SMTL ID : 3bnf.1

W. succinogenes NrfA Sulfite Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.195, Y.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:Y.196, A:K.252, H2O.3, H2O.8 CA.13: 5 residues within 4Å: Chain B: E.195, Y.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:Y.196, B:K.252, H2O.28, H2O.32

2 x SO3: SULFITE ION(Non-covalent)

SO3.2: 6 residues within 4Å: Chain A: F.70, R.92, Y.196, Q.254, H.255 Ligands: HEM.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.92, A:Y.196 SO3.14: 6 residues within 4Å: Chain B: F.70, R.92, Y.196, Q.254, H.255 Ligands: HEM.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.92, B:Y.196

6 x Y1: YTTRIUM ION(Non-covalent)

Y1.3: 2 residues within 4Å: Chain A: E.30 Ligands: ACT.7 No protein-ligand interaction detected (PLIP) Y1.4: 3 residues within 4Å: Chain A: P.77 Ligands: HEM.10, HEM.11 No protein-ligand interaction detected (PLIP) Y1.5: 7 residues within 4Å: Chain A: E.386 Chain B: E.386 Ligands: ACT.6, HEM.12, Y1.17, ACT.18, HEM.24 No protein-ligand interaction detected (PLIP) Y1.15: 2 residues within 4Å: Chain B: E.30 Ligands: ACT.19 No protein-ligand interaction detected (PLIP) Y1.16: 3 residues within 4Å: Chain B: P.77 Ligands: HEM.22, HEM.23 No protein-ligand interaction detected (PLIP) Y1.17: 7 residues within 4Å: Chain A: E.386 Chain B: E.386 Ligands: Y1.5, ACT.6, HEM.12, ACT.18, HEM.24 No protein-ligand interaction detected (PLIP)

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

ACT.6: 9 residues within 4Å: Chain A: G.264, I.265, P.385, E.386 Chain B: E.386 Ligands: Y1.5, HEM.12, Y1.17, HEM.24 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.386 Water bridges: A:A.384, A:E.387 Salt bridges: A:K.322, B:K.322 ACT.7: 5 residues within 4Å: Chain A: G.21, I.22, E.23, Y.34 Ligands: Y1.3 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.18: 9 residues within 4Å: Chain A: E.386 Chain B: G.264, I.265, P.385, E.386 Ligands: Y1.5, HEM.12, Y1.17, HEM.24 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.386 Water bridges: B:A.384, B:E.387 Salt bridges: B:K.322, A:K.322 ACT.19: 5 residues within 4Å: Chain B: G.21, I.22, E.23, Y.34 Ligands: Y1.15 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.21, B:E.23, B:Y.34 Water bridges: B:E.23

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

HEM.8: 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, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378 Ligands: SO3.2, HEM.10 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:T.90, A:T.93, A:L.104, A:Y.196, A:Y.196, A:Y.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.9: 20 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, A.274, M.278, Y.280, Y.288, S.289, H.291 Ligands: HEM.10 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:W.31, A:Y.35, A:Y.35, A:Q.38, A:F.39, A:W.42, A:L.157, A:V.188, A:A.274 Hydrogen bonds: A:Q.38, 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.10: 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, V.188, C.189, Q.191, C.192, H.193, C.273, H.277, M.278, V.293, G.294, N.295 Ligands: Y1.4, HEM.8, HEM.9, HEM.11 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:P.77, A:K.112, A:I.144, A:H.277, A:V.293 Hydrogen bonds: A:S.48, A:R.78, A:Y.82, A:D.86 Metal complexes: A:H.80, A:H.193 HEM.11: 21 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, H.378, G.379, F.381, F.382, H.383 Ligands: Y1.4, HEM.10, HEM.12 13 PLIP interactions: 13 interactions with chain A, Hydrophobic interactions: A:H.193, A:Y.261, A:Y.261, A:H.266, A:V.271, A:P.296, A:H.378, A:F.381, A:F.382, A:F.382 Hydrogen bonds: A:N.295 Metal complexes: A:H.277, A:H.383 HEM.12: 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: Y1.5, ACT.6, HEM.11, Y1.17, ACT.18, HEM.24 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:I.265, A:I.265, 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 Salt bridges: A:K.269, A:K.322, B:H.308 Metal complexes: A:H.266, A:H.308 HEM.20: 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, C.192, H.193, Y.196, F.198, V.216, H.255, A.376, H.378 Ligands: SO3.14, HEM.22 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:T.90, B:T.93, B:L.104, B:Y.196, B:Y.196, B:Y.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.21: 20 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, A.274, M.278, Y.280, Y.288, S.289, H.291 Ligands: HEM.22 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:W.31, B:Y.35, B:Y.35, B:Q.38, B:F.39, B:W.42, B:L.157, B:V.188, B:A.274 Hydrogen bonds: B:Q.38, 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.22: 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, V.188, C.189, Q.191, C.192, H.193, C.273, H.277, M.278, V.293, G.294, N.295 Ligands: Y1.16, HEM.20, HEM.21, HEM.23 11 PLIP interactions: 11 interactions with chain B, Hydrophobic interactions: B:P.77, B:K.112, B:I.144, B:H.277, B:V.293 Hydrogen bonds: B:S.48, B:R.78, B:Y.82, B:D.86 Metal complexes: B:H.80, B:H.193 HEM.23: 21 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, H.378, G.379, F.381, F.382, H.383 Ligands: Y1.16, HEM.22, HEM.24 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:H.193, B:Y.261, B:Y.261, B:H.266, B:V.271, B:P.296, B:H.378, B:F.381, B:F.382, B:F.382 Hydrogen bonds: B:N.295 Metal complexes: B:H.277, B:H.383 HEM.24: 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: Y1.5, ACT.6, HEM.12, Y1.17, ACT.18, HEM.23 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:I.265, B:I.265, 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 Salt bridges: B:K.269, B:K.322, A:H.308 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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