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

STRUCTURE OF THE N90S MUTANT OF NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.1: 7 residues within 4Å: Chain A: V.294, A.296, F.306, A.311, H.313 Chain C: L.100, E.133 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.133 PG4.10: 7 residues within 4Å: Chain A: L.100, E.133 Chain B: V.294, A.296, F.306, A.311, H.313 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.133 PG4.19: 7 residues within 4Å: Chain B: L.100, E.133 Chain C: V.294, A.296, F.306, A.311, H.313 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.133

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

CU.2: 4 residues within 4Å: Chain A: 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.3: 5 residues within 4Å: Chain A: D.92, H.94, H.129 Chain B: H.249, H.300 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.94, A:H.129, B:H.300, H2O.5 CU.11: 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.12: 5 residues within 4Å: Chain B: D.92, H.94, H.129 Chain C: H.249, H.300 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:H.94, B:H.129, C:H.300, H2O.18 CU.20: 4 residues within 4Å: Chain C: 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.21: 5 residues within 4Å: Chain A: H.249, H.300 Chain C: D.92, H.94, H.129 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.94, C:H.129, A:H.300, H2O.31

6 x ZN: ZINC ION(Non-covalent)

ZN.4: 3 residues within 4Å: Chain A: H.165, D.167, T.234 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.165, A:D.167, A:D.167, H2O.13 ZN.6: 3 residues within 4Å: Chain A: D.4, L.6, H.8 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.8, H2O.13, H2O.13 ZN.13: 3 residues within 4Å: Chain B: H.165, D.167, T.234 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.165, B:D.167, B:D.167, H2O.26 ZN.15: 3 residues within 4Å: Chain B: D.4, L.6, H.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.8, H2O.26, H2O.26 ZN.22: 3 residues within 4Å: Chain C: H.165, D.167, T.234 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.165, C:D.167, C:D.167, H2O.39 ZN.24: 3 residues within 4Å: Chain C: D.4, L.6, H.8 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.8, H2O.39, H2O.39

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.5: 3 residues within 4Å: Chain A: M.135, A.194, Y.197 No protein-ligand interaction detected (PLIP) PEG.9: 5 residues within 4Å: Chain A: D.121, R.122 Chain B: D.256, R.270, K.290 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.257, B:K.290 Water bridges: B:R.270, A:D.121, A:D.121 PEG.14: 3 residues within 4Å: Chain B: M.135, A.194, Y.197 No protein-ligand interaction detected (PLIP) PEG.18: 5 residues within 4Å: Chain B: D.121, R.122 Chain C: D.256, R.270, K.290 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:W.257, C:R.270, C:K.290 Water bridges: C:R.270, B:D.121, B:D.121 PEG.23: 3 residues within 4Å: Chain C: M.135, A.194, Y.197 No protein-ligand interaction detected (PLIP) PEG.27: 5 residues within 4Å: Chain A: D.256, R.270, K.290 Chain C: D.121, R.122 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Water bridges: C:D.121, C:D.121, A:R.270 Hydrogen bonds: A:W.257, A:K.290

6 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 6 residues within 4Å: Chain A: D.47, D.48, K.49, V.218, F.306, E.307 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.47, A:D.48, A:D.48, A:K.49 Salt bridges: A:K.49 MES.8: 5 residues within 4Å: Chain A: P.163, L.164, H.165, T.234, T.288 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.165 Water bridges: A:T.234 MES.16: 6 residues within 4Å: Chain B: D.47, D.48, K.49, V.218, F.306, E.307 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.47, B:D.48, B:D.48, B:K.49 Salt bridges: B:K.49 MES.17: 5 residues within 4Å: Chain B: P.163, L.164, H.165, T.234, T.288 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.165, B:H.165 Water bridges: B:T.234 MES.25: 6 residues within 4Å: Chain C: D.47, D.48, K.49, V.218, F.306, E.307 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.47, C:D.48, C:D.48, C:K.49 Salt bridges: C:K.49 MES.26: 5 residues within 4Å: Chain C: P.163, L.164, H.165, T.234, T.288 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.165 Water bridges: C:T.234

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hough, M.A. et al., Identification of the Proton Channel to the Active Site Type 2 Cu Centre of Nitrite Reductase: Structural and Enzymatic Properties of the His254Phe and Asn90Ser Mutants. Biochemistry (2008)

Release Date

2011-05-18

Peptides

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE

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