SMTL ID : 5jrd.1

E. coli Hydrogenase-1 variant P508A

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

hetero-2-2-mer

Ligands

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.1: 12 residues within 4Å: Chain A: H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, P.224, I.243 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.187, A:C.190, A:C.215, A:C.221 SF4.11: 11 residues within 4Å: Chain C: H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, I.243 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.187, C:C.190, C:C.215, C:C.221

2 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.2: 10 residues within 4Å: Chain A: T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain B: K.226 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.230, A:C.249, A:C.252 F3S.12: 10 residues within 4Å: Chain C: T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 Chain D: K.226 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.230, C:C.249, C:C.252

2 x SF3: FE4-S3 CLUSTER(Non-covalent)

SF3.3: 12 residues within 4Å: Chain A: E.16, C.17, T.18, C.19, C.20, E.76, T.114, C.115, C.120, G.148, C.149 Chain B: R.74 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Water interactions Salt bridges: A:E.16, A:E.76 Metal complexes: A:C.17, A:C.19, A:C.19, A:C.20, A:C.115, A:C.120, A:C.149, H2O.7, H2O.9 SF3.13: 12 residues within 4Å: Chain C: E.16, C.17, T.18, C.19, C.20, E.76, T.114, C.115, C.120, G.148, C.149 Chain D: R.74 10 PLIP interactions: 8 interactions with chain C, 2 Ligand-Water interactions Salt bridges: C:E.76 Metal complexes: C:C.17, C:C.19, C:C.19, C:C.20, C:C.115, C:C.120, C:C.149, H2O.31, H2O.35

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: T.114, W.118, C.120, G.256 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: I.12, H.13, D.46, K.98 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: T.114, W.118, C.120, G.256 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain C: I.12, H.13, D.46, K.98 Ligand excluded by PLIP

2 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.6: 13 residues within 4Å: Chain B: C.79, V.82, H.83, A.507, A.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.7 7 PLIP interactions: 6 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.509, B:R.509, B:T.532, B:T.532 Water bridges: B:A.508 Metal complexes: B:C.579, H2O.18 FCO.16: 13 residues within 4Å: Chain D: C.79, V.82, H.83, A.507, A.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.17 7 PLIP interactions: 6 interactions with chain D, 1 Ligand-Water interactions Hydrogen bonds: D:R.509, D:R.509, D:T.532, D:T.532 Water bridges: D:D.118 Metal complexes: D:C.579, H2O.43

2 x NI: NICKEL (II) ION(Non-covalent)

NI.7: 5 residues within 4Å: Chain B: C.76, C.79, C.576, C.579 Ligands: FCO.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.76, B:C.576, B:C.579, H2O.18 NI.17: 5 residues within 4Å: Chain D: C.76, C.79, C.576, C.579 Ligands: FCO.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.76, D:C.576, D:C.579, H2O.43

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain B: E.57, C.528, H.582 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.57, B:C.528, B:H.582, H2O.9, H2O.9, H2O.10 MG.18: 3 residues within 4Å: Chain D: E.57, C.528, H.582 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.57, D:C.528, D:H.582, H2O.35, H2O.35, H2O.35

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 5 residues within 4Å: Chain A: R.211 Chain B: G.480, N.481, L.482, A.483 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Salt bridges: A:R.211 Hydrogen bonds: B:L.482, B:A.483 SO4.10: 2 residues within 4Å: Chain B: K.157 Chain D: K.157 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Water bridges: D:R.266, D:R.266 Salt bridges: D:K.157, B:K.157 SO4.19: 2 residues within 4Å: Chain D: W.373, R.394 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.394

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brooke, E.J. et al., Importance of the Active Site "Canopy" Residues in an O2-Tolerant [NiFe]-Hydrogenase. Biochemistry (2017)

Release Date

2017-03-08

Peptides

Hydrogenase-1 small chain: AC
Hydrogenase-1 large chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

C
T

B
L

D
M

Hydrogenase-1 small chain

Hydrogenase-1 large chain

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