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

Protein crystallography data

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

Other elements in 5mte:

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:

Nickel (Ni) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 2 binding sites of Zinc 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 Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5mte

Go back to Zinc Binding Sites List in 5mte
Zinc binding site 1 out of 2 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 Zinc with other atoms in the Zn 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:Zn202

b:16.4
occ:1.00
NE2 A:HIS127 2.1 16.6 1.0
NE2 A:HIS131 2.1 16.2 1.0
O2 A:BB2201 2.2 16.6 1.0
O4 A:BB2201 2.2 19.2 1.0
SG A:CYS85 2.3 16.7 1.0
C3 A:BB2201 2.8 19.4 1.0
N1 A:BB2201 2.9 18.1 1.0
CD2 A:HIS127 3.0 16.2 1.0
CE1 A:HIS131 3.1 17.2 1.0
CD2 A:HIS131 3.1 15.7 1.0
CE1 A:HIS127 3.1 17.6 1.0
NE2 A:GLN47 3.2 18.3 1.0
CB A:CYS85 3.4 17.0 1.0
O A:HOH380 3.7 20.4 1.0
CA A:CYS85 3.8 17.0 1.0
CD A:GLN47 3.9 18.2 1.0
OE1 A:GLN47 4.1 18.3 1.0
CG A:HIS127 4.2 17.0 1.0
ND1 A:HIS127 4.2 17.9 1.0
N A:LEU86 4.2 17.7 1.0
ND1 A:HIS131 4.2 16.5 1.0
C5 A:BB2201 4.2 18.2 1.0
CG A:HIS131 4.3 15.5 1.0
C A:CYS85 4.5 17.4 1.0
OE1 A:GLU128 4.5 18.8 1.0
C6 A:BB2201 4.6 19.9 1.0
O A:HOH364 4.7 16.7 1.0
OE2 A:GLU128 4.9 18.2 1.0
CG A:GLN47 4.9 17.4 1.0
O A:GLY84 4.9 18.8 1.0
C7 A:BB2201 4.9 23.1 1.0

Zinc binding site 2 out of 2 in 5mte

Go back to Zinc Binding Sites List in 5mte
Zinc binding site 2 out of 2 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 Zinc with other atoms in the Zn 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:Zn202

b:17.6
occ:1.00
NE2 B:HIS127 2.1 15.7 1.0
NE2 B:HIS131 2.1 18.7 1.0
O2 B:BB2201 2.2 16.8 1.0
O4 B:BB2201 2.3 20.8 1.0
SG B:CYS85 2.3 18.3 1.0
C3 B:BB2201 2.8 20.4 1.0
N1 B:BB2201 2.8 19.8 1.0
CD2 B:HIS127 3.0 15.9 1.0
CE1 B:HIS131 3.1 17.3 1.0
CE1 B:HIS127 3.1 17.4 1.0
CD2 B:HIS131 3.1 16.7 1.0
NE2 B:GLN47 3.4 19.9 1.0
CB B:CYS85 3.4 18.3 1.0
O B:HOH361 3.7 18.9 1.0
CA B:CYS85 3.8 18.5 1.0
CD B:GLN47 3.9 18.8 1.0
OE1 B:GLN47 4.1 17.8 1.0
CG B:HIS127 4.2 16.6 1.0
ND1 B:HIS127 4.2 17.0 1.0
ND1 B:HIS131 4.2 16.9 1.0
C5 B:BB2201 4.2 20.8 1.0
CG B:HIS131 4.3 15.8 1.0
N B:LEU86 4.3 19.3 1.0
C B:CYS85 4.5 19.5 1.0
C6 B:BB2201 4.6 22.0 1.0
OE1 B:GLU128 4.6 18.9 1.0
O B:HOH358 4.7 16.4 1.0
C7 B:BB2201 4.9 24.1 1.0
O B:GLY84 4.9 20.0 1.0
OE2 B:GLU128 4.9 19.1 1.0

Reference:

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
Page generated: Wed Dec 16 06:33:45 2020

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