SMTL ID : 1fs9.1

CYTOCHROME C NITRITE REDUCTASE FROM WOLINELLA SUCCINOGENES-AZIDE COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: E.217, Y.218, Y.255, K.274, Q.276 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.217, A:Y.218, A:K.274, H2O.4, H2O.9 CA.11: 5 residues within 4Å: Chain B: E.217, Y.218, Y.255, K.274, Q.276 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.217, B:Y.218, B:K.274, H2O.20, H2O.25

6 x Y1: YTTRIUM ION(Non-covalent)

Y1.2: 1 residues within 4Å: Chain A: E.52 No protein-ligand interaction detected (PLIP) Y1.3: 3 residues within 4Å: Chain A: P.99 Ligands: HEC.8, HEC.9 No protein-ligand interaction detected (PLIP) Y1.4: 5 residues within 4Å: Chain A: E.408 Chain B: E.408 Ligands: HEC.10, Y1.14, HEC.20 No protein-ligand interaction detected (PLIP) Y1.12: 1 residues within 4Å: Chain B: E.52 No protein-ligand interaction detected (PLIP) Y1.13: 3 residues within 4Å: Chain B: P.99 Ligands: HEC.18, HEC.19 No protein-ligand interaction detected (PLIP) Y1.14: 5 residues within 4Å: Chain A: E.408 Chain B: E.408 Ligands: Y1.4, HEC.10, HEC.20 No protein-ligand interaction detected (PLIP)

2 x AZI: AZIDE ION(Non-covalent)

AZI.5: 5 residues within 4Å: Chain A: F.92, R.114, Y.218, Q.276 Ligands: HEC.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.114, A:R.114, A:Y.218, A:Q.276 AZI.15: 5 residues within 4Å: Chain B: F.92, R.114, Y.218, Q.276 Ligands: HEC.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.114, B:R.114, B:Y.218, B:Q.276

10 x HEC: HEME C(Covalent)

HEC.6: 24 residues within 4Å: Chain A: Y.96, N.97, P.99, D.108, N.109, T.112, R.114, T.115, L.126, C.130, C.133, K.134, Y.185, Q.213, C.214, H.215, Y.218, F.220, V.238, H.277, A.398, H.400 Ligands: AZI.5, HEC.8 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:P.99, A:T.112, A:T.115, A:L.126, A:Y.218, A:Y.218, A:F.220, A:V.238, A:H.277 Hydrogen bonds: A:N.97, A:A.398 Water bridges: A:R.114, A:R.114, A:H.400 Salt bridges: A:R.114, A:H.277, A:H.400 Metal complexes: H2O.1 HEC.7: 19 residues within 4Å: Chain A: W.53, Y.57, Q.60, F.61, W.64, G.167, C.168, C.171, H.172, L.179, H.203, R.207, M.300, Y.302, K.309, Y.310, S.311, H.313 Ligands: HEC.8 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:W.53, A:Y.57, A:Y.57, A:Q.60, A:F.61, A:W.64, A:L.179, A:L.179 Hydrogen bonds: A:Y.302, A:S.311 Water bridges: A:H.203 Salt bridges: A:H.203, A:R.207, A:H.313 Metal complexes: A:H.172, A:H.313 HEC.8: 25 residues within 4Å: Chain A: S.70, P.99, R.100, G.101, H.102, Y.104, A.105, D.108, C.133, K.134, I.166, V.210, C.211, Q.213, C.214, H.215, C.295, H.299, M.300, V.315, G.316 Ligands: Y1.3, HEC.6, HEC.7, HEC.9 10 PLIP interactions: 10 interactions with chain A, Hydrophobic interactions: A:A.105, A:K.134, A:I.166, A:H.299, A:V.315 Hydrogen bonds: A:S.70, A:Y.104, A:D.108 Metal complexes: A:H.102, A:H.215 HEC.9: 22 residues within 4Å: Chain A: P.99, C.211, H.215, W.280, Y.283, H.288, V.293, S.294, C.295, C.298, H.299, N.317, P.318, L.319, H.400, G.401, F.403, F.404, H.405 Ligands: Y1.3, HEC.8, HEC.10 11 PLIP interactions: 11 interactions with chain A, Hydrophobic interactions: A:H.215, A:Y.283, A:V.293, A:P.318, A:H.400, A:F.404, A:F.404 Hydrogen bonds: A:N.317, A:N.317 Metal complexes: A:H.299, A:H.405 HEC.10: 20 residues within 4Å: Chain A: I.287, H.288, V.293, C.298, P.318, S.325, C.326, C.329, H.330, L.337, I.340, K.344, F.404, P.407 Chain B: H.330, E.408 Ligands: Y1.4, HEC.9, Y1.14, HEC.20 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:I.287, A:I.287, A:V.293, A:P.318, A:L.337, A:I.340, A:F.404 Salt bridges: A:K.344, B:H.330 Metal complexes: A:H.288, A:H.330 HEC.16: 24 residues within 4Å: Chain B: Y.96, N.97, P.99, D.108, N.109, T.112, R.114, T.115, L.126, C.130, C.133, K.134, Y.185, Q.213, C.214, H.215, Y.218, F.220, V.238, H.277, A.398, H.400 Ligands: AZI.15, HEC.18 18 PLIP interactions: 17 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:P.99, B:T.112, B:T.115, B:L.126, B:Y.218, B:Y.218, B:F.220, B:V.238, B:H.277 Hydrogen bonds: B:N.97, B:A.398 Water bridges: B:R.114, B:R.114, B:H.400 Salt bridges: B:R.114, B:H.277, B:H.400 Metal complexes: H2O.17 HEC.17: 19 residues within 4Å: Chain B: W.53, Y.57, Q.60, F.61, W.64, G.167, C.168, C.171, H.172, L.179, H.203, R.207, M.300, Y.302, K.309, Y.310, S.311, H.313 Ligands: HEC.18 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:W.53, B:Y.57, B:Y.57, B:Q.60, B:F.61, B:W.64, B:L.179, B:L.179 Hydrogen bonds: B:Y.302, B:S.311 Water bridges: B:H.203 Salt bridges: B:H.203, B:R.207, B:H.313 Metal complexes: B:H.172, B:H.313 HEC.18: 25 residues within 4Å: Chain B: S.70, P.99, R.100, G.101, H.102, Y.104, A.105, D.108, C.133, K.134, I.166, V.210, C.211, Q.213, C.214, H.215, C.295, H.299, M.300, V.315, G.316 Ligands: Y1.13, HEC.16, HEC.17, HEC.19 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:A.105, B:K.134, B:I.166, B:H.299, B:V.315 Hydrogen bonds: B:S.70, B:S.70, B:R.100, B:Y.104, B:D.108 Metal complexes: B:H.102, B:H.215 HEC.19: 22 residues within 4Å: Chain B: P.99, C.211, H.215, W.280, Y.283, H.288, V.293, S.294, C.295, C.298, H.299, N.317, P.318, L.319, H.400, G.401, F.403, F.404, H.405 Ligands: Y1.13, HEC.18, HEC.20 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:H.215, B:Y.283, B:V.293, B:P.318, B:H.400, B:F.404, B:F.404 Hydrogen bonds: B:N.317, B:N.317 Water bridges: B:H.400, B:H.400 Metal complexes: B:H.299, B:H.405 HEC.20: 20 residues within 4Å: Chain A: H.330, E.408 Chain B: I.287, H.288, V.293, C.298, P.318, S.325, C.326, C.329, H.330, L.337, I.340, K.344, F.404, P.407 Ligands: Y1.4, HEC.10, Y1.14, HEC.19 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: B:I.287, B:I.287, B:V.293, B:P.318, B:L.337, B:I.340, B:F.404 Salt bridges: B:K.344, A:H.330 Metal complexes: B:H.288, B:H.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Einsle, O. et al., Cytochrome c nitrite reductase from Wolinella succinogenes. Structure at 1.6 A resolution, inhibitor binding, and heme-packing motifs. J.Biol.Chem. (2000)

Release Date

2001-01-17

Peptides

CYTOCHROME C NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

CYTOCHROME C NITRITE REDUCTASE