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Zinc in PDB 1xem: High Resolution Crystal Structure of Escherichia Coli Zinc- Peptide Deformylase Bound to Formate

Enzymatic activity of High Resolution Crystal Structure of Escherichia Coli Zinc- Peptide Deformylase Bound to Formate

All present enzymatic activity of High Resolution Crystal Structure of Escherichia Coli Zinc- Peptide Deformylase Bound to Formate:
3.5.1.88;

Protein crystallography data

The structure of High Resolution Crystal Structure of Escherichia Coli Zinc- Peptide Deformylase Bound to Formate, PDB code: 1xem was solved by R.Jain, B.Hao, R.-P.Liu, M.K.Chan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 14.88 / 1.76
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 54.640, 54.640, 224.000, 90.00, 90.00, 120.00
R / Rfree (%) 16.3 / 20.4

Zinc Binding Sites:

The binding sites of Zinc atom in the High Resolution Crystal Structure of Escherichia Coli Zinc- Peptide Deformylase Bound to Formate (pdb code 1xem). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the High Resolution Crystal Structure of Escherichia Coli Zinc- Peptide Deformylase Bound to Formate, PDB code: 1xem:

Zinc binding site 1 out of 1 in 1xem

Go back to Zinc Binding Sites List in 1xem
Zinc binding site 1 out of 1 in the High Resolution Crystal Structure of Escherichia Coli Zinc- Peptide Deformylase Bound to Formate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Crystal Structure of Escherichia Coli Zinc- Peptide Deformylase Bound to Formate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:14.7
occ:1.00
 NE2 A:HIS136 2.0 11.5 1.0
NE2 A:HIS132 2.1 15.3 1.0
O1 A:FMT501 2.1 20.3 1.0
SG A:CYS90 2.2 14.7 1.0
C A:FMT501 2.7 23.8 1.0
O2 A:FMT501 2.9 27.0 1.0
CE1 A:HIS136 3.0 13.0 1.0
CD2 A:HIS132 3.0 13.0 1.0
CD2 A:HIS136 3.1 13.9 1.0
CE1 A:HIS132 3.1 14.5 1.0
CB A:CYS90 3.3 14.4 1.0
NE2 A:GLN50 3.6 11.8 1.0
O A:HOH561 3.6 13.7 1.0
CA A:CYS90 3.8 14.1 1.0
CD A:GLN50 4.0 13.4 1.0
OE1 A:GLN50 4.0 13.8 1.0
ND1 A:HIS136 4.1 13.1 1.0
CG A:HIS132 4.2 12.5 1.0
CG A:HIS136 4.2 13.0 1.0
ND1 A:HIS132 4.2 14.0 1.0
OE2 A:GLU133 4.4 17.5 1.0
N A:LEU91 4.4 14.3 1.0
O A:HOH560 4.5 13.1 1.0
C A:CYS90 4.5 13.2 1.0
OE1 A:GLU133 4.5 17.3 1.0
O A:GLY89 4.6 16.9 1.0
CD A:GLU133 4.9 14.0 1.0
N A:CYS90 5.0 13.5 1.0

Reference:

R.Jain, B.Hao, R.-P.Liu, M.K.Chan. Structures of E. Coli Peptide Deformylase Bound to Formate: Insight Into the Preference For FE2+ Over ZN2+ As the Active Site Metal J.Am.Chem.Soc. V. 127 4558 2005.
ISSN: ISSN 0002-7863
PubMed: 15796505
DOI: 10.1021/JA0503074
Page generated: Wed Aug 20 00:17:21 2025

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