SMTL ID : 6syo.2 (1 other biounit)

Hydrogenase-2 variant R479K - As Isolated form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

hetero-1-1-mer

Ligands

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

FCO.1: 14 residues within 4Å: Chain A: 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.2, OXY.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.479, A:S.502 Metal complexes: A:C.64, A:C.549

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

NI.2: 6 residues within 4Å: Chain A: C.61, C.64, C.546, C.549 Ligands: FCO.1, OXY.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.61, A:C.64, A:C.546, A:C.549

3 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 2 residues within 4Å: Chain A: N.81, N.294 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: E.42, A.498, H.552 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.42, A:A.498, A:H.552, H2O.2, H2O.3, H2O.3 MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

1 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.5: 7 residues within 4Å: Chain A: C.61, V.63, C.64, K.479, C.546 Ligands: FCO.1, NI.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.64, A:K.479 Water bridges: A:K.479, A:K.479

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 4 residues within 4Å: Chain A: M.241, Y.443 Chain B: A.165, T.169 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.443, B:A.165 Water bridges: A:K.244

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

SF4.7: 11 residues within 4Å: Chain B: H.191, C.194, R.196, R.197, C.219, L.220, Y.221, C.225, G.227, P.228, V.248 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.191, B:C.194, B:C.219, B:C.225 SF4.9: 11 residues within 4Å: Chain B: E.20, C.21, G.23, C.24, G.117, S.118, C.119, V.125, G.152, C.153, P.154 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.21, B:C.24, B:C.119, B:C.153

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

F3S.8: 11 residues within 4Å: Chain B: I.190, T.230, C.234, F.239, W.246, P.247, C.254, Y.255, G.256, C.257, N.258 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.234, B:C.254, B:C.257

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 large chain: A
Hydrogenase-2 small chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
LLL

B
TTT

Hydrogenase-2 large chain

Hydrogenase-2 small chain

Related Entries With Identical Sequence