Zinc in PDB 6a6a: Vanyb in Complex with D-Alanine

All present enzymatic activity of Vanyb in Complex with D-Alanine:
3.4.16.4;

The structure of Vanyb in Complex with D-Alanine, PDB code: 6a6a 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)	36.46 / 2.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.368, 40.830, 114.672, 90.00, 109.08, 90.00
R / Rfree (%)	20.2 / 27.6

The binding sites of Zinc atom in the Vanyb in Complex with D-Alanine (pdb code 6a6a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Vanyb in Complex with D-Alanine, PDB code: 6a6a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Vanyb in Complex with D-Alanine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Vanyb in Complex with D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn305 b:23.9 occ:1.00 ND1 A:HIS241 2.0 27.4 1.0 OD1 A:ASP195 2.0 21.8 1.0 NE2 A:HIS188 2.0 27.0 1.0 O A:ACT304 2.2 25.6 1.0 OXT A:ACT304 2.2 25.0 1.0 C A:ACT304 2.5 26.3 1.0 CG A:ASP195 2.6 19.3 1.0 OD2 A:ASP195 2.6 16.6 1.0 CE1 A:HIS241 2.9 26.0 1.0 CD2 A:HIS188 3.0 26.2 1.0 CG A:HIS241 3.0 25.2 1.0 CE1 A:HIS188 3.0 26.2 1.0 CB A:HIS241 3.4 22.8 1.0 NH2 A:ARG146 3.7 27.5 1.0 CH3 A:ACT304 4.0 27.0 1.0 NE2 A:HIS241 4.0 21.8 1.0 CB A:ASP195 4.1 20.8 1.0 ND1 A:HIS188 4.1 23.1 1.0 CG A:HIS188 4.1 24.0 1.0 CD2 A:HIS241 4.1 23.7 1.0 OXT A:DAL301 4.2 24.2 1.0 CA A:HIS241 4.2 23.5 1.0 NH1 A:ARG146 4.3 28.6 1.0 CA A:DAL301 4.3 24.5 1.0 C A:DAL301 4.3 24.6 1.0 CD1 A:TRP240 4.4 26.4 1.0 CZ A:ARG146 4.4 33.0 1.0 NE1 A:TRP240 4.6 27.8 1.0 CA A:ASP195 4.7 21.4 1.0 N A:ASP195 4.8 22.5 1.0

Zinc binding site 2 out of 2 in the Vanyb in Complex with D-Alanine


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Vanyb in Complex with D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn305 b:27.3 occ:1.00 ND1 B:HIS241 1.9 32.2 1.0 NE2 B:HIS188 2.0 24.3 1.0 OD1 B:ASP195 2.1 31.6 1.0 OXT B:ACT304 2.2 18.0 1.0 O B:ACT304 2.5 21.2 1.0 C B:ACT304 2.7 21.9 1.0 CE1 B:HIS241 2.8 30.3 1.0 CG B:ASP195 2.9 30.3 1.0 CG B:HIS241 3.0 30.8 1.0 CD2 B:HIS188 3.0 25.6 1.0 CE1 B:HIS188 3.0 26.0 1.0 OD2 B:ASP195 3.1 28.9 1.0 CB B:HIS241 3.4 26.9 1.0 NH2 B:ARG146 3.8 24.1 1.0 NE2 B:HIS241 4.0 29.5 1.0 CD2 B:HIS241 4.1 31.3 1.0 CA B:DAL301 4.1 28.3 1.0 ND1 B:HIS188 4.1 26.1 1.0 CA B:HIS241 4.1 28.1 1.0 CG B:HIS188 4.1 27.1 1.0 CH3 B:ACT304 4.2 20.0 1.0 CB B:ASP195 4.3 29.7 1.0 C B:DAL301 4.4 29.0 1.0 O B:DAL301 4.4 29.2 1.0 NH1 B:ARG146 4.6 23.0 1.0 CD1 B:TRP240 4.6 31.1 1.0 CZ B:ARG146 4.6 25.0 1.0 N B:ASP195 4.6 29.1 1.0 NE1 B:TRP240 4.7 34.2 1.0 CA B:ASP195 4.7 29.8 1.0 C B:VAL194 4.9 29.9 1.0 O B:VAL194 4.9 26.2 1.0 N B:DAL301 4.9 33.2 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