SMTL ID : 5a4m.1

Mechanism of Hydrogen activation by NiFe-hydrogenases

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NFV: NI-FE OXIDIZED ACTIVE CENTER(Non-covalent)

NFV.1: 13 residues within 4Å: Chain A: C.76, C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 10 PLIP interactions: 9 interactions with chain A, 1 Ligand-Water interactions Hydrogen bonds: A:R.509, A:R.509, A:T.532 Metal complexes: A:C.76, A:C.79, A:C.79, A:C.576, A:C.579, A:C.579, H2O.5 NFV.3: 13 residues within 4Å: Chain B: C.76, C.79, V.82, H.83, A.507, P.508, R.509, L.512, V.530, P.531, T.532, C.576, C.579 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.509, B:R.509, B:T.532 Metal complexes: B:C.76, B:C.79, B:C.79, B:C.576, B:C.579, B:C.579

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.3, H2O.3, H2O.16 MG.4: 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.25, H2O.25, H2O.37

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

SF4.5: 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 SF4.9: 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.6: 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.10: 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)

SF3.7: 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 11 PLIP interactions: 8 interactions with chain C, 1 Ligand-Ligand interactions, 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, SF3.7, H2O.11, H2O.44 SF3.11: 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 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Water interactions 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, H2O.33, H2O.52

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

CL.8: 6 residues within 4Å: Chain C: T.114, W.118, G.119, C.120, N.255, G.256 Ligand excluded by PLIP CL.12: 5 residues within 4Å: Chain D: T.114, W.118, C.120, N.255, G.256 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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