SMTL ID : 5adu.1

The Mechanism of Hydrogen Activation by NiFe-hydrogenases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

hetero-2-2-mer

Ligands

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

FCO.1: 13 residues within 4Å: Chain A: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.2 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Hydrogen bonds: A:R.509, A:R.509, A:T.532, A:T.532 Metal complexes: A:C.579, H2O.3 FCO.4: 13 residues within 4Å: Chain B: C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 Ligands: NI.5 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.509, B:R.509, B:T.532, B:T.532 Metal complexes: B:C.579, H2O.19

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

NI.2: 5 residues within 4Å: Chain A: C.76, C.79, C.576, C.579 Ligands: FCO.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.76, A:C.576, A:C.579, H2O.3 NI.5: 5 residues within 4Å: Chain B: C.76, C.79, C.576, C.579 Ligands: FCO.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.76, B:C.576, B:C.579, H2O.19

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.57, C.528, H.582 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.57, A:C.528, A:H.582, H2O.2, H2O.2, H2O.12 MG.6: 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.18, H2O.18, H2O.27

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

SO4.7: 1 residues within 4Å: Chain B: R.394 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.394 SO4.14: 5 residues within 4Å: Chain A: G.480, N.481, L.482, A.483 Chain C: R.211 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:G.480, A:L.482, A:A.483 Salt bridges: C:R.211

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

SF4.8: 12 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, P.224, I.243 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.187, C:C.190, C:C.215, C:C.221 SF4.15: 11 residues within 4Å: Chain D: 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 D, Metal complexes: D:H.187, D:C.190, D:C.215, D:C.221

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

F3S.9: 10 residues within 4Å: Chain A: K.226 Chain C: T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.230, C:C.249, C:C.252 F3S.16: 10 residues within 4Å: Chain B: K.226 Chain D: T.226, N.228, C.230, W.235, P.242, C.249, L.250, G.251, C.252 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.230, D:C.249, D:C.252

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

SF3.10: 12 residues within 4Å: Chain A: R.74 Chain C: E.16, C.17, T.18, C.19, C.20, E.76, T.114, C.115, C.120, G.148, C.149 8 PLIP interactions: 8 interactions with chain C, 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 SF3.17: 12 residues within 4Å: Chain B: R.74 Chain D: E.16, C.17, T.18, C.19, C.20, E.76, T.114, C.115, C.120, G.148, C.149 8 PLIP interactions: 8 interactions with chain D, Salt bridges: D:E.76 Metal complexes: D:C.17, D:C.19, D:C.19, D:C.20, D:C.115, D:C.120, D:C.149

2 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.11: 10 residues within 4Å: Chain C: I.7, V.9, W.11, I.40, I.72, I.160, M.163, V.164, D.167, R.168 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:I.7, C:I.7, C:V.9, C:V.9, C:W.11, C:I.40, C:I.72, C:I.160, C:M.163 LMT.18: 10 residues within 4Å: Chain D: I.7, V.9, W.11, I.40, I.72, I.160, M.163, V.164, D.167, R.168 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:I.7, D:I.7, D:V.9, D:V.9, D:W.11, D:I.40, D:I.72, D:I.160, D:M.163, D:V.164

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

CL.12: 4 residues within 4Å: Chain C: T.114, W.118, C.120, G.256 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain C: I.12, H.13, D.46, K.98 Ligand excluded by PLIP CL.19: 4 residues within 4Å: Chain D: T.114, W.118, C.120, G.256 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain D: I.12, H.13, D.46, K.98 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, R.M. et al., Mechanism of hydrogen activation by [NiFe] hydrogenases. Nat. Chem. Biol. (2016)

Release Date

2015-11-25

Peptides

Hydrogenase-1 large chain: AB
Hydrogenase-1 small chain: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
M

C
S

D
T

Hydrogenase-1 large chain

Hydrogenase-1 small chain

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