Zinc in PDB 5jp6: Bdellovibrio Bacteriovorus Peptidoglycan Deacetylase BD3279

The structure of Bdellovibrio Bacteriovorus Peptidoglycan Deacetylase BD3279, PDB code: 5jp6 was solved by A.L.Lovering, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	97.37 / 1.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	112.434, 112.434, 79.859, 90.00, 90.00, 120.00
R / Rfree (%)	14.5 / 16.7

The structure of Bdellovibrio Bacteriovorus Peptidoglycan Deacetylase BD3279 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Bdellovibrio Bacteriovorus Peptidoglycan Deacetylase BD3279 (pdb code 5jp6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Bdellovibrio Bacteriovorus Peptidoglycan Deacetylase BD3279, PDB code: 5jp6:

Zinc binding site 1 out of 1 in the Bdellovibrio Bacteriovorus Peptidoglycan Deacetylase BD3279


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Bdellovibrio Bacteriovorus Peptidoglycan Deacetylase BD3279 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:37.3 occ:0.50 NE2 A:HIS227 2.1 28.9 1.0 OH A:TYR280 2.3 21.6 1.0 CD2 A:HIS227 2.3 21.2 1.0 OD2 A:ASP177 2.4 31.8 1.0 CZ A:TYR280 2.8 23.4 1.0 OD1 A:ASP177 3.0 30.9 1.0 CE2 A:TYR280 3.0 27.6 1.0 CG A:ASP177 3.0 24.5 1.0 CE1 A:HIS227 3.3 30.8 1.0 CG A:HIS227 3.6 24.8 1.0 OD2 A:ASP176 3.8 21.3 1.0 CD1 A:ILE229 3.8 57.3 1.0 CE1 A:TYR280 3.9 24.1 1.0 CB A:ASP176 4.0 18.0 1.0 ND1 A:HIS227 4.0 33.4 1.0 NE2 A:HIS335 4.1 22.1 1.0 CD2 A:TYR280 4.1 26.5 1.0 CD2 A:HIS335 4.2 19.8 1.0 CG A:ASP176 4.4 18.6 1.0 CB A:ASP177 4.4 20.6 1.0 CD1 A:TYR280 4.8 28.2 1.0 OA A:PXU279 4.8 31.3 1.0 CB A:HIS227 4.8 21.6 1.0 CG A:TYR280 4.9 26.8 1.0

C.Lambert, T.R.Lerner, N.K.Bui, H.Somers, S.Aizawa, S.Liddell, A.Clark, W.Vollmer, A.L.Lovering, R.E.Sockett. Interrupting Peptidoglycan Deacetylation During Bdellovibrio Predator-Prey Interaction Prevents Ultimate Destruction of Prey Wall, Liberating Bacterial-Ghosts. Sci Rep V. 6 26010 2016.
ISSN: ESSN 2045-2322
PubMed: 27211869
DOI: 10.1038/SREP26010