SMTL ID : 2zoo.1

Crystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-trimer

Ligands

3 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 12 residues within 4Å: Chain A: P.362, G.363 Chain B: K.307 Chain C: E.99, S.100, S.101, F.102, T.103, A.104, H.107, T.108, S.109 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:A.104, C:S.100, C:F.102, C:S.109 Water bridges: C:E.99, C:T.110, B:N.311, B:N.311 GLC-FRU.8: 12 residues within 4Å: Chain A: E.99, S.100, S.101, F.102, T.103, A.104, H.107, T.108, S.109 Chain B: P.362, G.363 Chain C: K.307 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:A.104, A:S.100, A:F.102, A:S.109 Water bridges: A:E.99, A:T.110, C:N.311, C:N.311 GLC-FRU.15: 12 residues within 4Å: Chain A: K.307 Chain B: E.99, S.100, S.101, F.102, T.103, A.104, H.107, T.108, S.109 Chain C: P.362, G.363 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.104, B:S.100, B:F.102, B:S.109 Water bridges: B:E.99, B:T.110, A:N.311, A:N.311

6 x CU: COPPER (II) ION(Non-covalent)

CU.2: 5 residues within 4Å: Chain A: P.83, H.84, C.125, H.133, M.138 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.84, A:C.125, A:H.133 CU.3: 5 residues within 4Å: Chain A: D.87, H.89, H.124 Chain C: H.230, H.279 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.279, A:H.89, A:H.124, H2O.16 CU.9: 5 residues within 4Å: Chain B: P.83, H.84, C.125, H.133, M.138 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.84, B:C.125, B:H.133 CU.10: 5 residues within 4Å: Chain A: H.230, H.279 Chain B: D.87, H.89, H.124 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: B:H.89, B:H.124, A:H.279, H2O.31 CU.16: 5 residues within 4Å: Chain C: P.83, H.84, C.125, H.133, M.138 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.84, C:C.125, C:H.133 CU.17: 5 residues within 4Å: Chain B: H.230, H.279 Chain C: D.87, H.89, H.124 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.89, C:H.124, B:H.279, H2O.47

3 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.4: 29 residues within 4Å: Chain A: N.349, C.350, C.353, H.354, A.364, F.365, P.366, P.367, L.368, S.371, Y.373, L.374, G.381, I.385, L.389, S.390, G.391, I.393, V.395, Y.400, N.401, G.402, V.403, M.404, P.405, L.409 Chain B: Q.321 Chain C: A.128, P.129 16 PLIP interactions: 1 interactions with chain C, 15 interactions with chain A, Hydrophobic interactions: C:P.129, A:F.365, A:P.366, A:L.368, A:L.368, A:Y.373, A:Y.373, A:L.374, A:L.389, A:V.395, A:M.404, A:L.409 Hydrogen bonds: A:S.371, A:G.402 Water bridges: A:N.401 Metal complexes: A:H.354 HEM.11: 29 residues within 4Å: Chain A: A.128, P.129 Chain B: N.349, C.350, C.353, H.354, A.364, F.365, P.366, P.367, L.368, S.371, Y.373, L.374, G.381, I.385, L.389, S.390, G.391, I.393, V.395, Y.400, N.401, G.402, V.403, M.404, P.405, L.409 Chain C: Q.321 16 PLIP interactions: 1 interactions with chain A, 15 interactions with chain B, Hydrophobic interactions: A:P.129, B:F.365, B:P.366, B:L.368, B:L.368, B:Y.373, B:Y.373, B:L.374, B:L.389, B:V.395, B:M.404, B:L.409 Hydrogen bonds: B:S.371, B:G.402 Water bridges: B:N.401 Metal complexes: B:H.354 HEM.18: 29 residues within 4Å: Chain A: Q.321 Chain B: A.128, P.129 Chain C: N.349, C.350, C.353, H.354, A.364, F.365, P.366, P.367, L.368, S.371, Y.373, L.374, G.381, I.385, L.389, S.390, G.391, I.393, V.395, Y.400, N.401, G.402, V.403, M.404, P.405, L.409 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain B, Hydrophobic interactions: C:F.365, C:P.366, C:L.368, C:L.368, C:Y.373, C:Y.373, C:L.374, C:L.389, C:V.395, C:M.404, C:L.409, B:P.129 Hydrogen bonds: C:S.371, C:G.402 Water bridges: C:N.401 Metal complexes: C:H.354

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

SO4.5: 4 residues within 4Å: Chain A: D.24, S.26, R.65, K.147 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.26 Salt bridges: A:R.65, A:K.147 SO4.6: 3 residues within 4Å: Chain A: N.334, K.335, K.431 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.335 Water bridges: A:N.334, A:D.336, A:K.431, A:K.431, A:K.431 Salt bridges: A:K.431 SO4.7: 4 residues within 4Å: Chain A: R.41, A.43, D.44, G.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.45 SO4.12: 4 residues within 4Å: Chain B: D.24, S.26, R.65, K.147 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.26 Salt bridges: B:R.65, B:K.147 SO4.13: 3 residues within 4Å: Chain B: N.334, K.335, K.431 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.335 Water bridges: B:N.334, B:D.336, B:K.431, B:K.431, B:K.431 Salt bridges: B:K.431 SO4.14: 4 residues within 4Å: Chain B: R.41, A.43, D.44, G.45 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.45 SO4.19: 4 residues within 4Å: Chain C: D.24, S.26, R.65, K.147 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.26 Salt bridges: C:R.65, C:K.147 SO4.20: 3 residues within 4Å: Chain C: N.334, K.335, K.431 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.335 Water bridges: C:N.334, C:D.336, C:K.431, C:K.431, C:K.431 Salt bridges: C:K.431 SO4.21: 4 residues within 4Å: Chain C: R.41, A.43, D.44, G.45 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.45

Links

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Citation

Nojiri, M. et al., Electron transfer processes within and between proteins containing the HEME C and blue Cu. To be Published

Release Date

2009-06-09

Peptides

Probable nitrite reductase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Probable nitrite reductase