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Zinc in PDB 1vev: Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5

Enzymatic activity of Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5

All present enzymatic activity of Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5:
3.5.1.88;

Protein crystallography data

The structure of Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5, PDB code: 1vev was solved by Z.Zhou, X.Song, Y.Li, W.Gong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.91 / 2.51
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 82.192, 82.192, 201.040, 90.00, 90.00, 90.00
R / Rfree (%) 25.8 / 29

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5 (pdb code 1vev). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5, PDB code: 1vev:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 1vev

Go back to Zinc Binding Sites List in 1vev
Zinc binding site 1 out of 2 in the Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1513

b:45.6
occ:1.00
NE2 A:HIS147 2.1 16.9 1.0
NE2 A:HIS143 2.3 25.5 1.0
O1 A:FMT1800 2.5 35.8 1.0
SG A:CYS101 2.8 22.3 1.0
C A:FMT1800 2.9 34.8 1.0
O2 A:FMT1800 2.9 33.4 1.0
CE1 A:HIS147 3.1 16.6 1.0
CD2 A:HIS147 3.1 16.4 1.0
CD2 A:HIS143 3.2 24.1 1.0
CE1 A:HIS143 3.3 24.9 1.0
O A:HOH3723 3.5 17.9 1.0
OE1 A:GLN53 3.5 20.2 1.0
CB A:CYS101 3.6 19.1 1.0
NE2 A:GLN53 3.7 21.0 1.0
CD A:GLN53 3.8 20.5 1.0
CA A:CYS101 4.1 20.4 1.0
ND1 A:HIS147 4.2 15.9 1.0
CG A:HIS147 4.3 17.6 1.0
CG A:HIS143 4.4 24.5 1.0
O A:HOH3722 4.4 24.9 1.0
ND1 A:HIS143 4.4 24.7 1.0
N A:LEU102 4.5 22.3 1.0
OE1 A:GLU144 4.5 27.1 1.0
OE2 A:GLU144 4.6 31.2 1.0
C A:CYS101 4.7 21.2 1.0
O3S A:MES1716 4.7 51.1 1.0
C8 A:MES1716 4.9 51.9 1.0
CD A:GLU144 4.9 28.0 1.0
O A:GLY100 4.9 20.9 1.0
CG A:GLN53 5.0 19.1 1.0

Zinc binding site 2 out of 2 in 1vev

Go back to Zinc Binding Sites List in 1vev
Zinc binding site 2 out of 2 in the Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Peptide Deformylase From Leptospira Interrogans (Lipdf) at PH6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2513

b:37.7
occ:1.00
NE2 B:HIS143 2.1 15.7 1.0
NE2 B:HIS147 2.2 16.8 1.0
O2 B:FMT2800 2.5 22.6 1.0
SG B:CYS101 2.6 22.2 1.0
O1 B:FMT2800 2.9 20.0 1.0
C B:FMT2800 3.0 21.2 1.0
CE1 B:HIS143 3.1 16.1 1.0
CD2 B:HIS147 3.1 15.8 1.0
CD2 B:HIS143 3.2 16.9 1.0
CE1 B:HIS147 3.2 15.4 1.0
CB B:CYS101 3.5 16.9 1.0
O B:HOH2812 3.6 11.6 1.0
OE1 B:GLN53 3.6 15.9 1.0
CA B:CYS101 3.9 16.9 1.0
NE2 B:GLN53 4.0 14.1 1.0
CD B:GLN53 4.0 15.1 1.0
O1S B:MES2716 4.1 49.5 1.0
ND1 B:HIS143 4.2 16.3 1.0
CG B:HIS147 4.3 15.5 1.0
ND1 B:HIS147 4.3 16.7 1.0
N B:LEU102 4.3 17.2 1.0
CG B:HIS143 4.3 16.4 1.0
OE2 B:GLU144 4.5 24.0 1.0
O B:HOH2809 4.5 17.9 1.0
C B:CYS101 4.6 17.2 1.0
O B:GLY100 4.8 17.4 1.0
C8 B:MES2716 4.8 49.6 1.0
OE1 B:GLU144 5.0 24.7 1.0

Reference:

Z.Zhou, X.Song, W.Gong. Novel Conformational States of Peptide Deformylase From Pathogenic Bacterium Leptospira Interrogans: Implications For Population Shift J.Biol.Chem. V. 280 42391 2005.
ISSN: ISSN 0021-9258
PubMed: 16239225
DOI: 10.1074/JBC.M506370200
Page generated: Fri Sep 25 23:54:02 2020
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