- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- homo-trimer
- Ligands
- 6 x CU: COPPER (II) ION(Non-covalent)
- 9 x ZN: ZINC ION(Non-covalent)
ZN.3: 6 residues within 4Å:- Chain A: D.92, H.94, H.129
- Chain C: H.249, H.300
- Ligands: CU.2
4 PLIP interactions:2 interactions with chain A, 1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: A:H.94, A:H.129, C:H.300, H2O.11
ZN.5: 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.11
ZN.9: 2 residues within 4Å:- Chain A: D.4, H.8
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:H.8, H2O.12
ZN.14: 6 residues within 4Å:- Chain A: H.249, H.300
- Chain B: D.92, H.94, H.129
- Ligands: CU.13
4 PLIP interactions:2 interactions with chain B, 1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: B:H.94, B:H.129, A:H.300, H2O.23
ZN.16: 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.23
ZN.20: 2 residues within 4Å:- Chain B: D.4, H.8
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:H.8, H2O.23
ZN.25: 6 residues within 4Å:- Chain B: H.249, H.300
- Chain C: D.92, H.94, H.129
- Ligands: CU.24
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.34
ZN.27: 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.34
ZN.31: 2 residues within 4Å:- Chain C: D.4, H.8
2 PLIP interactions:1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:H.8, H2O.34
- 9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.4: 1 residues within 4Å:- Chain A: A.194
No protein-ligand interaction detected (PLIP)PEG.10: 6 residues within 4Å:- Chain A: K.10, V.11, T.12, E.34, F.35, T.36
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.36
- Water bridges: A:F.35, A:Q.76
PEG.11: 6 residues within 4Å:- Chain A: A.25, D.154, P.163, L.164, H.165
- Ligands: MES.7
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.154, A:P.163
PEG.15: 1 residues within 4Å:- Chain B: A.194
No protein-ligand interaction detected (PLIP)PEG.21: 6 residues within 4Å:- Chain B: K.10, V.11, T.12, E.34, F.35, T.36
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:T.36
- Water bridges: B:F.35, B:Q.76
PEG.22: 6 residues within 4Å:- Chain B: A.25, D.154, P.163, L.164, H.165
- Ligands: MES.18
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:D.154, B:P.163
PEG.26: 1 residues within 4Å:- Chain C: A.194
No protein-ligand interaction detected (PLIP)PEG.32: 6 residues within 4Å:- Chain C: K.10, V.11, T.12, E.34, F.35, T.36
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:T.36
- Water bridges: C:F.35, C:Q.76
PEG.33: 6 residues within 4Å:- Chain C: A.25, D.154, P.163, L.164, H.165
- Ligands: MES.29
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:D.154, C:P.163
- 6 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
MES.6: 6 residues within 4Å:- Chain A: D.47, D.48, K.49, V.218, F.306, E.307
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.48, A:K.49
- Salt bridges: A:K.49
MES.7: 7 residues within 4Å:- Chain A: P.163, L.164, H.165, T.234, T.288, K.290
- Ligands: PEG.11
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:H.165
- Water bridges: A:G.232
- Salt bridges: A:K.290
MES.17: 6 residues within 4Å:- Chain B: D.47, D.48, K.49, V.218, F.306, E.307
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:D.48, B:K.49
- Salt bridges: B:K.49
MES.18: 7 residues within 4Å:- Chain B: P.163, L.164, H.165, T.234, T.288, K.290
- Ligands: PEG.22
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:H.165
- Water bridges: B:G.232
- Salt bridges: B:K.290
MES.28: 6 residues within 4Å:- Chain C: D.47, D.48, K.49, V.218, F.306, E.307
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:D.48, C:K.49
- Salt bridges: C:K.49
MES.29: 7 residues within 4Å:- Chain C: P.163, L.164, H.165, T.234, T.288, K.290
- Ligands: PEG.33
3 PLIP interactions:3 interactions with chain C- Hydrogen bonds: C:H.165
- Water bridges: C:G.232
- Salt bridges: C:K.290
- 3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.8: 7 residues within 4Å:- Chain A: V.294, A.296, F.306, A.311, H.313
- Chain B: L.100, E.133
No protein-ligand interaction detected (PLIP)PG4.19: 7 residues within 4Å:- Chain B: V.294, A.296, F.306, A.311, H.313
- Chain C: L.100, E.133
No protein-ligand interaction detected (PLIP)PG4.30: 7 residues within 4Å:- Chain A: L.100, E.133
- Chain C: V.294, A.296, F.306, A.311, H.313
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
AB
AC
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.50 Å
- Oligo State
- homo-trimer
- Ligands
- 6 x CU: COPPER (II) ION(Non-covalent)
- 9 x ZN: ZINC ION(Non-covalent)
- 9 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 6 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 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
AB
AC
A