SMTL ID : 4nfw.15 (17 other biounits)

Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 7 residues within 4Å: Chain A: E.51, E.54, E.55, D.98 Ligands: MN.2, SO4.3, SO4.4 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.51, A:E.55 MN.2: 6 residues within 4Å: Chain A: E.39, R.50, E.51, E.54 Ligands: MN.1, SO4.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.51, H2O.2 MN.6: 5 residues within 4Å: Chain B: E.51, E.54, E.55 Ligands: SO4.8, SO4.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.51, B:E.55 MN.7: 5 residues within 4Å: Chain B: H.37, E.39, R.50, E.51 Ligands: SO4.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.51

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 6 residues within 4Å: Chain A: G.36, H.37, E.51 Ligands: MN.1, MN.2, SO4.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.37 Water bridges: A:E.51 Salt bridges: A:H.37 SO4.4: 9 residues within 4Å: Chain A: E.23, N.32, A.35, G.36, E.51, E.55 Ligands: MN.1, SO4.3, SO4.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.32, A:A.35, A:E.55 SO4.5: 6 residues within 4Å: Chain A: T.7, N.32, A.35, G.36, R.81 Ligands: SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.7, A:N.32 Water bridges: A:R.81 Salt bridges: A:R.81 SO4.8: 6 residues within 4Å: Chain B: G.36, H.37, E.51 Ligands: MN.6, MN.7, SO4.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.37 Salt bridges: B:H.37 SO4.9: 6 residues within 4Å: Chain B: T.7, N.32, A.35, F.79, R.81 Ligands: SO4.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.32 Salt bridges: B:R.81 SO4.10: 10 residues within 4Å: Chain B: E.23, N.32, Q.33, A.35, G.36, E.55, R.119 Ligands: MN.6, SO4.8, SO4.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.32, B:A.35, B:A.35, B:R.119, B:R.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, M.K. et al., Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli. Acta Crystallogr.,Sect.D (2014)

Release Date

2014-05-14

Peptides

Putative Nudix hydrolase ymfB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
G

Putative Nudix hydrolase ymfB

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