SMTL ID : 3shd.2 (17 other biounits)

Crystal structure of Nudix hydrolase Orf153, ymfB, from Escherichia coli K-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.51, E.55 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: 4 residues within 4Å: Chain A: H.37, E.51 Ligands: MN.1, SO4.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.51, H2O.1

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

SO4.3: 7 residues within 4Å: Chain A: G.36, H.37, E.51, E.55 Ligands: MN.1, MN.2, SO4.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.37 Water bridges: A:R.50, A:D.100 Salt bridges: A:H.37 SO4.4: 8 residues within 4Å: Chain A: E.23, A.35, G.36, E.51, E.55 Ligands: MN.1, SO4.3, SO4.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.32, A:A.35, A:R.119 Water bridges: A:R.119, A:R.119 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, A:A.35 Salt bridges: A:R.81

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, M.K., Structure and atypical hydrolysis mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli. To be Published

Release Date

2012-06-27

Peptides

Phosphatase nudJ: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Phosphatase nudJ

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