SMTL ID : 3daf.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PO4.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

FE2.2: 5 residues within 4Å: Chain A: C.176 Ligands: CYN.3, CMO.4, CMO.5, FEG.6 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: A:C.176, H2O.1, CMO.4, CMO.5 FE2.8: 5 residues within 4Å: Chain B: C.176 Ligands: CYN.9, CMO.10, CMO.11, FEG.12 4 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: B:C.176, H2O.9, CMO.10, CMO.11

2 x CYN: CYANIDE ION(Non-covalent)

CYN.3: 5 residues within 4Å: Chain A: C.176 Ligands: FE2.2, CMO.4, CMO.5, FEG.6 No protein-ligand interaction detected (PLIP) CYN.9: 5 residues within 4Å: Chain B: C.176 Ligands: FE2.8, CMO.10, CMO.11, FEG.12 No protein-ligand interaction detected (PLIP)

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

CMO.4: 8 residues within 4Å: Chain A: W.148, A.175, C.176, P.202 Ligands: FE2.2, CYN.3, CMO.5, FEG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.176 CMO.5: 8 residues within 4Å: Chain A: W.148, C.204, V.205, P.206 Ligands: FE2.2, CYN.3, CMO.4, FEG.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:C.204 CMO.10: 8 residues within 4Å: Chain B: W.148, A.175, C.176, P.202 Ligands: FE2.8, CYN.9, CMO.11, FEG.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.176 CMO.11: 8 residues within 4Å: Chain B: W.148, C.204, V.205, P.206 Ligands: FE2.8, CYN.9, CMO.10, FEG.12 1 PLIP interactions: 1 interactions with chain B Water bridges: B:C.204

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

FEG.6: 25 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: FE2.2, CYN.3, CMO.4, CMO.5 15 PLIP interactions: 15 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:S.63, A:C.176 Water bridges: A:S.42, A:S.133 Salt bridges: A:H.14, A:D.64, A:D.135 pi-Cation interactions: A:K.151 FEG.12: 25 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: FE2.8, CYN.9, CMO.10, CMO.11 16 PLIP interactions: 16 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:S.42, B:S.133 Salt bridges: B:H.14, B:D.64, B:D.135 pi-Cation interactions: B:K.151

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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