SMTL ID : 3bnh.1

W. succinogenes NrfA Y218F Nitrite Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x NO2: NITRITE ION(Non-covalent)

NO2.1: 6 residues within 4Å: Chain A: F.70, R.92, F.196, Q.254, H.255 Ligands: HEM.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.255 NO2.14: 6 residues within 4Å: Chain B: F.70, R.92, F.196, Q.254, H.255 Ligands: HEM.22 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.112, B:H.255

2 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain A: E.195, F.196, K.252, Q.254 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.195, A:F.196, A:K.252, H2O.4, H2O.8 CA.15: 4 residues within 4Å: Chain B: E.195, F.196, K.252, Q.254 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.195, B:F.196, B:K.252, H2O.29, H2O.33

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: G.21, I.22, E.23, Y.34 Ligands: Y1.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.21, A:E.23, A:Y.34 Water bridges: A:E.23 ACT.4: 5 residues within 4Å: Chain A: A.170, A.171, S.221, K.222, G.223 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.171 ACT.16: 5 residues within 4Å: Chain B: G.21, I.22, E.23, Y.34 Ligands: Y1.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.21, B:E.23, B:Y.34 Water bridges: B:E.23 ACT.17: 5 residues within 4Å: Chain B: A.170, A.171, S.221, K.222, G.223 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.171

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 11 residues within 4Å: Chain A: G.264, I.265, P.385, E.386 Chain B: K.322, R.325, E.386 Ligands: Y1.8, HEM.13, Y1.21, HEM.26 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:I.265, A:E.386, B:R.325 Water bridges: A:H.266, A:E.387, B:K.322 Salt bridges: B:K.322 SO4.18: 11 residues within 4Å: Chain A: K.322, R.325, E.386 Chain B: G.264, I.265, P.385, E.386 Ligands: Y1.8, HEM.13, Y1.21, HEM.26 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.325, B:I.265, B:E.386 Water bridges: A:K.322, B:H.266, B:E.387 Salt bridges: A:K.322

6 x Y1: YTTRIUM ION(Non-covalent)

Y1.6: 2 residues within 4Å: Chain A: E.30 Ligands: ACT.3 No protein-ligand interaction detected (PLIP) Y1.7: 3 residues within 4Å: Chain A: P.77 Ligands: HEM.11, HEM.12 No protein-ligand interaction detected (PLIP) Y1.8: 8 residues within 4Å: Chain A: E.386 Chain B: K.322, E.386 Ligands: SO4.5, HEM.13, SO4.18, Y1.21, HEM.26 No protein-ligand interaction detected (PLIP) Y1.19: 2 residues within 4Å: Chain B: E.30 Ligands: ACT.16 No protein-ligand interaction detected (PLIP) Y1.20: 3 residues within 4Å: Chain B: P.77 Ligands: HEM.24, HEM.25 No protein-ligand interaction detected (PLIP) Y1.21: 8 residues within 4Å: Chain A: K.322, E.386 Chain B: E.386 Ligands: SO4.5, Y1.8, HEM.13, SO4.18, HEM.26 No protein-ligand interaction detected (PLIP)

10 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.9: 25 residues within 4Å: Chain A: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, A.107, C.108, C.111, K.112, Y.163, Q.191, C.192, H.193, F.196, F.198, V.216, H.255, A.376, H.378 Ligands: NO2.1, HEM.11 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:P.77, A:T.90, A:T.93, A:L.104, A:F.196, A:F.196, A:F.196, A:F.198, A:V.216, A:H.255 Hydrogen bonds: A:N.75, A:A.376 Water bridges: A:R.92, A:R.92 Salt bridges: A:R.92, A:H.255, A:H.378 pi-Stacking: A:H.255 HEM.10: 18 residues within 4Å: Chain A: W.31, Y.35, Q.38, F.39, W.42, G.145, C.146, C.149, H.150, L.157, H.181, R.185, M.278, Y.280, Y.288, S.289, H.291 Ligands: HEM.11 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:W.31, A:Y.35, A:Y.35, A:Q.38, A:Q.38, A:F.39, A:W.42 Hydrogen bonds: A:Q.38, A:Y.280, A:S.289 Water bridges: A:R.185 Salt bridges: A:H.181, A:R.185, A:H.291 Metal complexes: A:H.150, A:H.291 HEM.11: 26 residues within 4Å: Chain A: S.48, P.77, R.78, G.79, H.80, Y.82, A.83, D.86, C.111, K.112, I.144, N.148, V.188, C.189, Q.191, C.192, H.193, C.273, H.277, M.278, V.293, G.294 Ligands: Y1.7, HEM.9, HEM.10, HEM.12 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:P.77, A:K.112, A:H.277 Hydrogen bonds: A:S.48, A:R.78, A:Y.82, A:D.86 Water bridges: A:S.48, A:V.293, A:N.295 Metal complexes: A:H.80, A:H.193 HEM.12: 23 residues within 4Å: Chain A: P.77, C.189, H.193, D.257, W.258, Y.261, H.266, V.271, S.272, C.273, C.276, H.277, N.295, P.296, L.297, H.378, G.379, F.381, F.382, H.383 Ligands: Y1.7, HEM.11, HEM.13 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:H.193, A:D.257, A:W.258, A:Y.261, A:Y.261, A:Y.261, A:Y.261, A:H.266, A:V.271, A:L.297, A:L.297, A:H.378, A:F.382, A:F.382 Hydrogen bonds: A:N.295, A:N.295 Metal complexes: A:H.277, A:H.383 HEM.13: 25 residues within 4Å: Chain A: I.265, H.266, K.269, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, I.318, V.319, K.322, F.382, P.385 Chain B: I.265, H.308, E.386 Ligands: SO4.5, Y1.8, HEM.12, SO4.18, Y1.21, HEM.26 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:I.265, A:I.265, A:K.269, A:V.271, A:P.296, A:L.315, A:L.315, A:I.318, A:V.319, A:F.382 Salt bridges: A:K.322, B:H.308 Metal complexes: A:H.266, A:H.308 Water bridges: B:R.309 HEM.22: 25 residues within 4Å: Chain B: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, A.107, C.108, C.111, K.112, Y.163, Q.191, C.192, H.193, F.196, F.198, V.216, H.255, A.376, H.378 Ligands: NO2.14, HEM.24 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:P.77, B:T.90, B:T.93, B:L.104, B:F.196, B:F.196, B:F.196, B:F.198, B:V.216, B:H.255 Hydrogen bonds: B:N.75, B:A.376 Water bridges: B:R.92, B:R.92 Salt bridges: B:R.92, B:H.255, B:H.378 pi-Stacking: B:H.255 HEM.23: 18 residues within 4Å: Chain B: W.31, Y.35, Q.38, F.39, W.42, G.145, C.146, C.149, H.150, L.157, H.181, R.185, M.278, Y.280, Y.288, S.289, H.291 Ligands: HEM.24 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.31, B:Y.35, B:Y.35, B:Q.38, B:Q.38, B:F.39, B:W.42 Hydrogen bonds: B:Q.38, B:Y.280, B:S.289 Water bridges: B:R.185 Salt bridges: B:H.181, B:R.185, B:H.291 Metal complexes: B:H.150, B:H.291 HEM.24: 26 residues within 4Å: Chain B: S.48, P.77, R.78, G.79, H.80, Y.82, A.83, D.86, C.111, K.112, I.144, N.148, V.188, C.189, Q.191, C.192, H.193, C.273, H.277, M.278, V.293, G.294 Ligands: Y1.20, HEM.22, HEM.23, HEM.25 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:P.77, B:K.112, B:H.277 Hydrogen bonds: B:S.48, B:R.78, B:Y.82, B:D.86 Water bridges: B:S.48, B:V.293, B:N.295 Metal complexes: B:H.80, B:H.193 HEM.25: 23 residues within 4Å: Chain B: P.77, C.189, H.193, D.257, W.258, Y.261, H.266, V.271, S.272, C.273, C.276, H.277, N.295, P.296, L.297, H.378, G.379, F.381, F.382, H.383 Ligands: Y1.20, HEM.24, HEM.26 18 PLIP interactions: 18 interactions with chain B, Hydrophobic interactions: B:H.193, B:D.257, B:W.258, B:Y.261, B:Y.261, B:Y.261, B:Y.261, B:H.266, B:V.271, B:L.297, B:L.297, B:H.378, B:F.382, B:F.382 Hydrogen bonds: B:N.295, B:N.295 Metal complexes: B:H.277, B:H.383 HEM.26: 25 residues within 4Å: Chain A: I.265, H.308, E.386 Chain B: I.265, H.266, K.269, V.271, C.276, P.296, S.303, C.304, C.307, H.308, L.315, I.318, V.319, K.322, F.382, P.385 Ligands: SO4.5, Y1.8, HEM.13, SO4.18, Y1.21, HEM.25 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:I.265, B:I.265, B:K.269, B:V.271, B:P.296, B:L.315, B:L.315, B:I.318, B:V.319, B:F.382 Salt bridges: B:K.322, A:H.308 Metal complexes: B:H.266, B:H.308 Water bridges: A:R.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lukat, P. et al., Binding and Reduction of Sulfite by Cytochrome c Nitrite Reductase. Biochemistry (2008)

Release Date

2008-02-26

Peptides

Cytochrome c-552: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome c-552

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