Zinc in PDB 5zhf: Structure of Vanyb Unbound

All present enzymatic activity of Structure of Vanyb Unbound:
3.4.16.4;

The structure of Structure of Vanyb Unbound, PDB code: 5zhf was solved by H.S.Kim, H.Hahn, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.65
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.339, 40.902, 115.401, 90.00, 108.44, 90.00
R / Rfree (%)	17.7 / 20.9

The binding sites of Zinc atom in the Structure of Vanyb Unbound (pdb code 5zhf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Vanyb Unbound, PDB code: 5zhf:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Vanyb Unbound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Vanyb Unbound within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:19.6 occ:1.00 OD1 A:ASP195 2.0 19.4 1.0 ND1 A:HIS241 2.0 18.6 1.0 NE2 A:HIS188 2.1 18.9 1.0 O A:HOH526 2.2 19.6 1.0 CG A:ASP195 2.8 18.4 1.0 CE1 A:HIS241 2.9 19.7 1.0 OD2 A:ASP195 2.9 20.3 1.0 CG A:HIS241 3.1 17.8 1.0 CD2 A:HIS188 3.1 21.2 1.0 CE1 A:HIS188 3.1 20.9 1.0 CB A:HIS241 3.5 18.4 1.0 NE2 A:HIS241 4.0 18.8 1.0 NH2 A:ARG146 4.1 25.5 1.0 CD2 A:HIS241 4.1 18.4 1.0 ND1 A:HIS188 4.2 20.6 1.0 CG A:HIS188 4.2 20.9 1.0 CB A:ASP195 4.2 18.6 1.0 CA A:HIS241 4.3 17.7 1.0 CD1 A:TRP240 4.3 20.7 1.0 NE1 A:TRP240 4.4 21.5 1.0 O A:HOH470 4.7 33.8 1.0 OE1 A:GLU238 4.7 25.9 1.0 CA A:ASP195 4.7 18.1 1.0 N A:ASP195 4.8 17.7 1.0 O A:HOH519 4.8 31.2 1.0 CZ A:ARG146 4.9 25.2 1.0 NH1 A:ARG146 4.9 24.8 1.0

Zinc binding site 2 out of 2 in the Structure of Vanyb Unbound


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Vanyb Unbound within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:19.5 occ:1.00 OD1 B:ASP195 1.9 21.0 1.0 ND1 B:HIS241 2.1 20.1 1.0 NE2 B:HIS188 2.1 20.8 1.0 O B:HOH505 2.3 19.6 1.0 CG B:ASP195 2.8 20.8 1.0 OD2 B:ASP195 2.9 19.8 1.0 CE1 B:HIS241 3.0 20.3 1.0 CE1 B:HIS188 3.0 22.1 1.0 CG B:HIS241 3.1 19.5 1.0 CD2 B:HIS188 3.1 20.4 1.0 CB B:HIS241 3.5 19.6 1.0 NE2 B:HIS241 4.1 19.6 1.0 ND1 B:HIS188 4.2 20.8 1.0 NH2 B:ARG146 4.2 24.3 1.0 CD2 B:HIS241 4.2 19.6 1.0 CB B:ASP195 4.2 20.8 1.0 CG B:HIS188 4.2 19.5 1.0 CA B:HIS241 4.3 19.0 1.0 CD1 B:TRP240 4.3 22.3 1.0 NE1 B:TRP240 4.4 22.4 1.0 N B:ASP195 4.7 18.9 1.0 CA B:ASP195 4.7 19.9 1.0 O B:HOH493 4.7 39.3 1.0 OE1 B:GLU238 4.8 25.6 1.0 CZ B:ARG146 4.8 23.1 1.0 NH1 B:ARG146 4.9 22.9 1.0 O B:HOH502 4.9 14.6 1.0

H.S.Kim, H.Hahn, J.Kim, D.M.Jang, J.Y.Lee, J.M.Back, H.N.Im, H.Kim, B.W.Han, S.W.Suh. Structural Basis For the Substrate Recognition of Peptidoglycan Pentapeptides By Enterococcus Faecalis Vanyb. Int. J. Biol. Macromol. V. 119 335 2018.
ISSN: ISSN 1879-0003
PubMed: 30016658
DOI: 10.1016/J.IJBIOMAC.2018.07.081