SMTL ID : 2xwz.1 (1 other biounit)

STRUCTURE OF THE RECOMBINANT NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed with nitrite

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: P.88, H.89, C.130, H.139, M.144 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.89, A:C.130, A:H.139 CU.2: 5 residues within 4Å: Chain A: D.92, H.94, H.129 Chain C: H.300 Ligands: NO2.3 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Metal complexes: C:H.300, A:H.94, A:H.129 CU.16: 4 residues within 4Å: Chain B: H.89, C.130, H.139, M.144 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.89, B:C.130, B:H.139 CU.17: 5 residues within 4Å: Chain A: H.300 Chain B: D.92, H.94, H.129 Ligands: NO2.6 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:H.94, B:H.129, A:H.300 CU.29: 5 residues within 4Å: Chain C: P.88, H.89, C.130, H.139, M.144 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.89, C:C.130, C:H.139 CU.30: 6 residues within 4Å: Chain B: H.249, H.300 Chain C: D.92, H.94, H.129 Ligands: NO.38 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: C:H.94, C:H.129, B:H.300, NO.38

2 x NO2: NITRITE ION(Non-covalent)

NO2.3: 7 residues within 4Å: Chain A: D.92, H.94, H.129 Chain C: H.249, I.251, H.300 Ligands: CU.2 No protein-ligand interaction detected (PLIP) NO2.6: 7 residues within 4Å: Chain A: H.249, I.251, H.300 Chain B: D.92, H.94, H.129 Ligands: CU.17 No protein-ligand interaction detected (PLIP)

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

SO4.4: 3 residues within 4Å: Chain A: G.293, V.294 Chain B: K.104 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain A: V.14, A.15 Ligand excluded by PLIP SO4.8: 4 residues within 4Å: Chain A: H.22, E.23, Q.24, H.165 Ligand excluded by PLIP SO4.9: 2 residues within 4Å: Chain A: Q.327, P.331 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain A: T.222, G.223, H.313 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: P.152, R.153, D.154 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain A: G.223, A.224 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: T.222, G.223, H.313 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain B: G.293, V.294 Chain C: K.104 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain B: R.270 Ligands: ACT.28 Ligand excluded by PLIP SO4.20: 2 residues within 4Å: Chain B: Q.327, P.331 Ligand excluded by PLIP SO4.21: 1 residues within 4Å: Chain A: R.270 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain B: K.42, M.44 Ligand excluded by PLIP SO4.23: 4 residues within 4Å: Chain B: H.22, E.23, Q.24, H.165 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: P.152, R.153, D.154 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain B: L.13, V.14, A.15 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain C: H.22, E.23, Q.24, A.25, H.165 Ligand excluded by PLIP SO4.32: 1 residues within 4Å: Chain C: R.270 Ligand excluded by PLIP SO4.33: 2 residues within 4Å: Chain C: V.14, A.15 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain C: S.28, G.29, K.31 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain C: Q.327, A.330, P.331 Ligand excluded by PLIP SO4.36: 4 residues within 4Å: Chain C: E.71, P.152, R.153, D.154 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain A: K.104 Chain C: G.293, V.294 Ligand excluded by PLIP

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

ACT.5: 7 residues within 4Å: Chain A: G.134, M.135, V.136, P.137, W.138, Y.197 Chain C: E.307 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.197 Hydrogen bonds: A:M.135, A:W.138 ACT.14: 8 residues within 4Å: Chain A: E.307 Chain B: G.134, M.135, V.136, P.137, W.138, Y.197, M.204 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:E.307, B:P.137 Hydrogen bonds: A:E.307, A:E.307, B:W.138 ACT.15: 6 residues within 4Å: Chain B: N.90, L.100, K.104, N.107, A.131, E.133 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.100, B:E.133 Hydrogen bonds: B:N.90, B:N.107, B:A.131 Water bridges: B:E.133 Salt bridges: B:K.104 ACT.26: 7 residues within 4Å: Chain B: E.307 Chain C: G.134, M.135, P.137, W.138, Y.197 Ligands: ACT.27 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:M.135, C:W.138, B:E.307 ACT.27: 6 residues within 4Å: Chain B: F.306 Chain C: G.134, M.135, V.136, P.137 Ligands: ACT.26 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:F.306 Hydrogen bonds: C:G.134, C:V.136 ACT.28: 6 residues within 4Å: Chain B: R.270, D.271, K.290 Chain C: D.121, R.122 Ligands: SO4.19 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:D.121 Water bridges: C:R.122 Salt bridges: C:R.122, B:R.270, B:K.290

1 x NO: NITRIC OXIDE(Non-covalent)

NO.38: 7 residues within 4Å: Chain B: H.249, I.251, H.300 Chain C: D.92, H.94, H.129 Ligands: CU.30 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leferink, N.G.H. et al., Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase. Biochemistry (2011)

Release Date

2011-05-18

Peptides

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

C
E

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE

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