- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)
- 2 x ICG: iron-sulfur-molybdenum cluster with interstitial carbon with selenium incorporated(Non-covalent)
ICG.2: 15 residues within 4Å:- Chain A: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442
- Ligands: HCA.1
2 PLIP interactions:2 interactions with chain A,- Salt bridges: A:E.380
- Metal complexes: A:C.275
ICG.13: 15 residues within 4Å:- Chain C: V.70, R.96, H.195, Y.229, I.231, C.275, S.278, I.355, G.356, G.357, L.358, R.359, F.381, H.442
- Ligands: HCA.12
2 PLIP interactions:2 interactions with chain C,- Salt bridges: C:E.380
- Metal complexes: C:C.275
- 9 x IMD: IMIDAZOLE(Non-covalent)
IMD.3: 2 residues within 4Å:- Chain A: E.287, W.294
3 PLIP interactions:3 interactions with chain A- Water bridges: A:W.294
- pi-Stacking: A:W.294, A:W.294
IMD.6: 5 residues within 4Å:- Chain B: L.253, D.256, G.275, T.276, E.280
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:K.241
- Water bridges: B:G.275
IMD.7: 7 residues within 4Å:- Chain B: I.469, S.482, T.483, T.484, Q.492, I.493, T.496
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:Y.233, B:S.482, B:Q.492
IMD.8: 5 residues within 4Å:- Chain A: G.157, L.158, F.186
- Chain B: E.120, A.123
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:E.120
- Water bridges: A:R.187
IMD.14: 2 residues within 4Å:- Chain C: E.287, W.294
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:E.287
- Water bridges: C:E.287, C:E.296
- pi-Stacking: C:W.294
IMD.16: 6 residues within 4Å:- Chain C: G.406, Y.407, E.410, I.430
- Chain D: F.269, M.271
No protein-ligand interaction detected (PLIP)IMD.18: 7 residues within 4Å:- Chain D: I.469, S.482, T.483, T.484, Q.492, I.493, T.496
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:T.483, D:T.496
- Water bridges: D:S.482
IMD.19: 5 residues within 4Å:- Chain D: L.253, D.256, G.275, T.276, E.280
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:E.280
IMD.20: 5 residues within 4Å:- Chain C: G.157, L.158, F.186
- Chain D: E.120, A.123
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain C- Hydrogen bonds: D:E.120
- Water bridges: C:R.187
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)
CLF.5: 18 residues within 4Å:- Chain A: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185
- Chain B: C.70, P.72, S.92, G.94, C.95, Y.98, T.152, C.153, S.188
9 PLIP interactions:5 interactions with chain A, 4 interactions with chain B,- Salt bridges: A:E.153
- Metal complexes: A:C.62, A:C.88, A:C.88, A:C.154, B:C.70, B:C.95, B:C.95, B:C.153
CLF.17: 19 residues within 4Å:- Chain C: C.62, Y.64, P.85, G.87, C.88, Y.91, E.153, C.154, G.185
- Chain D: C.70, P.72, S.92, G.94, C.95, Y.98, F.99, T.152, C.153, S.188
9 PLIP interactions:4 interactions with chain D, 5 interactions with chain C,- Metal complexes: D:C.70, D:C.95, D:C.95, D:C.153, C:C.62, C:C.88, C:C.88, C:C.154
- Salt bridges: C:E.153
- 2 x FE2: FE (II) ION(Non-covalent)
FE2.9: 4 residues within 4Å:- Chain B: D.353, D.357
- Chain D: R.108, E.109
6 PLIP interactions:2 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: D:R.108, D:E.109, B:D.353, B:D.357, H2O.15, H2O.47
FE2.11: 4 residues within 4Å:- Chain B: R.108, E.109
- Chain D: D.353, D.357
6 PLIP interactions:2 interactions with chain D, 2 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: D:D.353, D:D.357, B:R.108, B:E.109, H2O.21, H2O.43
- 2 x SE: SELENIUM ATOM(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Spatzal, T. et al., Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor. Elife (2015)
- Release Date
- 2015-12-30
- Peptides
- Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CB
BD
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.60 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 2 x HCA: 3-HYDROXY-3-CARBOXY-ADIPIC ACID(Non-covalent)
- 2 x ICG: iron-sulfur-molybdenum cluster with interstitial carbon with selenium incorporated(Non-covalent)
- 9 x IMD: IMIDAZOLE(Non-covalent)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x CLF: FE(8)-S(7) CLUSTER(Non-covalent)
- 2 x FE2: FE (II) ION(Non-covalent)
- 2 x SE: SELENIUM ATOM(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Spatzal, T. et al., Catalysis-dependent selenium incorporation and migration in the nitrogenase active site iron-molybdenum cofactor. Elife (2015)
- Release Date
- 2015-12-30
- Peptides
- Nitrogenase molybdenum-iron protein alpha chain: AC
Nitrogenase molybdenum-iron protein beta chain: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AC
CB
BD
D