Zinc in PDB 1y6h: Crystal Structure of Lipdf

All present enzymatic activity of Crystal Structure of Lipdf:
3.5.1.88;

The structure of Crystal Structure of Lipdf, PDB code: 1y6h 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)	25.14 / 2.20
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	91.032, 91.032, 86.380, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 22.8

The binding sites of Zinc atom in the Crystal Structure of Lipdf (pdb code 1y6h). 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 Lipdf, PDB code: 1y6h:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Lipdf


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 Lipdf within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn513 b:46.3 occ:1.00 NE2 A:HIS147 2.2 18.0 1.0 O1 A:FMT723 2.3 32.1 1.0 NE2 A:HIS143 2.4 16.4 1.0 C A:FMT723 2.5 33.2 1.0 SG A:CYS101 2.7 22.9 1.0 O2 A:FMT723 2.7 33.9 1.0 CD2 A:HIS143 3.1 16.3 1.0 CE1 A:HIS147 3.2 16.8 1.0 CD2 A:HIS147 3.2 15.2 1.0 NE2 A:GLN53 3.3 14.3 1.0 CE1 A:HIS143 3.5 17.0 1.0 CB A:CYS101 3.6 18.8 1.0 O A:HOH727 3.7 16.1 1.0 CD A:GLN53 3.8 17.6 1.0 OE1 A:GLN53 3.8 17.1 1.0 CA A:CYS101 4.0 17.6 1.0 N A:LEU102 4.2 18.9 1.0 OE2 A:GLU144 4.3 23.3 1.0 ND1 A:HIS147 4.3 16.2 1.0 CG A:HIS147 4.3 15.5 1.0 CG A:HIS143 4.3 17.2 1.0 ND1 A:HIS143 4.5 16.0 1.0 C A:CYS101 4.6 19.6 1.0 O A:HOH738 4.6 14.5 1.0 OE1 A:GLU144 4.7 25.6 1.0 CD A:GLU144 4.8 22.6 1.0 O A:GLY100 4.8 19.9 1.0 CG A:GLN53 4.9 16.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Lipdf


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 Lipdf within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn513 b:39.8 occ:1.00 NE2 B:HIS147 2.1 17.4 1.0 NE2 B:HIS143 2.2 16.6 1.0 O2 B:FMT716 2.3 24.9 1.0 SG B:CYS101 2.4 19.4 1.0 O1 B:FMT716 2.6 23.1 1.0 C B:FMT716 2.7 25.7 1.0 CD2 B:HIS143 3.0 15.3 1.0 CE1 B:HIS147 3.1 15.6 1.0 CD2 B:HIS147 3.2 15.9 1.0 CE1 B:HIS143 3.3 16.0 1.0 CB B:CYS101 3.3 17.7 1.0 O B:HOH1005 3.5 9.5 1.0 NE2 B:GLN53 3.5 13.2 1.0 CA B:CYS101 3.8 17.3 1.0 CD B:GLN53 4.0 17.3 1.0 OE1 B:GLN53 4.0 16.9 1.0 CG B:HIS143 4.2 15.8 1.0 ND1 B:HIS147 4.3 16.9 1.0 N B:LEU102 4.3 17.0 1.0 CG B:HIS147 4.3 15.4 1.0 ND1 B:HIS143 4.4 15.8 1.0 OE2 B:GLU144 4.4 23.5 1.0 C B:CYS101 4.5 18.3 1.0 O B:HOH1010 4.5 16.1 1.0 O1 B:FMT717 4.6 23.8 1.0 O B:GLY100 4.7 15.9 1.0 N B:GLY1001 4.8 33.4 1.0 OE1 B:GLU144 4.8 25.3 1.0 CD B:GLU144 5.0 24.1 1.0

Z.Zhou, X.Song, Y.Li, W.Gong. Unique Structural Characteristics of Peptide Deformylase From Pathogenic Bacterium Leptospira Interrogans J.Mol.Biol. V. 339 207 2004.
ISSN: ISSN 0022-2836
PubMed: 15123432
DOI: 10.1016/J.JMB.2004.03.045