- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.20 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)
- 2 x D6N: FeV(Non-covalent)
D6N.2: 16 residues within 4Å:- Chain A: V.57, K.83, Q.176, H.180, F.211, I.213, C.257, S.260, G.336, P.338, R.339, K.361, F.362, H.423
- Ligands: HCA.1, CO3.3
1 PLIP interactions:1 interactions with chain A,- Metal complexes: A:C.257
D6N.11: 16 residues within 4Å:- Chain D: V.57, K.83, Q.176, H.180, F.211, I.213, C.257, S.260, G.336, P.338, R.339, K.361, F.362, H.423
- Ligands: HCA.12, CO3.13
1 PLIP interactions:1 interactions with chain D,- Metal complexes: D:C.257
- 2 x CO3: CARBONATE ION(Non-functional Binders)
CO3.3: 6 residues within 4Å:- Chain A: T.335, G.336, G.337, P.338, R.339
- Ligands: D6N.2
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.335, A:G.337, A:R.339
CO3.13: 6 residues within 4Å:- Chain D: T.335, G.336, G.337, P.338, R.339
- Ligands: D6N.11
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:G.336, D:G.337, D:G.337
- 2 x H2S: HYDROSULFURIC ACID(Non-covalent)
- 2 x ZN: ZINC ION(Non-covalent)
ZN.5: 2 residues within 4Å:- Chain A: H.448
- Chain E: H.379
4 PLIP interactions:1 interactions with chain A, 1 interactions with chain E, 2 Ligand-Water interactions- Metal complexes: A:H.448, E:H.379, H2O.90, H2O.90
ZN.9: 2 residues within 4Å:- Chain B: H.379
- Chain D: H.448
4 PLIP interactions:1 interactions with chain D, 1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: D:H.448, B:H.379, H2O.23, H2O.68
- 2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)
CLF.6: 19 residues within 4Å:- Chain A: C.49, F.51, P.72, G.74, C.75, D.78, T.137, C.138, G.170
- Chain B: C.31, P.33, G.53, Q.54, G.55, C.56, F.59, T.114, C.115, S.153
9 PLIP interactions:4 interactions with chain B, 5 interactions with chain A,- Metal complexes: B:C.31, B:C.56, B:C.56, B:C.115, A:C.49, A:C.75, A:C.75, A:C.138
- Salt bridges: A:D.78
CLF.15: 19 residues within 4Å:- Chain D: C.49, F.51, P.72, G.74, C.75, D.78, T.137, C.138, G.170
- Chain E: C.31, P.33, G.53, Q.54, G.55, C.56, F.59, T.114, C.115, S.153
9 PLIP interactions:5 interactions with chain D, 4 interactions with chain E,- Salt bridges: D:D.78
- Metal complexes: D:C.49, D:C.75, D:C.75, D:C.138, E:C.31, E:C.56, E:C.56, E:C.115
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.7: 2 residues within 4Å:- Chain B: E.70
- Chain E: D.314
6 PLIP interactions:1 interactions with chain B, 1 interactions with chain E, 4 Ligand-Water interactions- Metal complexes: B:E.70, E:D.314, H2O.26, H2O.31, H2O.76, H2O.88
MG.8: 2 residues within 4Å:- Chain B: D.314
- Chain E: E.70
6 PLIP interactions:1 interactions with chain E, 1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: E:E.70, B:D.314, H2O.26, H2O.37, H2O.77, H2O.83
MG.10: 1 residues within 4Å:- Chain C: E.14
No protein-ligand interaction detected (PLIP)MG.16: 1 residues within 4Å:- Chain F: E.14
No protein-ligand interaction detected (PLIP)- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Sippel, D. et al., A bound reaction intermediate sheds light on the mechanism of nitrogenase. Science (2018)
- Release Date
- 2018-03-28
- Peptides
- Nitrogenase protein alpha chain: AD
Vanadium nitrogenase beta subunit, vnfK: BE
Vanadium nitrogenase, delta subunit, VnfG: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.20 Å
- Oligo State
- hetero-2-2-2-mer
- Ligands
- 2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)
- 2 x D6N: FeV(Non-covalent)
- 2 x CO3: CARBONATE ION(Non-functional Binders)
- 2 x H2S: HYDROSULFURIC ACID(Non-covalent)
- 2 x ZN: ZINC ION(Non-covalent)
- 2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Sippel, D. et al., A bound reaction intermediate sheds light on the mechanism of nitrogenase. Science (2018)
- Release Date
- 2018-03-28
- Peptides
- Nitrogenase protein alpha chain: AD
Vanadium nitrogenase beta subunit, vnfK: BE
Vanadium nitrogenase, delta subunit, VnfG: CF - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AD
DB
BE
EC
CF
F