Nickel 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:

Zinc

(Zn)

2 atoms

The binding sites of Nickel 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 Nickel atom.
In total 3 binding sites of Nickel where determined in the Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T - Crystal Form II, PDB code: 5mtd:
Jump to Nickel binding site number: 1; 2; 3;

Nickel binding site 1 out of 3 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 Nickel with other atoms in the Ni 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:Ni203 b:20.2 occ:1.00 O A:HOH378 2.1 26.2 1.0 O A:MET1 2.1 24.2 1.0 O A:HOH373 2.1 26.9 1.0 NE2 B:HIS74 2.1 18.7 1.0 O A:HOH370 2.1 24.2 1.0 N A:MET1 2.2 24.4 1.0 C A:MET1 2.8 23.5 1.0 CA A:MET1 3.0 23.9 1.0 CD2 B:HIS74 3.1 16.8 1.0 CE1 B:HIS74 3.1 20.4 1.0 O B:HOH390 4.0 23.3 1.0 N A:LYS2 4.1 23.2 1.0 O A:HOH329 4.1 26.9 1.0 O A:HOH431 4.1 24.0 1.0 CB A:MET1 4.2 22.6 1.0 ND1 B:HIS74 4.2 18.7 1.0 CG B:HIS74 4.2 17.4 1.0 O B:HOH399 4.6 31.3 1.0 CA A:LYS2 4.8 24.1 1.0 O A:HOH409 4.8 30.8 1.0 O B:HOH451 4.9 32.9 1.0 NH2 B:ARG98 4.9 23.0 1.0

Nickel binding site 2 out of 3 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 Nickel with other atoms in the Ni 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 A:Ni204 b:43.7 occ:1.00 NE2 A:HIS12 2.1 28.6 1.0 CE1 A:HIS12 3.0 29.5 1.0 O A:HOH308 3.2 39.7 1.0 CD2 A:HIS12 3.2 28.2 1.0 ND1 A:HIS12 4.2 28.5 1.0 CG A:HIS12 4.3 25.9 1.0 O A:ASP6 4.4 28.3 1.0 O A:HOH422 4.4 41.6 1.0 OH A:TYR88 4.7 26.4 1.0

Nickel binding site 3 out of 3 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 Nickel with other atoms in the Ni binding site number 3 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:Ni205 b:27.6 occ:1.00 NE2 A:HIS74 2.1 26.0 1.0 O A:HOH412 2.2 36.9 1.0 CD2 A:HIS74 3.1 24.9 1.0 CE1 A:HIS74 3.1 27.3 1.0 ND1 A:HIS74 4.2 23.7 1.0 CG A:HIS74 4.2 23.0 1.0 O A:HOH358 4.5 38.5 1.0 NH2 A:ARG98 4.9 30.1 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