Nickel in PDB 5mte: Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T in Complex with Actinonin - Crystal Form II

The structure of Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T in Complex with Actinonin - Crystal Form II, PDB code: 5mte 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 / 1.40
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.620, 64.620, 124.890, 90.00, 90.00, 120.00
R / Rfree (%)	18.7 / 20.3

The structure of Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T in Complex with Actinonin - 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 in Complex with Actinonin - Crystal Form II (pdb code 5mte). 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 in Complex with Actinonin - Crystal Form II, PDB code: 5mte:
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 in Complex with Actinonin - 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 in Complex with Actinonin - Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:22.5 occ:1.00 NE2 B:HIS74 2.1 20.5 1.0 O A:HOH349 2.1 26.8 1.0 N A:MET1 2.1 27.6 1.0 O A:MET1 2.1 26.9 1.0 O A:HOH362 2.1 29.4 1.0 O A:HOH389 2.2 30.2 1.0 C A:MET1 2.8 26.8 1.0 CA A:MET1 3.0 27.2 1.0 CD2 B:HIS74 3.0 19.3 1.0 CE1 B:HIS74 3.1 21.6 1.0 O B:HOH387 4.0 26.7 1.0 O A:HOH358 4.0 27.4 1.0 N A:LYS2 4.1 26.6 1.0 O A:HOH420 4.1 25.8 1.0 CB A:MET1 4.1 26.4 1.0 ND1 B:HIS74 4.2 19.8 1.0 CG B:HIS74 4.2 17.9 1.0 O A:HOH400 4.7 40.7 1.0 CA A:LYS2 4.8 27.4 1.0 NH2 B:ARG98 4.9 24.1 1.0 O B:HOH428 4.9 47.9 1.0 O B:HOH443 4.9 33.2 1.0

Nickel binding site 2 out of 3 in the Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T in Complex with Actinonin - 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 in Complex with Actinonin - Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni203 b:35.8 occ:1.00 OD1 B:ASP76 2.0 28.1 1.0 O B:HOH322 2.2 36.6 1.0 CG B:ASP76 3.0 28.9 1.0 OD2 B:ASP76 3.4 32.6 1.0 O B:HOH376 4.0 27.4 1.0 O B:ASP76 4.0 24.0 1.0 O B:HOH306 4.1 22.0 1.0 O B:HOH373 4.3 37.5 1.0 C B:ASP76 4.3 24.1 1.0 CB B:ASP76 4.4 25.8 1.0 N B:GLY77 4.7 23.8 1.0 CA B:GLY77 4.7 23.8 1.0 O B:HOH419 4.8 47.0 1.0 CA B:ASP76 4.9 24.4 1.0 O B:HOH372 5.0 30.2 1.0

Nickel binding site 3 out of 3 in the Crystal Structure of Pdf From the Vibrio Parahaemolyticus Bacteriophage VP16T in Complex with Actinonin - 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 in Complex with Actinonin - Crystal Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni204 b:42.0 occ:1.00 O B:HOH303 1.8 33.3 1.0 OD1 B:ASP26 1.9 39.6 1.0 OD2 B:ASP30 2.0 33.6 1.0 O B:HOH312 2.3 41.4 1.0 CG B:ASP30 3.0 31.4 1.0 CG B:ASP26 3.0 36.8 1.0 OD1 B:ASP30 3.3 32.5 1.0 OD2 B:ASP26 3.5 41.1 1.0 O B:ASP26 4.0 29.7 1.0 CB B:ASP26 4.2 33.9 1.0 C B:ASP26 4.3 30.0 1.0 CB B:ASP30 4.3 27.8 1.0 O B:HOH332 4.3 45.8 1.0 N B:LEU27 4.6 28.1 1.0 CA B:LEU27 4.8 26.4 1.0 CA B:ASP26 4.8 32.1 1.0

R.Grzela, J.Nusbaum, S.Fieulaine, F.Lavecchia, M.Desmadril, N.Nhiri, A.Van Dorsselaer, S.Cianferani, E.Jacquet, T.Meinnel, C.Giglione. Peptide Deformylases From Vibrio Parahaemolyticus Phage and Bacteria Display Similar Deformylase Activity and Inhibitor Binding Clefts. Biochim. Biophys. Acta V.1866 348 2018.
ISSN: ISSN 0006-3002
PubMed: 29101077
DOI: 10.1016/J.BBAPAP.2017.10.007