- 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.2: 6 residues within 4Å:- Chain A: D.92, H.94, H.129
- Chain C: H.249, H.300
- Ligands: CU.4
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.12
ZN.8: 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.12
ZN.12: 4 residues within 4Å:- Chain A: A.3, D.4, L.6, H.8
2 PLIP interactions:1 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:H.8, H2O.13
ZN.14: 6 residues within 4Å:- Chain A: H.249, H.300
- Chain B: D.92, H.94, H.129
- Ligands: CU.16
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.25
ZN.20: 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.25
ZN.24: 4 residues within 4Å:- Chain B: A.3, D.4, L.6, H.8
2 PLIP interactions:1 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:H.8, H2O.25
ZN.26: 6 residues within 4Å:- Chain B: H.249, H.300
- Chain C: D.92, H.94, H.129
- Ligands: CU.28
4 PLIP interactions:1 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: B:H.300, C:H.94, C:H.129, H2O.37
ZN.32: 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.37
ZN.36: 4 residues within 4Å:- Chain C: A.3, D.4, L.6, H.8
2 PLIP interactions:1 interactions with chain C, 1 Ligand-Water interactions- Metal complexes: C:H.8, H2O.37
- 6 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
MES.3: 6 residues within 4Å:- Chain A: P.163, L.164, H.165, T.234, T.288, K.290
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:H.165
- Salt bridges: A:K.290
MES.10: 6 residues within 4Å:- Chain A: D.47, D.48, K.49, V.218, F.306, E.307
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.48, A:K.49
- Water bridges: A:K.49
- Salt bridges: A:K.49
MES.15: 6 residues within 4Å:- Chain B: P.163, L.164, H.165, T.234, T.288, K.290
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:H.165
- Salt bridges: B:K.290
MES.22: 6 residues within 4Å:- Chain B: D.47, D.48, K.49, V.218, F.306, E.307
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:D.48, B:K.49
- Water bridges: B:K.49
- Salt bridges: B:K.49
MES.27: 6 residues within 4Å:- Chain C: P.163, L.164, H.165, T.234, T.288, K.290
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:H.165
- Salt bridges: C:K.290
MES.34: 6 residues within 4Å:- Chain C: D.47, D.48, K.49, V.218, F.306, E.307
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:D.48, C:K.49
- Water bridges: C:K.49
- Salt bridges: C:K.49
- 12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
PEG.5: 3 residues within 4Å:- Chain A: P.21, H.22, E.23
1 PLIP interactions:1 interactions with chain A- Water bridges: A:E.23
PEG.6: 6 residues within 4Å:- Chain A: K.10, V.11, T.12, V.14, H.20, P.21
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.12
PEG.7: 8 residues within 4Å:- Chain A: K.10, V.11, E.34, F.35, T.36, Q.76, L.77, T.78
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:V.11, A:F.35, A:Q.76, A:T.78, A:T.78
PEG.9: 3 residues within 4Å:- Chain A: M.87, M.135, A.194
No protein-ligand interaction detected (PLIP)PEG.17: 3 residues within 4Å:- Chain B: P.21, H.22, E.23
1 PLIP interactions:1 interactions with chain B- Water bridges: B:E.23
PEG.18: 6 residues within 4Å:- Chain B: K.10, V.11, T.12, V.14, H.20, P.21
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:T.12
PEG.19: 8 residues within 4Å:- Chain B: K.10, V.11, E.34, F.35, T.36, Q.76, L.77, T.78
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:V.11, B:F.35, B:Q.76, B:T.78, B:T.78
PEG.21: 3 residues within 4Å:- Chain B: M.87, M.135, A.194
No protein-ligand interaction detected (PLIP)PEG.29: 3 residues within 4Å:- Chain C: P.21, H.22, E.23
1 PLIP interactions:1 interactions with chain C- Water bridges: C:E.23
PEG.30: 6 residues within 4Å:- Chain C: K.10, V.11, T.12, V.14, H.20, P.21
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:T.12
PEG.31: 8 residues within 4Å:- Chain C: K.10, V.11, E.34, F.35, T.36, Q.76, L.77, T.78
5 PLIP interactions:5 interactions with chain C- Hydrogen bonds: C:V.11, C:F.35, C:Q.76, C:T.78, C:T.78
PEG.33: 3 residues within 4Å:- Chain C: M.87, M.135, A.194
No protein-ligand interaction detected (PLIP)- 3 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
PG4.11: 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)PG4.23: 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)PG4.35: 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
BB
BC
B
- 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)
- 6 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)
- 12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 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
BB
BC
B