SMTL ID : 1wa0.1

Crystal Structure Of W138H Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-trimer

Ligands

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

CU.1: 5 residues within 4Å: Chain A: H.89, C.130, P.132, 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.249, H.300 4 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:H.300, A:H.94, A:H.129, H2O.7 CU.8: 5 residues within 4Å: Chain B: H.89, C.130, P.132, H.139, M.144 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.89, B:C.130, B:H.139 CU.9: 5 residues within 4Å: Chain A: H.249, H.300 Chain B: D.92, H.94, H.129 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.300, B:H.94, B:H.129, H2O.23 CU.15: 5 residues within 4Å: Chain C: H.89, C.130, P.132, H.139, M.144 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.89, C:C.130, C:H.139 CU.16: 5 residues within 4Å: Chain B: H.249, H.300 Chain C: D.92, H.94, H.129 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:H.94, C:H.129, B:H.300, H2O.39

6 x ZN: ZINC ION(Non-covalent)

ZN.3: 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.16 ZN.4: 3 residues within 4Å: Chain A: A.3, D.4, H.8 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.8, H2O.16 ZN.10: 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.32 ZN.11: 3 residues within 4Å: Chain B: A.3, D.4, H.8 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.8, H2O.32 ZN.17: 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.48 ZN.18: 3 residues within 4Å: Chain C: A.3, D.4, H.8 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.8, H2O.48

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

SO4.5: 4 residues within 4Å: Chain A: D.47, D.48, K.49, V.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.48, A:K.49 Salt bridges: A:K.49 SO4.12: 4 residues within 4Å: Chain B: D.47, D.48, K.49, V.218 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.48, B:K.49 Salt bridges: B:K.49 SO4.19: 4 residues within 4Å: Chain C: D.47, D.48, K.49, V.218 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.48, C:K.49 Salt bridges: C:K.49

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

PG4.6: 6 residues within 4Å: Chain A: V.294, A.296, F.306, A.311, H.313 Chain B: L.100 No protein-ligand interaction detected (PLIP) PG4.13: 6 residues within 4Å: Chain B: V.294, A.296, F.306, A.311, H.313 Chain C: L.100 No protein-ligand interaction detected (PLIP) PG4.20: 6 residues within 4Å: Chain A: L.100 Chain C: V.294, A.296, F.306, A.311, H.313 No protein-ligand interaction detected (PLIP)

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

MES.7: 5 residues within 4Å: Chain A: P.163, L.164, H.165, T.234, T.288 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.165 MES.14: 5 residues within 4Å: Chain B: P.163, L.164, H.165, T.234, T.288 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.165 MES.21: 5 residues within 4Å: Chain C: P.163, L.164, H.165, T.234, T.288 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.165

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barrett, M.L. et al., Insights Into Redox Partner Interactions and Substrate Binding in Nitrite Reductase from Alcaligenes Xylosoxidans: Crystal Structures of the Trp138His and His313Gln Mutants. Biochemistry (2004)

Release Date

2005-01-04

Peptides

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
X

B
X

C
X

DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE