SMTL ID : 4uqp.1 (1 other biounit)

High-resolution structure of the D. fructosovorans NiFe-hydrogenase L122A mutant after exposure to air

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.185, C.188, R.190, L.191, F.194, C.213, L.214, Y.215, C.219, G.221, P.222, V.240 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.185, A:C.188, A:C.213, A:C.219 SF4.3: 12 residues within 4Å: Chain A: E.17, C.18, G.20, C.21, G.113, T.114, C.115, G.147, C.148, P.149 Chain B: R.84, H.242 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.76 Metal complexes: A:C.18, A:C.21, A:C.115, A:C.148

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

F3S.2: 12 residues within 4Å: Chain A: T.224, N.226, C.228, F.233, W.238, P.239, C.246, L.247, G.248, C.249 Chain B: K.239, Q.244 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.228, A:C.246, A:C.249

1 x SOT: morpholine-4-sulfonic acid(Covalent)

SOT.4: 3 residues within 4Å: Chain A: Y.215, P.222, V.223 No protein-ligand interaction detected (PLIP)

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.5: 4 residues within 4Å: Chain A: H.6, S.9, D.69 Chain B: Q.189 No protein-ligand interaction detected (PLIP)

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 9 residues within 4Å: Chain B: R.114, N.118, F.309, A.310, T.311, Q.324, W.456, E.459 Ligands: GOL.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.114, B:R.114, B:N.118, B:F.309 GOL.7: 7 residues within 4Å: Chain B: L.320, A.321, S.327, V.338, D.339, N.340, K.409 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:S.327, B:S.327, B:V.338, B:K.409 Water bridges: B:N.340, B:N.340, B:N.340 GOL.8: 5 residues within 4Å: Chain B: Q.324, K.455, W.456, E.459 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.324, B:W.456 GOL.9: 3 residues within 4Å: Chain A: K.209 Chain B: T.258, N.468 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.468 GOL.10: 7 residues within 4Å: Chain B: P.29, V.31, M.45, V.46, E.47, W.57, K.379 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.379, B:K.379

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

FCO.11: 13 residues within 4Å: Chain B: C.89, V.92, H.93, A.488, P.489, R.490, L.493, V.511, P.512, S.513, C.557, C.560 Ligands: NI.12 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:H.93, B:R.490, B:R.490, B:S.513 Metal complexes: B:C.560, H2O.12

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

NI.12: 5 residues within 4Å: Chain B: C.86, C.89, C.557, C.560 Ligands: FCO.11 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.86, B:C.560, H2O.12

1 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 3 residues within 4Å: Chain B: E.67, L.509, H.563 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.67, B:L.509, B:H.563, H2O.12, H2O.13, H2O.13

1 x GLY: GLYCINE(Non-covalent)

GLY.14: 8 residues within 4Å: Chain B: I.38, E.39, V.88, V.131, H.132, A.136, R.490, D.555 4 PLIP interactions: 4 interactions with chain B Water bridges: B:E.39, B:E.39, B:R.490 Salt bridges: B:R.490

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., Crystallographic Studies of [Nife]-Hydrogenase Mutants: Towards Consensus Structures for the Elusive Unready Oxidized States. J.Biol.Inorg.Chem. (2015)

Release Date

2014-10-29

Peptides

PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT: A
PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
R

PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT

PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT

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