SMTL ID : 3dag.1

The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

FE2.1: 4 residues within 4Å: Chain A: C.176 Ligands: FEG.2, CMO.3, CMO.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.176, H2O.1, H2O.1 FE2.5: 4 residues within 4Å: Chain B: C.176 Ligands: FEG.6, CMO.7, CMO.8 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.176, H2O.8, H2O.8

2 x FEG: 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine(Non-covalent)

FEG.2: 24 residues within 4Å: Chain A: L.6, G.7, A.8, G.9, C.10, T.13, H.14, S.63, D.64, P.65, P.114, P.115, C.118, D.135, W.148, L.149, P.150, I.158, A.175, C.176, T.177 Ligands: FE2.1, CMO.3, CMO.4 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:W.148, A:T.177 Hydrogen bonds: A:A.8, A:G.9, A:G.9, A:C.10, A:C.10, A:T.13, A:S.63, A:C.176 Salt bridges: A:H.14, A:D.64, A:D.135 FEG.6: 24 residues within 4Å: Chain B: L.6, G.7, A.8, G.9, C.10, T.13, H.14, S.63, D.64, P.65, P.114, P.115, C.118, D.135, W.148, L.149, P.150, I.158, A.175, C.176, T.177 Ligands: FE2.5, CMO.7, CMO.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:W.148, B:T.177 Hydrogen bonds: B:A.8, B:G.9, B:G.9, B:C.10, B:C.10, B:T.13, B:S.63, B:C.176 Water bridges: B:D.135 Salt bridges: B:H.14, B:D.64, B:D.135

4 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.3: 7 residues within 4Å: Chain A: W.148, A.175, C.176, P.202 Ligands: FE2.1, FEG.2, CMO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.176 Water bridges: A:G.203 CMO.4: 7 residues within 4Å: Chain A: W.148, C.204, V.205, P.206 Ligands: FE2.1, FEG.2, CMO.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.14 CMO.7: 7 residues within 4Å: Chain B: W.148, A.175, C.176, P.202 Ligands: FE2.5, FEG.6, CMO.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.176 Water bridges: B:G.203 CMO.8: 7 residues within 4Å: Chain B: W.148, C.204, V.205, P.206 Ligands: FE2.5, FEG.6, CMO.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.14

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shima, S. et al., The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site. Science (2008)

Release Date

2008-12-09

Peptides

5,10-methenyltetrahydromethanopterin hydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

5,10-methenyltetrahydromethanopterin hydrogenase

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