SMTL ID : 1oah.1

Cytochrome c Nitrite Reductase from Desulfovibrio desulfuricans ATCC 27774: The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

10 x HEC: HEME C(Covalent)

HEC.1: 19 residues within 4Å: Chain A: Y.112, N.113, T.115, D.124, F.125, I.128, R.130, C.146, C.149, K.150, C.233, H.234, Y.237, F.239, F.252, H.299, N.429 Ligands: HEC.3, CL.8 19 PLIP interactions: 18 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:T.115, A:F.125, A:F.125, A:I.128, A:Y.237, A:Y.237, A:F.239, A:F.252 Hydrogen bonds: A:N.113, A:A.427, A:N.429 Water bridges: A:Y.112, A:Y.112, A:N.113, A:R.130 Salt bridges: A:R.130, A:H.299 pi-Stacking: A:H.299 Metal complexes: H2O.6 HEC.2: 18 residues within 4Å: Chain A: F.54, Q.57, Y.61, G.187, C.188, C.191, H.192, M.197, L.199, R.222, R.226, V.229, M.322, I.332, S.333, H.335, M.337 Ligands: HEC.3 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:F.54, A:F.54, A:Q.57, A:Q.57, A:Y.61, A:Y.61, A:L.199, A:V.229 Hydrogen bonds: A:Q.57, A:S.333 Salt bridges: A:R.222, A:R.226 Metal complexes: A:H.192, A:H.335 HEC.3: 26 residues within 4Å: Chain A: G.75, S.76, T.115, R.116, G.117, H.118, Y.120, A.121, D.124, C.149, K.150, I.186, N.190, Y.202, V.229, C.230, Q.232, C.233, H.234, H.321, M.337, T.338 Ligands: HEC.1, HEC.2, HEC.4, CA.7 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:K.150, A:I.186, A:Y.202, A:H.321 Hydrogen bonds: A:T.115, A:R.116, A:Y.120, A:D.124, A:M.337, A:T.338 Water bridges: A:S.76, A:S.339, A:S.339 Salt bridges: A:K.342 Metal complexes: A:H.118, A:H.234 HEC.4: 26 residues within 4Å: Chain A: T.71, K.74, G.75, E.114, T.115, C.230, H.234, E.301, Y.302, F.305, H.310, V.315, S.316, C.317, C.320, H.321, S.339, P.340, M.341, Q.369, N.429, F.433, H.434 Ligands: HEC.3, HEC.5, CA.7 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:H.234, A:E.301, A:E.301, A:F.305, A:F.305, A:V.315, A:N.429, A:F.433, A:F.433 Hydrogen bonds: A:T.71, A:G.75, A:S.339, A:S.339, A:Q.369 Water bridges: A:Y.73, A:Y.73, A:S.339 Salt bridges: A:K.74 Metal complexes: A:H.321, A:H.434 HEC.5: 22 residues within 4Å: Chain A: P.309, H.310, A.313, V.315, D.319, C.320, P.340, M.346, A.348, C.349, Q.351, C.352, H.353, R.364, V.365, F.433, P.436 Chain B: P.309, H.353, K.356 Ligands: HEC.4, HEC.17 16 PLIP interactions: 13 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:A.313, A:V.315, A:D.319, A:P.340, A:R.364, A:V.365, A:F.433 Water bridges: A:R.364, A:R.364, A:T.368, A:T.368, B:P.309 Metal complexes: A:H.310, A:H.353 Salt bridges: B:H.353, B:K.356 HEC.13: 20 residues within 4Å: Chain B: Y.112, N.113, T.115, D.124, F.125, I.128, R.130, L.142, C.146, C.149, K.150, C.233, H.234, Y.237, F.239, F.252, H.299, N.429 Ligands: HEC.15, CL.20 18 PLIP interactions: 17 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:T.115, B:F.125, B:F.125, B:I.128, B:L.142, B:Y.237, B:Y.237, B:F.239, B:F.252 Hydrogen bonds: B:N.113, B:N.429, B:N.429 Water bridges: B:N.113, B:R.130 Salt bridges: B:R.130, B:H.299 pi-Stacking: B:H.299 Metal complexes: H2O.16 HEC.14: 19 residues within 4Å: Chain B: F.54, Q.57, Y.61, G.187, C.188, C.191, H.192, M.197, L.199, R.222, R.226, V.229, M.322, Y.324, I.332, S.333, H.335, M.337 Ligands: HEC.15 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:F.54, B:F.54, B:Q.57, B:Q.57, B:Y.61, B:Y.61, B:L.199, B:V.229 Hydrogen bonds: B:Q.57, B:S.333 Water bridges: B:R.222, B:R.222 Salt bridges: B:R.222, B:R.226 Metal complexes: B:H.192, B:H.335 HEC.15: 27 residues within 4Å: Chain B: G.75, S.76, T.115, R.116, G.117, H.118, Y.120, A.121, D.124, C.149, K.150, I.186, N.190, Y.202, V.229, C.230, Q.232, C.233, H.234, H.321, M.322, M.337, T.338 Ligands: HEC.13, HEC.14, HEC.16, CA.19 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:K.150, B:I.186, B:Y.202, B:H.321 Hydrogen bonds: B:R.116, B:Y.120, B:M.337, B:T.338 Water bridges: B:S.76, B:S.339, B:S.339 Salt bridges: B:K.342 Metal complexes: B:H.118, B:H.234 HEC.16: 27 residues within 4Å: Chain B: T.71, K.74, G.75, E.114, T.115, C.230, H.234, E.301, Y.302, F.305, H.310, V.315, S.316, C.317, C.320, H.321, S.339, P.340, M.341, Q.369, N.429, S.430, F.433, H.434 Ligands: HEC.15, HEC.17, CA.19 21 PLIP interactions: 21 interactions with chain B, Hydrophobic interactions: B:H.234, B:E.301, B:E.301, B:F.305, B:F.305, B:H.310, B:V.315, B:N.429, B:F.433, B:F.433 Hydrogen bonds: B:G.75, B:S.339, B:S.339, B:Q.369 Water bridges: B:Y.73, B:Y.73, B:T.115, B:S.339 Salt bridges: B:K.74 Metal complexes: B:H.321, B:H.434 HEC.17: 22 residues within 4Å: Chain A: P.309, H.353, K.356 Chain B: P.309, H.310, A.313, V.315, D.319, C.320, P.340, M.346, A.348, C.349, Q.351, C.352, H.353, R.364, V.365, F.433, P.436 Ligands: HEC.5, HEC.16 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A, Hydrophobic interactions: B:A.313, B:V.315, B:V.315, B:D.319, B:P.340, B:R.364, B:V.365, B:F.433 Water bridges: B:R.364, B:T.368, B:T.368, B:T.368, A:P.309, A:Y.360 Metal complexes: B:H.310, B:H.353 Salt bridges: A:H.353, A:K.356

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: E.236, Y.237, K.296, Q.298 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.236, A:Y.237, A:K.296, H2O.6, H2O.6 CA.7: 5 residues within 4Å: Chain A: G.75, E.114, T.115 Ligands: HEC.3, HEC.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:G.75, A:E.114, A:T.115, A:T.115 CA.18: 4 residues within 4Å: Chain B: E.236, Y.237, K.296, Q.298 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.236, B:Y.237, B:K.296, H2O.15, H2O.15 CA.19: 5 residues within 4Å: Chain B: G.75, E.114, T.115 Ligands: HEC.15, HEC.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:G.75, B:E.114, B:T.115, B:T.115

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 4 residues within 4Å: Chain A: P.107, F.108, R.130 Ligands: HEC.1 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: K.93, H.94 Ligands: ZN.9 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: H.399, D.462 Ligands: ZN.10 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: P.107, F.108, R.130 Ligands: HEC.13 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 2 residues within 4Å: Chain A: H.94 Ligands: CL.11 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.94 ZN.10: 3 residues within 4Å: Chain A: H.399, D.462 Ligands: CL.12 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.399, A:D.462

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cunha, C.A. et al., Cytochrome C Nitrite Reductase from Desulfovibrio Desulfuricans Atcc 27774. The Relevance of the Two Calcium Sites in the Structure of the Catalytic Subunit (Nrfa). J.Biol.Chem. (2003)

Release Date

2003-05-08

Peptides

CYTOCHROME C NITRITE REDUCTASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CYTOCHROME C NITRITE REDUCTASE