Zinc in PDB 5mtd: Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II

The structure of Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II, PDB code: 5mtd was solved by S.Fieulaine, R.Grzela, C.Giglione, T.Meinnel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.67 / 1.50
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.260, 64.260, 125.690, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 21

The structure of Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II also contains other interesting chemical elements:

Nickel

(Ni)

3 atoms

The binding sites of Zinc atom in the Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II (pdb code 5mtd). 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 Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II, PDB code: 5mtd:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II


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 Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:15.4 occ:1.00 NE2 A:HIS127 2.0 14.3 1.0 NE2 A:HIS131 2.0 16.0 1.0 O A:HOH344 2.1 20.9 1.0 SG A:CYS85 2.2 15.4 1.0 O A:HOH391 2.9 32.0 1.0 CD2 A:HIS127 2.9 15.1 1.0 CE1 A:HIS131 3.0 14.7 1.0 CD2 A:HIS131 3.0 14.4 1.0 CE1 A:HIS127 3.1 15.5 1.0 CB A:CYS85 3.3 15.9 1.0 NE2 A:GLN47 3.5 14.1 1.0 O A:HOH374 3.5 16.5 1.0 CA A:CYS85 3.8 15.3 1.0 CD A:GLN47 3.9 15.5 1.0 OE1 A:GLN47 4.0 14.9 1.0 CG A:HIS127 4.1 15.1 1.0 ND1 A:HIS131 4.1 13.4 1.0 ND1 A:HIS127 4.2 15.0 1.0 CG A:HIS131 4.2 13.7 1.0 N A:LEU86 4.3 15.6 1.0 C A:CYS85 4.5 15.4 1.0 OE1 A:GLU128 4.5 21.4 1.0 O A:HOH366 4.5 15.7 1.0 OE2 A:GLU128 4.6 19.0 1.0 O A:GLY84 4.7 16.1 1.0 O4 A:PGE201 4.8 39.9 1.0 CD A:GLU128 4.9 19.1 1.0 CG A:GLN47 5.0 14.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II


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 Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:17.6 occ:1.00 NE2 B:HIS131 2.1 17.7 1.0 NE2 B:HIS127 2.1 15.1 1.0 O B:HOH305 2.1 18.5 1.0 SG B:CYS85 2.2 17.5 1.0 CD2 B:HIS127 3.0 16.6 1.0 CD2 B:HIS131 3.0 16.0 1.0 CE1 B:HIS131 3.1 15.4 1.0 CE1 B:HIS127 3.1 16.3 1.0 CB B:CYS85 3.2 18.2 1.0 O B:HOH368 3.5 18.2 1.0 NE2 B:GLN47 3.6 17.7 1.0 O B:HOH382 3.7 31.7 1.0 CA B:CYS85 3.8 18.8 1.0 CD B:GLN47 4.0 17.1 1.0 OE1 B:GLN47 4.0 16.1 1.0 CG B:HIS127 4.1 15.2 1.0 ND1 B:HIS131 4.2 14.0 1.0 CG B:HIS131 4.2 14.2 1.0 ND1 B:HIS127 4.2 15.7 1.0 OE2 B:GLU128 4.2 21.7 1.0 C6 B:PGE201 4.3 37.7 1.0 O B:HOH357 4.4 16.6 1.0 N B:LEU86 4.5 18.7 1.0 C B:CYS85 4.6 18.6 1.0 OE1 B:GLU128 4.6 18.8 1.0 O B:GLY84 4.7 19.2 1.0 CD B:GLU128 4.8 19.1 1.0

R.Grzela, J.Nusbaum, S.Fieulaine, F.Lavecchia, W.V.Bienvenut, C.Dian, T.Meinnel, C.Giglione. The C-Terminal Residue of Phage VP16 Pdf, the Smallest Peptide Deformylase, Acts As An Offset Element Locking the Active Conformation. Sci Rep V. 7 11041 2017.
ISSN: ESSN 2045-2322
PubMed: 28887476
DOI: 10.1038/S41598-017-11329-3