SMTL ID : 4ko1.2 (1 other biounit)

High X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 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, W.257, C.258, C.264, I.265, G.266, C.267 Chain B: R.186, Q.191 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.69, H.189 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

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.5: 2 residues within 4Å: Chain A: D.271, G.275 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.271, A:G.275, H2O.1, H2O.3, H2O.13 CA.6: 2 residues within 4Å: Chain A: D.195, D.196 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.195, A:D.196, H2O.4, H2O.8, H2O.13 CA.9: 3 residues within 4Å: Chain B: E.52, I.445, H.499 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.52, B:I.445, B:H.499, H2O.15, H2O.15, H2O.15

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

FCO.7: 11 residues within 4Å: Chain B: C.74, H.78, A.424, P.425, R.426, L.429, A.448, T.449, U.493, C.496 Ligands: NI.8 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.426, B:R.426, B:T.449 Metal complexes: B:C.74, B:C.496, H2O.14

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

NI.8: 7 residues within 4Å: Chain B: E.24, C.71, C.74, U.493, G.495, C.496 Ligands: FCO.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.71, B:C.496

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.10: 6 residues within 4Å: Chain B: C.74, T.76, A.77, F.106, N.109, P.425 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain B: D.40, R.456, G.460, R.462 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.40, B:R.456, B:G.460, B:R.462 Water bridges: B:R.462 GOL.12: 4 residues within 4Å: Chain B: A.157, T.158, Y.161, T.231 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.157

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., Structural foundations for the O2 resistance of Desulfomicrobium baculatum [NiFeSe]-hydrogenase. Chem.Commun.(Camb.) (2013)

Release Date

2013-07-10

Peptides

Periplasmic [NiFeSe] hydrogenase small subunit: A
Nickel-dependent hydrogenase large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
T

B
M

Periplasmic [NiFeSe] hydrogenase small subunit

Nickel-dependent hydrogenase large subunit

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