- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.30 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x F3S: FE3-S4 CLUSTER(Non-covalent)
F3S.2: 13 residues within 4Å:- Chain A: I.190, T.230, C.234, F.239, W.246, P.247, C.254, Y.255, G.256, C.257, N.258
- Chain B: K.211, Q.216
3 PLIP interactions:3 interactions with chain A,- Metal complexes: A:C.234, A:C.254, A:C.257
F3S.16: 13 residues within 4Å:- Chain C: I.190, T.230, C.234, F.239, W.246, P.247, C.254, Y.255, G.256, C.257, N.258
- Chain D: K.211, Q.216
3 PLIP interactions:3 interactions with chain C,- Metal complexes: C:C.234, C:C.254, C:C.257
- 7 x GOL: GLYCEROL(Non-functional Binders)
GOL.4: 7 residues within 4Å:- Chain A: K.207, E.208, F.209, L.223, H.269
- Chain B: F.458, K.460
8 PLIP interactions:3 interactions with chain B, 5 interactions with chain A- Hydrogen bonds: B:K.460, A:F.209
- Water bridges: B:R.51, B:R.51, A:K.207, A:H.222, A:H.222, A:L.223
GOL.5: 5 residues within 4Å:- Chain A: A.165, T.169
- Chain D: M.241, Y.443, I.447
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:A.165, A:T.169
GOL.6: 7 residues within 4Å:- Chain A: G.267, I.268, H.269, Q.270
- Chain B: D.49, R.51, D.52
6 PLIP interactions:4 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:H.269, B:D.52
- Water bridges: A:G.267, A:G.267, A:Q.270, B:D.49
GOL.10: 4 residues within 4Å:- Chain B: M.241, Y.443
- Chain C: A.165, T.169
2 PLIP interactions:1 interactions with chain B, 1 interactions with chain C- Hydrogen bonds: B:Y.443, C:A.165
GOL.14: 5 residues within 4Å:- Chain A: H.199, R.204, W.218
- Chain C: R.188, E.192
2 PLIP interactions:1 interactions with chain C, 1 interactions with chain A- Hydrogen bonds: C:R.188, A:R.204
GOL.19: 7 residues within 4Å:- Chain C: G.267, I.268, H.269, Q.270
- Chain D: D.49, R.51, D.52
5 PLIP interactions:2 interactions with chain D, 3 interactions with chain C- Water bridges: D:D.49, D:D.49, C:G.267
- Hydrogen bonds: C:H.269, C:H.269
GOL.23: 8 residues within 4Å:- Chain C: E.47, K.70, Y.71
- Chain D: G.162, Q.163, L.164, G.165, A.168
5 PLIP interactions:2 interactions with chain D, 3 interactions with chain C- Hydrogen bonds: D:L.164, D:G.165, C:K.70, C:K.70, C:Y.71
- 2 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)
FCO.7: 14 residues within 4Å:- Chain B: C.64, T.67, H.68, A.477, P.478, K.479, L.482, V.500, P.501, S.502, C.546, C.549
- Ligands: NI.8, OXY.13
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:K.479, B:S.502
- Metal complexes: B:C.64, B:C.549
FCO.20: 14 residues within 4Å:- Chain D: C.64, T.67, H.68, A.477, P.478, K.479, L.482, V.500, P.501, S.502, C.546, C.549
- Ligands: NI.21, OXY.25
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:K.479, D:S.502
- Metal complexes: D:C.64, D:C.549
- 2 x NI: NICKEL (II) ION(Non-covalent)
NI.8: 6 residues within 4Å:- Chain B: C.61, C.64, C.546, C.549
- Ligands: FCO.7, OXY.13
4 PLIP interactions:4 interactions with chain B- Metal complexes: B:C.61, B:C.64, B:C.546, B:C.549
NI.21: 6 residues within 4Å:- Chain D: C.61, C.64, C.546, C.549
- Ligands: FCO.20, OXY.25
4 PLIP interactions:4 interactions with chain D- Metal complexes: D:C.61, D:C.64, D:C.546, D:C.549
- 4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.9: 3 residues within 4Å:- Chain B: E.42, A.498, H.552
6 PLIP interactions:3 interactions with chain B, 3 Ligand-Water interactions- Metal complexes: B:E.42, B:A.498, B:H.552, H2O.15, H2O.15, H2O.15
MG.11: 2 residues within 4Å:- Chain B: N.81, N.294
No protein-ligand interaction detected (PLIP)MG.18: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.22: 3 residues within 4Å:- Chain D: E.42, A.498, H.552
6 PLIP interactions:3 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: D:E.42, D:A.498, D:H.552, H2O.49, H2O.50, H2O.51
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x OXY: OXYGEN MOLECULE(Non-covalent)
OXY.13: 7 residues within 4Å:- Chain B: C.61, V.63, C.64, K.479, C.546
- Ligands: FCO.7, NI.8
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:C.64, B:K.479
- Water bridges: B:K.479, B:K.479, B:K.479
OXY.25: 8 residues within 4Å:- Chain D: C.61, V.63, C.64, K.479, C.546, C.549
- Ligands: FCO.20, NI.21
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:C.64, D:K.479
- Water bridges: D:K.479, D:K.479
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Beaton, S.E. et al., Hydrogen activation by NiFe-hydrogenases - consolidating the role of the pendant arginine. To Be Published
- Release Date
- 2020-10-14
- Peptides
- Hydrogenase-2 small chain: AC
Hydrogenase-2 large chain: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
SSSC
TTTB
LLLD
MMM
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.30 Å
- Oligo State
- hetero-2-2-mer
- Ligands
- 4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)
- 2 x F3S: FE3-S4 CLUSTER(Non-covalent)
- 7 x GOL: GLYCEROL(Non-functional Binders)
- 2 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)
- 2 x NI: NICKEL (II) ION(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 2 x CL: CHLORIDE ION(Non-functional Binders)
- 2 x OXY: OXYGEN MOLECULE(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Beaton, S.E. et al., Hydrogen activation by NiFe-hydrogenases - consolidating the role of the pendant arginine. To Be Published
- Release Date
- 2020-10-14
- Peptides
- Hydrogenase-2 small chain: AC
Hydrogenase-2 large chain: BD - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
SSSC
TTTB
LLLD
MMM