SMTL ID : 2zpe.2 (1 other biounit)

nitrosylated Fe-type nitrile hydratase with tert-butylisonitrile

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

hetero-2-2-mer

Ligands

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

FE.1: 5 residues within 4Å: Chain A: C.109, C.112, S.113, C.114 Ligands: NO.2 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.109 FE.10: 5 residues within 4Å: Chain C: C.109, C.112, S.113, C.114 Ligands: NO.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.109

2 x NO: NITRIC OXIDE(Non-covalent)

NO.2: 5 residues within 4Å: Chain A: C.112, S.113, C.114 Ligands: FE.1, TB0.7 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Q.90, A:T.115, A:T.115, A:W.117 NO.11: 5 residues within 4Å: Chain C: C.112, S.113, C.114 Ligands: FE.10, TB0.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.113 Water bridges: C:T.115, C:T.115, C:T.115

12 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: G.180 No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain A: E.139 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.139, H2O.9, H2O.11, H2O.19, H2O.20, H2O.21 MG.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain C: G.180 No protein-ligand interaction detected (PLIP) MG.15: 1 residues within 4Å: Chain C: E.139 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.139, H2O.36, H2O.38, H2O.46, H2O.47, H2O.48 MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x TB0: tert-butyl isocyanide(Non-covalent)

TB0.7: 11 residues within 4Å: Chain A: Q.90, C.112, S.113 Chain B: Y.37, M.40, V.52, V.55, R.56, Y.72, Y.76 Ligands: NO.2 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.37, B:R.56 TB0.16: 11 residues within 4Å: Chain C: Q.90, C.112, S.113 Chain D: Y.37, M.40, V.52, V.55, R.56, Y.72, Y.76 Ligands: NO.11 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.37, D:R.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hashimoto, K. et al., Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile. J.Biol.Chem. (2008)

Release Date

2008-10-21

Peptides

Nitrile hydratase subunit alpha: AC
Nitrile hydratase subunit beta: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Nitrile hydratase subunit alpha

Nitrile hydratase subunit beta

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