Nickel in PDB 5mtc: Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form I

The structure of Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form I, PDB code: 5mtc 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)	42.26 / 1.70
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.730, 64.730, 128.530, 90.00, 90.00, 120.00
R / Rfree (%)	17.1 / 20.1

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

Zinc

(Zn)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form I (pdb code 5mtc). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form I, PDB code: 5mtc:
Jump to Nickel binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni202 b:21.1 occ:1.00 O A:MET1 2.1 23.8 1.0 NE2 B:HIS74 2.1 20.7 1.0 O A:HOH339 2.2 32.0 1.0 N A:MET1 2.2 25.7 1.0 O A:HOH358 2.2 27.3 1.0 O A:HOH365 2.2 29.8 1.0 C A:MET1 2.9 23.7 1.0 CA A:MET1 3.0 25.5 1.0 CD2 B:HIS74 3.1 19.6 1.0 CE1 B:HIS74 3.1 22.1 1.0 CB A:MET1 3.8 24.4 1.0 N A:LYS2 4.1 22.6 1.0 ND1 B:HIS74 4.2 19.9 1.0 CG B:HIS74 4.2 19.1 1.0 O B:HOH318 4.3 41.7 1.0 O A:HOH377 4.8 50.1 1.0 CA A:LYS2 4.8 22.3 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form I within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:29.8 occ:1.00 NE2 A:HIS12 2.0 23.3 1.0 O A:HOH318 2.2 25.0 1.0 CE1 A:HIS12 2.8 23.0 1.0 CD2 A:HIS12 3.2 24.7 1.0 ND1 A:HIS12 4.0 22.8 1.0 O A:ASP6 4.0 25.3 1.0 CG A:HIS12 4.2 19.7 1.0 OH A:TYR88 4.6 22.9 1.0 CA A:ASP7 4.9 25.1 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