SMTL ID : 4ci0.3 (2 other biounits)

Electron cryo-microscopy of F420-reducing NiFe hydrogenase Frh

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY 3.36 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: C.66, A.326, V.349, P.350, C.383 Ligands: NI.2 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.66, A:C.383

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

NI.2: 5 residues within 4Å: Chain A: C.63, C.66, C.380, C.383 Ligands: FE.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:C.66, A:C.380, A:C.383

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

FE2.3: 3 residues within 4Å: Chain A: E.44, A.347, H.386 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.44, A:E.44, A:A.347, A:H.386

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

SF4.4: 15 residues within 4Å: Chain A: R.61, H.150 Chain B: G.56, C.57, T.58, G.59, D.60, E.102, G.130, S.131, C.132, C.137, G.170, C.171, P.172 9 PLIP interactions: 9 interactions with chain B, Salt bridges: B:D.60, B:D.60, B:D.60, B:E.102 Metal complexes: B:C.57, B:D.60, B:D.60, B:C.132, B:C.171 SF4.5: 12 residues within 4Å: Chain B: A.229, C.230, T.232, A.234, L.235, C.249, I.250, K.251, C.252, G.253, I.254, C.255 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.230, B:C.249, B:C.252, B:C.255 SF4.6: 11 residues within 4Å: Chain B: C.220, I.221, G.222, C.223, G.224, T.225, C.226, M.237, P.242, C.259, P.260 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.220, B:C.223, B:C.226, B:C.259 SF4.8: 11 residues within 4Å: Chain B: I.221 Chain C: I.102, P.103, C.104, C.134, M.135, E.136, N.137, C.192, C.195, K.261 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.104, C:C.134, C:C.192, C:C.195

1 x ZN: ZINC ION(Non-covalent)

ZN.7: 2 residues within 4Å: Chain B: C.206, C.208 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.206, B:C.208

1 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.9: 32 residues within 4Å: Chain C: A.23, Q.24, D.25, G.26, G.27, I.28, V.29, T.30, V.47, A.48, A.71, A.72, G.73, T.74, K.75, Y.76, T.77, S.79, N.81, V.100, I.102, Q.105, I.132, Y.133, C.134, M.135, N.137, Y.198, T.207, G.208, S.209, V.210 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:T.74, C:Y.76, C:I.102, C:I.132, C:N.137 Hydrogen bonds: C:Q.24, C:D.25, C:G.26, C:G.27, C:I.28, C:V.29, C:T.30, C:T.30, C:A.48, C:A.48, C:G.73, C:T.74, C:T.74, C:K.75, C:K.75, C:Y.76, C:T.77, C:S.79, C:N.81, C:M.135, C:Y.198, C:Y.198, C:S.209, C:V.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Allegretti, M. et al., Atomic Model of the F420-Reducing [Nife] Hydrogenase by Electron Cryo-Electron Microscopy Using a Direct Electron Detector. Elife (2014)

Release Date

2014-02-26

Peptides

F420-REDUCING HYDROGENASE, SUBUNIT ALPHA: A
F420-REDUCING HYDROGENASE, SUBUNIT GAMMA: B
F420-REDUCING HYDROGENASE, SUBUNIT BETA: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

F420-REDUCING HYDROGENASE, SUBUNIT ALPHA

F420-REDUCING HYDROGENASE, SUBUNIT GAMMA

F420-REDUCING HYDROGENASE, SUBUNIT BETA

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