SMTL ID : 1cc1.1

CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.207, H.208, C.211, Y.213, L.214, Y.217, C.231, K.232, A.233, C.237, G.239, P.240, V.259 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.208, A:C.211, A:C.231, A:C.237 SF4.2: 11 residues within 4Å: Chain A: T.242, C.246, W.251, C.258, C.264, I.265, G.266, C.267, V.268 Chain B: R.185, Q.190 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.246, A:C.258, A:C.264, A:C.267 SF4.3: 13 residues within 4Å: Chain A: G.17, C.18, G.20, C.21, E.77, G.124, T.125, C.126, G.163, C.164, P.165 Chain B: R.68, H.188 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.77 Metal complexes: A:C.18, A:C.21, A:C.126, A:C.164

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

NI.4: 5 residues within 4Å: Chain B: C.70, C.73, U.492, C.495 Ligands: FCO.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.70, B:C.73, B:C.495

1 x FE2: FE (II) ION(Non-covalent)

FE2.5: 3 residues within 4Å: Chain B: E.51, I.444, H.498 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.51, B:I.444, B:H.498, H2O.6, H2O.6, H2O.6

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

FCO.6: 12 residues within 4Å: Chain B: C.73, H.77, A.423, P.424, R.425, L.428, S.446, A.447, T.448, U.492, C.495 Ligands: NI.4 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.425, B:R.425, B:T.448, B:T.448 Metal complexes: B:C.73, B:C.495

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.7: 6 residues within 4Å: Chain B: C.73, T.75, A.76, F.105, N.108, P.424 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcin, E. et al., The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center. Structure Fold.Des. (1999)

Release Date

1999-06-01

Peptides

HYDROGENASE (SMALL SUBUNIT): A
HYDROGENASE (LARGE SUBUNIT): B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
L

HYDROGENASE (SMALL SUBUNIT)

HYDROGENASE (LARGE SUBUNIT)