SMTL ID : 3bng.1

W. succinogenes NrfA Y218F

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

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

ACT.1: 5 residues within 4Å: Chain A: G.21, I.22, E.23, Y.34 Ligands: Y1.7 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.2: 6 residues within 4Å: Chain A: A.170, A.171, G.172, S.221, K.222, G.223 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.222 ACT.3: 2 residues within 4Å: Chain A: S.48, N.50 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.50 Water bridges: A:S.48, A:N.295 ACT.16: 5 residues within 4Å: Chain B: G.21, I.22, E.23, Y.34 Ligands: Y1.22 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: 6 residues within 4Å: Chain B: A.170, A.171, G.172, S.221, K.222, G.223 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.222 ACT.18: 2 residues within 4Å: Chain B: S.48, N.50 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.50 Water bridges: B:S.48, B:N.295

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

SO4.4: 9 residues within 4Å: Chain A: T.263, G.264, I.265, H.383, A.384, P.385, E.386, E.387 Chain B: R.325 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:I.265, A:H.383, A:E.386, A:E.387 Water bridges: A:Q.268, A:Q.268, A:E.386, B:K.322 Salt bridges: B:R.325 SO4.5: 3 residues within 4Å: Chain A: S.311, E.312 Ligands: Y1.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.312 Water bridges: A:S.311, A:Q.313 SO4.19: 9 residues within 4Å: Chain A: R.325 Chain B: T.263, G.264, I.265, H.383, A.384, P.385, E.386, E.387 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Water bridges: A:K.322, A:K.322, B:Q.268, B:Q.268 Salt bridges: A:R.325 Hydrogen bonds: B:I.265, B:H.383, B:E.386, B:E.387 SO4.20: 3 residues within 4Å: Chain B: S.311, E.312 Ligands: Y1.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.312 Water bridges: B:S.311, B:Q.313

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: E.195, F.196, Y.233, 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.21: 5 residues within 4Å: Chain B: E.195, F.196, Y.233, 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

8 x Y1: YTTRIUM ION(Non-covalent)

Y1.7: 2 residues within 4Å: Chain A: E.30 Ligands: ACT.1 No protein-ligand interaction detected (PLIP) Y1.8: 3 residues within 4Å: Chain A: P.77 Ligands: HEM.13, HEM.14 No protein-ligand interaction detected (PLIP) Y1.9: 3 residues within 4Å: Chain A: D.301, E.312 Ligands: SO4.5 No protein-ligand interaction detected (PLIP) Y1.10: 5 residues within 4Å: Chain A: E.386 Chain B: E.386 Ligands: HEM.15, Y1.25, HEM.30 No protein-ligand interaction detected (PLIP) Y1.22: 2 residues within 4Å: Chain B: E.30 Ligands: ACT.16 No protein-ligand interaction detected (PLIP) Y1.23: 3 residues within 4Å: Chain B: P.77 Ligands: HEM.28, HEM.29 No protein-ligand interaction detected (PLIP) Y1.24: 3 residues within 4Å: Chain B: D.301, E.312 Ligands: SO4.20 No protein-ligand interaction detected (PLIP) Y1.25: 5 residues within 4Å: Chain A: E.386 Chain B: E.386 Ligands: Y1.10, HEM.15, HEM.30 No protein-ligand interaction detected (PLIP)

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

HEM.11: 23 residues within 4Å: Chain A: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, 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: HEM.13 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:P.77, A:T.90, A:T.93, A:L.104, A:F.196, A:F.196, A:F.198, A:V.216, A:H.255 Hydrogen bonds: A:N.75 Water bridges: A:R.92, A:D.257, A:A.376 Salt bridges: A:R.92, A:H.255, A:H.378 pi-Stacking: A:H.255 Metal complexes: H2O.21 HEM.12: 19 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, V.188, M.278, Y.280, Y.288, S.289, H.291 Ligands: HEM.13 20 PLIP interactions: 20 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, A:L.157, A:L.157, A:V.188 Hydrogen bonds: A:Q.38, A:Y.280, A:S.289 Water bridges: A:K.287 Salt bridges: A:H.181, A:R.185, A:K.287, A:H.291 Metal complexes: A:H.150, A:H.291 HEM.13: 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, C.149, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294 Ligands: Y1.8, HEM.11, HEM.12, HEM.14 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:P.77, A:K.112, A:I.144, A:H.277 Hydrogen bonds: A:S.48, A:Y.82, A:D.86 Water bridges: A:N.87 Metal complexes: A:H.80, A:H.193 HEM.14: 22 residues within 4Å: Chain A: P.77, C.189, H.193, 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: Y1.8, HEM.13, HEM.15 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:H.193, A:Y.261, A:Y.261, A:Y.261, A:Y.261, A:V.271, A:P.296, A:L.297, A:H.378, A:F.382, A:F.382 Hydrogen bonds: A:N.295, A:N.295 Water bridges: A:H.378 Metal complexes: A:H.277, A:H.383 HEM.15: 24 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.310, E.386 Ligands: Y1.10, HEM.14, Y1.25, HEM.30 16 PLIP interactions: 1 interactions with chain B, 15 interactions with chain A, Salt bridges: B:H.308, A:K.322 Hydrophobic interactions: 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 Water bridges: A:K.269, A:K.322, A:K.322 Metal complexes: A:H.266, A:H.308 HEM.26: 23 residues within 4Å: Chain B: Y.74, N.75, P.77, D.86, N.87, T.90, R.92, T.93, L.104, 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: HEM.28 18 PLIP interactions: 17 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.77, B:T.90, B:T.93, B:L.104, B:F.196, B:F.196, B:F.198, B:V.216, B:H.255 Hydrogen bonds: B:N.75 Water bridges: B:R.92, B:D.257, B:A.376 Salt bridges: B:R.92, B:H.255, B:H.378 pi-Stacking: B:H.255 Metal complexes: H2O.46 HEM.27: 19 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, V.188, M.278, Y.280, Y.288, S.289, H.291 Ligands: HEM.28 20 PLIP interactions: 20 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, B:L.157, B:L.157, B:V.188 Hydrogen bonds: B:Q.38, B:Y.280, B:S.289 Water bridges: B:K.287 Salt bridges: B:H.181, B:R.185, B:K.287, B:H.291 Metal complexes: B:H.150, B:H.291 HEM.28: 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, C.149, V.188, C.189, C.192, H.193, C.273, H.277, M.278, V.293, G.294 Ligands: Y1.23, HEM.26, HEM.27, HEM.29 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:P.77, B:K.112, B:I.144, B:H.277 Hydrogen bonds: B:S.48, B:Y.82, B:D.86 Water bridges: B:N.87 Metal complexes: B:H.80, B:H.193 HEM.29: 22 residues within 4Å: Chain B: P.77, C.189, H.193, 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: Y1.23, HEM.28, HEM.30 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:H.193, B:Y.261, B:Y.261, B:Y.261, B:Y.261, B:V.271, B:P.296, B:L.297, B:H.378, B:F.382, B:F.382 Hydrogen bonds: B:N.295, B:N.295 Water bridges: B:H.378 Metal complexes: B:H.277, B:H.383 HEM.30: 24 residues within 4Å: Chain A: I.265, H.308, E.310, 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: Y1.10, HEM.15, Y1.25, HEM.29 16 PLIP interactions: 1 interactions with chain A, 15 interactions with chain B, Salt bridges: A:H.308, B:K.322 Hydrophobic interactions: 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 Water bridges: B:K.269, B:K.322, B:K.322 Metal complexes: B:H.266, B:H.308

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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