SMTL ID : 3f47.1

The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

2 x I2C: 5'-O-[(S)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxoethyl)pyridin-4-yl]oxy}phosphoryl]guanosine(Non-covalent)

I2C.1: 24 residues within 4Å: Chain A: L.6, G.7, A.8, G.9, C.10, T.13, 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, P.202 Ligands: FE2.2, CMO.3, CMO.4 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:W.148, A:W.148, A:A.175, 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 Salt bridges: A:D.64, A:D.135 pi-Cation interactions: A:K.151 I2C.6: 24 residues within 4Å: Chain B: L.6, G.7, A.8, G.9, C.10, T.13, 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, P.202 Ligands: FE2.7, CMO.8, CMO.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:W.148, B:W.148, B:A.175, B:T.177 Hydrogen bonds: B:A.8, B:G.9, B:G.9, B:C.10, B:C.10, B:S.63, B:C.176 Water bridges: B:T.13, B:S.42, B:D.135 Salt bridges: B:D.64, B:D.135 pi-Cation interactions: B:K.151

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

FE2.2: 4 residues within 4Å: Chain A: C.176 Ligands: I2C.1, CMO.3, CMO.4 4 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions, 2 Ligand-Ligand interactions Metal complexes: A:C.176, H2O.1, CMO.3, CMO.4 FE2.7: 4 residues within 4Å: Chain B: C.176 Ligands: I2C.6, CMO.8, CMO.9 4 PLIP interactions: 1 interactions with chain B, 2 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: B:C.176, CMO.8, CMO.9, H2O.10

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

CMO.3: 7 residues within 4Å: Chain A: W.148, C.204, V.205, P.206 Ligands: I2C.1, FE2.2, CMO.4 No protein-ligand interaction detected (PLIP) CMO.4: 8 residues within 4Å: Chain A: C.176, H.201, P.202, G.203, C.204 Ligands: I2C.1, FE2.2, CMO.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.203, A:C.204, A:C.204 CMO.8: 7 residues within 4Å: Chain B: W.148, C.204, V.205, P.206 Ligands: I2C.6, FE2.7, CMO.9 No protein-ligand interaction detected (PLIP) CMO.9: 8 residues within 4Å: Chain B: C.176, H.201, P.202, G.203, C.204 Ligands: I2C.6, FE2.7, CMO.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.203, B:C.204, B:C.204

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 4 residues within 4Å: Chain A: L.51, V.54, P.55, V.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.55 NA.10: 4 residues within 4Å: Chain B: L.51, V.54, P.55, V.57 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hiromoto, T. et al., The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex. Febs Lett. (2009)

Release Date

2009-02-10

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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