SMTL ID : 4q0t.1

Free form of TvNiR, low dose data set

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-hexamer

Ligands

48 x HEC: HEME C(Covalent)

HEC.1: 22 residues within 4Å: Chain A: H.112, A.113, P.115, D.124, H.125, V.128, R.130, A.131, A.178, C.183, C.186, K.187, R.241, C.298, H.299, V.300, Y.302, C.304, F.326, H.360, N.485 Ligands: HEC.3 22 PLIP interactions: 21 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:P.115, A:V.128, A:A.131, A:V.300, A:Y.302, A:Y.302, A:F.326 Hydrogen bonds: A:A.113, A:A.483, A:N.485 Water bridges: A:H.112, A:H.112, A:H.112, A:R.130, A:H.360 Salt bridges: A:K.89, A:H.112, A:R.130, A:H.360 pi-Stacking: A:Y.302, A:H.360 Metal complexes: H2O.1 HEC.2: 18 residues within 4Å: Chain A: C.65, H.69, Q.72, F.73, L.224, N.225, C.226, C.229, H.230, A.289, S.291, M.294, M.383, Y.394, T.395, H.397 Ligands: HEC.3, HEC.7 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:H.69, A:Q.72, A:Q.72, A:L.224, A:A.289, A:T.395 Hydrogen bonds: A:Q.72, A:T.395, A:T.395 Salt bridges: A:K.385 Metal complexes: A:H.230, A:H.397 HEC.3: 25 residues within 4Å: Chain A: R.80, S.83, P.115, R.116, S.117, H.118, F.120, M.121, D.124, C.186, K.187, L.224, M.228, M.294, C.295, C.298, H.299, C.378, H.382, M.383, Q.399, R.400 Ligands: HEC.1, HEC.2, HEC.4 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:P.115, A:L.224, A:H.382 Hydrogen bonds: A:S.83, A:P.115, A:R.116, A:F.120, A:D.124 Metal complexes: A:H.118, A:H.299 HEC.4: 24 residues within 4Å: Chain A: R.95, N.292, C.295, H.299, E.362, A.363, F.366, H.371, V.376, A.377, C.378, C.381, H.382, T.401, P.402, R.403, I.426, K.430, N.485, S.486, F.489, H.490 Ligands: HEC.3, HEC.5 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:H.299, A:E.362, A:E.362, A:F.366, A:F.366, A:V.376, A:P.402, A:I.426, A:N.485, A:F.489, A:F.489 Hydrogen bonds: A:R.95, A:T.401, A:T.401 Water bridges: A:S.83, A:K.430, A:N.485 Salt bridges: A:R.403, A:K.430 Metal complexes: A:H.382, A:H.490 HEC.5: 18 residues within 4Å: Chain A: V.370, H.371, N.374, V.376, C.381, P.402, A.409, C.410, C.413, H.414, W.417, A.422, I.426, F.489 Chain C: N.140, W.141, Q.142 Ligands: HEC.4 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain C, Hydrophobic interactions: A:V.370, A:V.376, A:P.402, A:W.417, A:W.417, A:I.426, A:F.489, C:W.141, C:Q.142 Metal complexes: A:H.371, A:H.414 Hydrogen bonds: C:W.141 HEC.6: 25 residues within 4Å: Chain A: A.10, C.13, F.14, H.17, I.20, H.24, V.32, N.33, C.34, C.37, H.38, T.58, R.59, M.60, I.192, L.193, F.227, P.232, H.233, R.238, F.273, R.275, R.281 Ligands: HEC.7, HEC.8 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:A.10, A:F.14, A:I.20, A:V.32, A:T.58, A:I.192, A:L.193, A:F.227, A:P.232, A:F.273 Water bridges: A:R.281 Salt bridges: A:R.238, A:R.275, A:R.281, A:R.281 Metal complexes: A:H.38, A:H.233 HEC.7: 17 residues within 4Å: Chain A: K.28, H.29, V.32, H.36, A.64, C.65, T.67, C.68, H.69, C.226, H.230, A.235 Chain B: H.36, T.67, C.68 Ligands: HEC.2, HEC.6 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:K.28, A:T.67 Salt bridges: A:K.28, A:K.28 Metal complexes: A:H.29, A:H.69 Hydrogen bonds: B:T.67 HEC.8: 23 residues within 4Å: Chain A: V.8, Q.12, C.13, C.16, H.17, C.34, H.38, A.40, H.43, V.44, A.47, S.48, S.49, R.51, M.52, R.55, P.56, T.58, L.193, Q.274, R.275, G.276 Ligands: HEC.6 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:V.8, A:V.44, A:A.47, A:M.52, A:P.56 Hydrogen bonds: A:G.276 Water bridges: A:R.275, A:R.275, A:R.275 Salt bridges: A:R.55, A:R.275, A:R.275 Metal complexes: A:H.17, A:H.43 HEC.11: 22 residues within 4Å: Chain B: H.112, A.113, D.124, H.125, V.128, R.130, A.131, A.178, C.183, C.186, K.187, R.241, C.298, H.299, V.300, Y.302, C.304, F.326, H.360, A.483, N.485 Ligands: HEC.13 21 PLIP interactions: 20 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:V.128, B:A.131, B:V.300, B:Y.302, B:Y.302, B:F.326, B:H.360 Hydrogen bonds: B:A.113, B:A.483, B:N.485 Water bridges: B:H.112, B:R.130, B:H.360 Salt bridges: B:K.89, B:H.112, B:H.112, B:R.130, B:H.360 pi-Stacking: B:Y.302, B:H.360 Metal complexes: H2O.26 HEC.12: 18 residues within 4Å: Chain B: C.65, H.69, Q.72, F.73, L.224, N.225, C.226, C.229, H.230, A.289, S.291, M.294, M.383, Y.394, T.395, H.397 Ligands: HEC.13, HEC.17 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:H.69, B:Q.72, B:Q.72, B:L.224, B:A.289, B:T.395 Hydrogen bonds: B:Q.72, B:T.395 Salt bridges: B:K.385 Metal complexes: B:H.230, B:H.397 HEC.13: 25 residues within 4Å: Chain B: R.80, S.83, P.115, R.116, S.117, H.118, F.120, M.121, D.124, C.186, K.187, L.224, M.228, M.294, C.295, C.298, H.299, C.378, H.382, M.383, Q.399, R.400 Ligands: HEC.11, HEC.12, HEC.14 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:P.115, B:L.224, B:H.382 Hydrogen bonds: B:S.83, B:R.116, B:F.120 Water bridges: B:S.117, B:Q.399 Metal complexes: B:H.118, B:H.299 HEC.14: 24 residues within 4Å: Chain B: R.95, N.292, C.295, H.299, E.362, A.363, F.366, H.371, V.376, A.377, C.378, C.381, H.382, T.401, P.402, R.403, I.426, K.430, N.485, S.486, F.489, H.490 Ligands: HEC.13, HEC.15 20 PLIP interactions: 20 interactions with chain B, Hydrophobic interactions: B:H.299, B:E.362, B:E.362, B:F.366, B:V.376, B:P.402, B:I.426, B:N.485, B:F.489, B:F.489 Hydrogen bonds: B:R.95, B:T.401 Water bridges: B:S.83, B:R.95, B:K.430, B:N.485 Salt bridges: B:R.403, B:K.430 Metal complexes: B:H.382, B:H.490 HEC.15: 18 residues within 4Å: Chain B: V.370, H.371, N.374, C.381, P.402, A.409, C.410, C.413, H.414, W.417, A.422, I.426, F.489, P.492 Chain F: N.140, W.141, Q.142 Ligands: HEC.14 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain F, Hydrophobic interactions: B:V.370, B:P.402, B:W.417, B:W.417, B:I.426, B:F.489, F:Q.142 Metal complexes: B:H.371, B:H.414 Hydrogen bonds: F:W.141 HEC.16: 23 residues within 4Å: Chain B: A.10, C.13, F.14, H.17, I.20, H.24, V.32, N.33, C.34, C.37, H.38, T.58, I.192, L.193, F.227, P.232, H.233, R.238, F.273, R.275, R.281 Ligands: HEC.17, HEC.18 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:A.10, B:F.14, B:I.20, B:V.32, B:T.58, B:I.192, B:L.193, B:F.227, B:P.232, B:P.232, B:F.273 Water bridges: B:R.281 Salt bridges: B:R.238, B:R.275, B:R.281, B:R.281 Metal complexes: B:H.38, B:H.233 HEC.17: 17 residues within 4Å: Chain A: H.36, T.67, C.68 Chain B: K.28, H.29, V.32, H.36, A.64, C.65, T.67, C.68, H.69, C.226, H.230, A.235 Ligands: HEC.12, HEC.16 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:K.28, B:K.28, B:T.67 Salt bridges: B:K.28, B:K.28 Metal complexes: B:H.29, B:H.69 Water bridges: A:T.67, A:T.67 HEC.18: 22 residues within 4Å: Chain B: Q.12, C.13, C.16, H.17, C.34, H.38, A.40, H.43, V.44, A.47, S.48, S.49, R.50, R.51, M.52, R.55, P.56, T.58, L.193, Q.274, R.275 Ligands: HEC.16 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:A.40, B:V.44, B:M.52, B:P.56 Water bridges: B:R.275, B:R.275 Salt bridges: B:R.55, B:R.275 Metal complexes: B:H.17, B:H.43 HEC.23: 22 residues within 4Å: Chain C: H.112, A.113, P.115, D.124, H.125, V.128, R.130, A.131, A.178, C.183, C.186, K.187, R.241, C.298, H.299, V.300, Y.302, C.304, F.326, H.360, N.485 Ligands: HEC.25 21 PLIP interactions: 20 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: C:P.115, C:V.128, C:A.131, C:V.300, C:Y.302, C:Y.302, C:F.326 Hydrogen bonds: C:A.113, C:A.483, C:N.485 Water bridges: C:H.112, C:A.113, C:R.130, C:H.360 Salt bridges: C:K.89, C:H.112, C:R.130, C:H.360 pi-Stacking: C:Y.302, C:H.360 Metal complexes: H2O.51 HEC.24: 18 residues within 4Å: Chain C: C.65, H.69, Q.72, F.73, L.224, N.225, C.226, C.229, H.230, A.289, S.291, M.294, M.383, Y.394, T.395, H.397 Ligands: HEC.25, HEC.29 12 PLIP interactions: 12 interactions with chain C, Hydrophobic interactions: C:H.69, C:Q.72, C:Q.72, C:L.224, C:A.289, C:T.395 Hydrogen bonds: C:Q.72, C:T.395, C:T.395 Salt bridges: C:K.385 Metal complexes: C:H.230, C:H.397 HEC.25: 25 residues within 4Å: Chain C: R.80, S.83, P.115, R.116, S.117, H.118, F.120, M.121, D.124, C.186, K.187, L.224, M.228, M.294, C.295, C.298, H.299, C.378, H.382, M.383, Q.399, R.400 Ligands: HEC.23, HEC.24, HEC.26 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:P.115, C:L.224, C:H.382 Hydrogen bonds: C:S.83, C:P.115, C:R.116, C:F.120 Metal complexes: C:H.118, C:H.299 HEC.26: 24 residues within 4Å: Chain C: R.95, N.292, C.295, H.299, E.362, A.363, F.366, H.371, V.376, A.377, C.378, C.381, H.382, T.401, P.402, R.403, I.426, K.430, N.485, S.486, F.489, H.490 Ligands: HEC.25, HEC.27 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:H.299, C:E.362, C:E.362, C:F.366, C:F.366, C:V.376, C:P.402, C:I.426, C:N.485, C:F.489, C:F.489 Hydrogen bonds: C:R.95, C:T.401, C:T.401 Water bridges: C:S.83, C:K.430, C:N.485 Salt bridges: C:R.403, C:K.430 Metal complexes: C:H.382, C:H.490 HEC.27: 18 residues within 4Å: Chain C: V.370, H.371, N.374, V.376, C.381, P.402, A.409, C.410, C.413, H.414, W.417, A.422, I.426, F.489 Chain E: N.140, W.141, Q.142 Ligands: HEC.26 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain E, Hydrophobic interactions: C:V.370, C:V.376, C:P.402, C:W.417, C:W.417, C:I.426, C:F.489, E:W.141, E:Q.142 Metal complexes: C:H.371, C:H.414 Hydrogen bonds: E:W.141 HEC.28: 25 residues within 4Å: Chain C: A.10, C.13, F.14, H.17, I.20, H.24, V.32, N.33, C.34, C.37, H.38, T.58, R.59, M.60, I.192, L.193, F.227, P.232, H.233, R.238, F.273, R.275, R.281 Ligands: HEC.29, HEC.30 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:A.10, C:F.14, C:I.20, C:V.32, C:T.58, C:I.192, C:L.193, C:F.227, C:P.232, C:F.273 Water bridges: C:R.281 Salt bridges: C:R.238, C:R.275, C:R.281, C:R.281 Metal complexes: C:H.38, C:H.233 HEC.29: 17 residues within 4Å: Chain C: K.28, H.29, V.32, H.36, A.64, C.65, T.67, C.68, H.69, C.226, H.230, A.235 Chain D: H.36, T.67, C.68 Ligands: HEC.24, HEC.28 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: C:K.28, C:T.67 Salt bridges: C:K.28, C:K.28 Metal complexes: C:H.29, C:H.69 Hydrogen bonds: D:T.67 HEC.30: 23 residues within 4Å: Chain C: V.8, Q.12, C.13, C.16, H.17, C.34, H.38, A.40, H.43, V.44, A.47, S.48, S.49, R.51, M.52, R.55, P.56, T.58, L.193, Q.274, R.275, G.276 Ligands: HEC.28 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:V.8, C:V.44, C:A.47, C:M.52, C:P.56 Hydrogen bonds: C:G.276 Water bridges: C:R.275, C:R.275, C:R.275 Salt bridges: C:R.55, C:R.275, C:R.275 Metal complexes: C:H.17, C:H.43 HEC.33: 22 residues within 4Å: Chain D: H.112, A.113, D.124, H.125, V.128, R.130, A.131, A.178, C.183, C.186, K.187, R.241, C.298, H.299, V.300, Y.302, C.304, F.326, H.360, A.483, N.485 Ligands: HEC.35 21 PLIP interactions: 20 interactions with chain D, 1 Ligand-Water interactions Hydrophobic interactions: D:V.128, D:A.131, D:V.300, D:Y.302, D:Y.302, D:F.326, D:H.360 Hydrogen bonds: D:A.113, D:A.483, D:N.485 Water bridges: D:H.112, D:R.130, D:H.360 Salt bridges: D:K.89, D:H.112, D:H.112, D:R.130, D:H.360 pi-Stacking: D:Y.302, D:H.360 Metal complexes: H2O.77 HEC.34: 18 residues within 4Å: Chain D: C.65, H.69, Q.72, F.73, L.224, N.225, C.226, C.229, H.230, A.289, S.291, M.294, M.383, Y.394, T.395, H.397 Ligands: HEC.35, HEC.39 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:H.69, D:Q.72, D:Q.72, D:L.224, D:A.289, D:T.395 Hydrogen bonds: D:Q.72, D:T.395 Salt bridges: D:K.385 Metal complexes: D:H.230, D:H.397 HEC.35: 25 residues within 4Å: Chain D: R.80, S.83, P.115, R.116, S.117, H.118, F.120, M.121, D.124, C.186, K.187, L.224, M.228, M.294, C.295, C.298, H.299, C.378, H.382, M.383, Q.399, R.400 Ligands: HEC.33, HEC.34, HEC.36 11 PLIP interactions: 11 interactions with chain D, Hydrophobic interactions: D:P.115, D:L.224, D:H.382 Hydrogen bonds: D:S.83, D:R.116, D:F.120, D:D.124 Water bridges: D:S.117, D:Q.399 Metal complexes: D:H.118, D:H.299 HEC.36: 24 residues within 4Å: Chain D: R.95, N.292, C.295, H.299, E.362, A.363, F.366, H.371, V.376, A.377, C.378, C.381, H.382, T.401, P.402, R.403, I.426, K.430, N.485, S.486, F.489, H.490 Ligands: HEC.35, HEC.37 21 PLIP interactions: 21 interactions with chain D, Hydrophobic interactions: D:H.299, D:E.362, D:E.362, D:F.366, D:V.376, D:P.402, D:I.426, D:N.485, D:F.489, D:F.489 Hydrogen bonds: D:R.95, D:T.401, D:T.401 Water bridges: D:S.83, D:R.95, D:K.430, D:N.485 Salt bridges: D:R.403, D:K.430 Metal complexes: D:H.382, D:H.490 HEC.37: 18 residues within 4Å: Chain B: N.140, W.141, Q.142 Chain D: V.370, H.371, N.374, C.381, P.402, A.409, C.410, C.413, H.414, W.417, A.422, I.426, F.489, P.492 Ligands: HEC.36 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain D, Hydrophobic interactions: B:Q.142, D:V.370, D:P.402, D:W.417, D:W.417, D:I.426, D:F.489 Hydrogen bonds: B:W.141 Metal complexes: D:H.371, D:H.414 HEC.38: 23 residues within 4Å: Chain D: A.10, C.13, F.14, H.17, I.20, H.24, V.32, N.33, C.34, C.37, H.38, T.58, I.192, L.193, F.227, P.232, H.233, R.238, F.273, R.275, R.281 Ligands: HEC.39, HEC.40 18 PLIP interactions: 18 interactions with chain D, Hydrophobic interactions: D:A.10, D:F.14, D:I.20, D:V.32, D:T.58, D:I.192, D:L.193, D:F.227, D:P.232, D:P.232, D:F.273 Water bridges: D:R.281 Salt bridges: D:R.238, D:R.275, D:R.281, D:R.281 Metal complexes: D:H.38, D:H.233 HEC.39: 17 residues within 4Å: Chain C: H.36, T.67, C.68 Chain D: K.28, H.29, V.32, H.36, A.64, C.65, T.67, C.68, H.69, C.226, H.230, A.235 Ligands: HEC.34, HEC.38 9 PLIP interactions: 7 interactions with chain D, 2 interactions with chain C, Hydrophobic interactions: D:K.28, D:K.28, D:T.67 Salt bridges: D:K.28, D:K.28 Metal complexes: D:H.29, D:H.69 Water bridges: C:T.67, C:T.67 HEC.40: 22 residues within 4Å: Chain D: Q.12, C.13, C.16, H.17, C.34, H.38, A.40, H.43, V.44, A.47, S.48, S.49, R.50, R.51, M.52, R.55, P.56, T.58, L.193, Q.274, R.275 Ligands: HEC.38 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:A.40, D:V.44, D:M.52, D:P.56 Water bridges: D:R.275, D:R.275 Salt bridges: D:R.55, D:R.275 Metal complexes: D:H.17, D:H.43 HEC.45: 22 residues within 4Å: Chain E: H.112, A.113, P.115, D.124, H.125, V.128, R.130, A.131, A.178, C.183, C.186, K.187, R.241, C.298, H.299, V.300, Y.302, C.304, F.326, H.360, N.485 Ligands: HEC.47 22 PLIP interactions: 21 interactions with chain E, 1 Ligand-Water interactions Hydrophobic interactions: E:P.115, E:V.128, E:A.131, E:V.300, E:Y.302, E:Y.302, E:F.326 Hydrogen bonds: E:A.113, E:A.483, E:N.485 Water bridges: E:H.112, E:H.112, E:H.112, E:R.130, E:H.360 Salt bridges: E:K.89, E:H.112, E:R.130, E:H.360 pi-Stacking: E:Y.302, E:H.360 Metal complexes: H2O.102 HEC.46: 18 residues within 4Å: Chain E: C.65, H.69, Q.72, F.73, L.224, N.225, C.226, C.229, H.230, A.289, S.291, M.294, M.383, Y.394, T.395, H.397 Ligands: HEC.47, HEC.51 12 PLIP interactions: 12 interactions with chain E, Hydrophobic interactions: E:H.69, E:Q.72, E:Q.72, E:L.224, E:A.289, E:T.395 Hydrogen bonds: E:Q.72, E:T.395, E:T.395 Salt bridges: E:K.385 Metal complexes: E:H.230, E:H.397 HEC.47: 25 residues within 4Å: Chain E: R.80, S.83, P.115, R.116, S.117, H.118, F.120, M.121, D.124, C.186, K.187, L.224, M.228, M.294, C.295, C.298, H.299, C.378, H.382, M.383, Q.399, R.400 Ligands: HEC.45, HEC.46, HEC.48 9 PLIP interactions: 9 interactions with chain E, Hydrophobic interactions: E:P.115, E:L.224, E:H.382 Hydrogen bonds: E:S.83, E:P.115, E:R.116, E:F.120 Metal complexes: E:H.118, E:H.299 HEC.48: 24 residues within 4Å: Chain E: R.95, N.292, C.295, H.299, E.362, A.363, F.366, H.371, V.376, A.377, C.378, C.381, H.382, T.401, P.402, R.403, I.426, K.430, N.485, S.486, F.489, H.490 Ligands: HEC.47, HEC.49 20 PLIP interactions: 20 interactions with chain E, Hydrophobic interactions: E:H.299, E:E.362, E:E.362, E:F.366, E:F.366, E:V.376, E:P.402, E:I.426, E:N.485, E:F.489, E:F.489 Hydrogen bonds: E:R.95, E:T.401 Water bridges: E:S.83, E:K.430, E:N.485 Salt bridges: E:R.403, E:K.430 Metal complexes: E:H.382, E:H.490 HEC.49: 18 residues within 4Å: Chain A: N.140, W.141, Q.142 Chain E: V.370, H.371, N.374, V.376, C.381, P.402, A.409, C.410, C.413, H.414, W.417, A.422, I.426, F.489 Ligands: HEC.48 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain A, Hydrophobic interactions: E:V.370, E:V.376, E:P.402, E:W.417, E:W.417, E:I.426, E:F.489, A:W.141, A:Q.142 Metal complexes: E:H.371, E:H.414 Hydrogen bonds: A:W.141 HEC.50: 25 residues within 4Å: Chain E: A.10, C.13, F.14, H.17, I.20, H.24, V.32, N.33, C.34, C.37, H.38, T.58, R.59, M.60, I.192, L.193, F.227, P.232, H.233, R.238, F.273, R.275, R.281 Ligands: HEC.51, HEC.52 17 PLIP interactions: 17 interactions with chain E, Hydrophobic interactions: E:A.10, E:F.14, E:I.20, E:V.32, E:T.58, E:I.192, E:L.193, E:F.227, E:P.232, E:F.273 Water bridges: E:R.281 Salt bridges: E:R.238, E:R.275, E:R.281, E:R.281 Metal complexes: E:H.38, E:H.233 HEC.51: 17 residues within 4Å: Chain E: K.28, H.29, V.32, H.36, A.64, C.65, T.67, C.68, H.69, C.226, H.230, A.235 Chain F: H.36, T.67, C.68 Ligands: HEC.46, HEC.50 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain F, Hydrophobic interactions: E:K.28, E:T.67 Salt bridges: E:K.28, E:K.28 Metal complexes: E:H.29, E:H.69 Hydrogen bonds: F:T.67 HEC.52: 23 residues within 4Å: Chain E: V.8, Q.12, C.13, C.16, H.17, C.34, H.38, A.40, H.43, V.44, A.47, S.48, S.49, R.51, M.52, R.55, P.56, T.58, L.193, Q.274, R.275, G.276 Ligands: HEC.50 14 PLIP interactions: 14 interactions with chain E, Hydrophobic interactions: E:V.8, E:V.44, E:A.47, E:M.52, E:P.56 Hydrogen bonds: E:G.276 Water bridges: E:R.275, E:R.275, E:R.275 Salt bridges: E:R.55, E:R.275, E:R.275 Metal complexes: E:H.17, E:H.43 HEC.55: 22 residues within 4Å: Chain F: H.112, A.113, D.124, H.125, V.128, R.130, A.131, A.178, C.183, C.186, K.187, R.241, C.298, H.299, V.300, Y.302, C.304, F.326, H.360, A.483, N.485 Ligands: HEC.57 21 PLIP interactions: 20 interactions with chain F, 1 Ligand-Water interactions Hydrophobic interactions: F:V.128, F:A.131, F:V.300, F:Y.302, F:Y.302, F:F.326, F:H.360 Hydrogen bonds: F:A.113, F:A.483, F:N.485 Water bridges: F:H.112, F:R.130, F:H.360 Salt bridges: F:K.89, F:H.112, F:H.112, F:R.130, F:H.360 pi-Stacking: F:Y.302, F:H.360 Metal complexes: H2O.128 HEC.56: 18 residues within 4Å: Chain F: C.65, H.69, Q.72, F.73, L.224, N.225, C.226, C.229, H.230, A.289, S.291, M.294, M.383, Y.394, T.395, H.397 Ligands: HEC.57, HEC.61 11 PLIP interactions: 11 interactions with chain F, Hydrophobic interactions: F:H.69, F:Q.72, F:Q.72, F:L.224, F:A.289, F:T.395 Hydrogen bonds: F:Q.72, F:T.395 Salt bridges: F:K.385 Metal complexes: F:H.230, F:H.397 HEC.57: 25 residues within 4Å: Chain F: R.80, S.83, P.115, R.116, S.117, H.118, F.120, M.121, D.124, C.186, K.187, L.224, M.228, M.294, C.295, C.298, H.299, C.378, H.382, M.383, Q.399, R.400 Ligands: HEC.55, HEC.56, HEC.58 11 PLIP interactions: 11 interactions with chain F, Hydrophobic interactions: F:P.115, F:L.224, F:H.382 Hydrogen bonds: F:S.83, F:R.116, F:F.120, F:D.124 Water bridges: F:S.117, F:Q.399 Metal complexes: F:H.118, F:H.299 HEC.58: 24 residues within 4Å: Chain F: R.95, N.292, C.295, H.299, E.362, A.363, F.366, H.371, V.376, A.377, C.378, C.381, H.382, T.401, P.402, R.403, I.426, K.430, N.485, S.486, F.489, H.490 Ligands: HEC.57, HEC.59 20 PLIP interactions: 20 interactions with chain F, Hydrophobic interactions: F:H.299, F:E.362, F:E.362, F:F.366, F:V.376, F:P.402, F:I.426, F:N.485, F:F.489, F:F.489 Hydrogen bonds: F:R.95, F:T.401 Water bridges: F:S.83, F:R.95, F:K.430, F:N.485 Salt bridges: F:R.403, F:K.430 Metal complexes: F:H.382, F:H.490 HEC.59: 18 residues within 4Å: Chain D: N.140, W.141, Q.142 Chain F: V.370, H.371, N.374, C.381, P.402, A.409, C.410, C.413, H.414, W.417, A.422, I.426, F.489, P.492 Ligands: HEC.58 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain D, Hydrophobic interactions: F:V.370, F:P.402, F:W.417, F:W.417, F:I.426, F:F.489, D:Q.142 Metal complexes: F:H.371, F:H.414 Hydrogen bonds: D:W.141 HEC.60: 23 residues within 4Å: Chain F: A.10, C.13, F.14, H.17, I.20, H.24, V.32, N.33, C.34, C.37, H.38, T.58, I.192, L.193, F.227, P.232, H.233, R.238, F.273, R.275, R.281 Ligands: HEC.61, HEC.62 18 PLIP interactions: 18 interactions with chain F, Hydrophobic interactions: F:A.10, F:F.14, F:I.20, F:V.32, F:T.58, F:I.192, F:L.193, F:F.227, F:P.232, F:P.232, F:F.273 Water bridges: F:R.281 Salt bridges: F:R.238, F:R.275, F:R.281, F:R.281 Metal complexes: F:H.38, F:H.233 HEC.61: 17 residues within 4Å: Chain E: H.36, T.67, C.68 Chain F: K.28, H.29, V.32, H.36, A.64, C.65, T.67, C.68, H.69, C.226, H.230, A.235 Ligands: HEC.56, HEC.60 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain E, Hydrophobic interactions: F:K.28, F:K.28, F:T.67 Salt bridges: F:K.28, F:K.28 Metal complexes: F:H.29, F:H.69 Water bridges: E:T.67, E:T.67 HEC.62: 22 residues within 4Å: Chain F: Q.12, C.13, C.16, H.17, C.34, H.38, A.40, H.43, V.44, A.47, S.48, S.49, R.50, R.51, M.52, R.55, P.56, T.58, L.193, Q.274, R.275 Ligands: HEC.60 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: F:A.40, F:V.44, F:M.52, F:P.56 Water bridges: F:R.275, F:R.275 Salt bridges: F:R.55, F:R.275 Metal complexes: F:H.17, F:H.43

6 x CA: CALCIUM ION(Non-covalent)

CA.9: 4 residues within 4Å: Chain A: E.301, Y.302, K.357, Q.359 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.301, A:Y.302, A:K.357, H2O.8, H2O.8 CA.19: 4 residues within 4Å: Chain B: E.301, Y.302, K.357, Q.359 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.301, B:Y.302, B:K.357, H2O.34, H2O.34 CA.31: 4 residues within 4Å: Chain C: E.301, Y.302, K.357, Q.359 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.301, C:Y.302, C:K.357, H2O.59, H2O.59 CA.41: 4 residues within 4Å: Chain D: E.301, Y.302, K.357, Q.359 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.301, D:Y.302, D:K.357, H2O.85, H2O.85 CA.53: 4 residues within 4Å: Chain E: E.301, Y.302, K.357, Q.359 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.301, E:Y.302, E:K.357, H2O.110, H2O.110 CA.63: 4 residues within 4Å: Chain F: E.301, Y.302, K.357, Q.359 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:E.301, F:Y.302, F:K.357, H2O.136, H2O.136

6 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.10: 9 residues within 4Å: Chain A: R.86, V.127, Q.137, F.138, W.141, V.144 Chain E: Y.428, Y.432, R.496 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:F.138, A:W.141, A:W.141, A:W.141, A:V.144, E:Y.428, E:Y.432 Hydrogen bonds: A:R.86, A:R.86, A:F.138 MPD.20: 9 residues within 4Å: Chain B: R.86, V.127, Q.137, F.138, W.141, V.144 Chain D: Y.428, Y.432, R.496 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:F.138, B:W.141, B:W.141, B:W.141, B:V.144, D:Y.428, D:Y.432 Hydrogen bonds: B:R.86, B:R.86, B:F.138 MPD.32: 9 residues within 4Å: Chain A: Y.428, Y.432, R.496 Chain C: R.86, V.127, Q.137, F.138, W.141, V.144 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:F.138, C:W.141, C:W.141, C:W.141, C:V.144, A:Y.428, A:Y.432 Hydrogen bonds: C:R.86, C:R.86, C:F.138 MPD.42: 9 residues within 4Å: Chain D: R.86, V.127, Q.137, F.138, W.141, V.144 Chain F: Y.428, Y.432, R.496 10 PLIP interactions: 2 interactions with chain F, 8 interactions with chain D Hydrophobic interactions: F:Y.428, F:Y.432, D:F.138, D:W.141, D:W.141, D:W.141, D:V.144 Hydrogen bonds: D:R.86, D:R.86, D:F.138 MPD.54: 9 residues within 4Å: Chain C: Y.428, Y.432, R.496 Chain E: R.86, V.127, Q.137, F.138, W.141, V.144 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:F.138, E:W.141, E:W.141, E:W.141, E:V.144, C:Y.428, C:Y.432 Hydrogen bonds: E:R.86, E:R.86, E:F.138 MPD.64: 9 residues within 4Å: Chain B: Y.428, Y.432, R.496 Chain F: R.86, V.127, Q.137, F.138, W.141, V.144 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain B Hydrophobic interactions: F:F.138, F:W.141, F:W.141, F:W.141, F:V.144, B:Y.428, B:Y.432 Hydrogen bonds: F:R.86, F:R.86, F:F.138

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 6 residues within 4Å: Chain B: Y.197, K.270, T.272, D.279, F.280, R.281 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.270, B:R.281 Water bridges: B:D.250, B:K.270 GOL.43: 6 residues within 4Å: Chain D: Y.197, K.270, T.272, D.279, F.280, R.281 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.270, D:R.281 Water bridges: D:K.270, D:R.321 GOL.65: 6 residues within 4Å: Chain F: Y.197, K.270, T.272, D.279, F.280, R.281 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.270, F:R.281 Water bridges: F:K.270, F:R.321

3 x CIT: CITRIC ACID(Non-functional Binders)

CIT.22: 3 residues within 4Å: Chain B: S.48, S.49, R.50 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.49, B:S.49 Salt bridges: B:R.50 CIT.44: 3 residues within 4Å: Chain D: S.48, S.49, R.50 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.49, D:S.49 Salt bridges: D:R.50 CIT.66: 3 residues within 4Å: Chain F: S.48, S.49, R.50 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.49, F:S.49 Salt bridges: F:R.50

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lazarenko, V.A. et al., X-ray-induced changes in the active site structure of octaheme cytochrome c nitrite reductase and its substrate complexes. TO BE PUBLISHED

Release Date

2014-09-10

Peptides

Eight-heme nitrite reductase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Eight-heme nitrite reductase