Copper in PDB 5zhw: Vanyb in Complex with D-Alanine-D-Alanine

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

The structure of Vanyb in Complex with D-Alanine-D-Alanine, PDB code: 5zhw 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 / 2.18
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.861, 40.578, 115.449, 90.00, 108.62, 90.00
R / Rfree (%)	15.9 / 20.8

The binding sites of Copper atom in the Vanyb in Complex with D-Alanine-D-Alanine (pdb code 5zhw). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Vanyb in Complex with D-Alanine-D-Alanine, PDB code: 5zhw:
Jump to Copper binding site number: 1; 2;

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Vanyb in Complex with D-Alanine-D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu301 b:27.3 occ:1.00 OD1 A:ASP195 1.9 26.1 1.0 O A:DAL303 2.0 42.2 1.0 ND1 A:HIS241 2.0 24.4 1.0 NE2 A:HIS188 2.1 25.6 1.0 CG A:ASP195 2.7 24.4 1.0 OD2 A:ASP195 2.9 24.7 1.0 CE1 A:HIS241 2.9 25.9 1.0 C A:DAL303 3.0 53.4 1.0 CE1 A:HIS188 3.0 24.7 1.0 CG A:HIS241 3.1 25.4 1.0 CD2 A:HIS188 3.1 23.7 1.0 CB A:HIS241 3.5 24.9 1.0 N A:DAL302 3.7 57.2 1.0 CA A:DAL302 3.8 48.8 1.0 NE2 A:HIS241 4.0 23.9 1.0 CA A:DAL303 4.1 58.3 1.0 CD2 A:HIS241 4.1 25.3 1.0 ND1 A:HIS188 4.1 25.7 1.0 CB A:ASP195 4.1 26.2 1.0 NH2 A:ARG146 4.2 32.2 1.0 CG A:HIS188 4.2 25.8 1.0 CA A:HIS241 4.3 26.0 1.0 CD1 A:TRP240 4.5 28.2 1.0 C A:DAL302 4.5 39.1 1.0 OE1 A:GLU238 4.6 39.8 1.0 NE1 A:TRP240 4.6 29.5 1.0 OXT A:DAL302 4.6 44.6 1.0 CA A:ASP195 4.6 25.3 1.0 N A:ASP195 4.7 24.7 1.0 N A:DAL303 4.8 57.6 1.0 CZ A:ARG146 4.9 30.0 1.0 NH1 A:ARG146 4.9 30.3 1.0

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


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Vanyb in Complex with D-Alanine-D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu301 b:27.4 occ:1.00 OD1 B:ASP195 1.9 24.9 1.0 ND1 B:HIS241 2.0 26.6 1.0 NE2 B:HIS188 2.1 25.6 1.0 O B:DAL303 2.2 52.1 1.0 CG B:ASP195 2.7 25.7 1.0 OD2 B:ASP195 2.8 28.1 1.0 CE1 B:HIS241 2.8 29.5 1.0 CD2 B:HIS188 3.0 24.3 1.0 CG B:HIS241 3.0 27.3 1.0 C B:DAL303 3.1 65.8 1.0 CE1 B:HIS188 3.1 25.5 1.0 CA B:DAL302 3.5 51.1 1.0 CB B:HIS241 3.5 26.5 1.0 N B:DAL302 3.6 61.9 1.0 NE2 B:HIS241 4.0 29.8 1.0 NH2 B:ARG146 4.0 29.8 1.0 CD2 B:HIS241 4.1 29.3 1.0 CB B:ASP195 4.1 25.6 1.0 ND1 B:HIS188 4.2 24.1 1.0 CG B:HIS188 4.2 25.0 1.0 CA B:HIS241 4.2 27.1 1.0 C B:DAL302 4.3 41.1 1.0 CA B:DAL303 4.3 69.2 1.0 O B:DAL302 4.5 51.8 1.0 CB B:DAL303 4.5 70.0 1.0 CD1 B:TRP240 4.6 35.9 1.0 N B:ASP195 4.6 24.1 1.0 CA B:ASP195 4.6 24.8 1.0 CB B:DAL302 4.6 51.2 1.0 NE1 B:TRP240 4.7 37.9 1.0 CZ B:ARG146 4.8 28.4 1.0 OE1 B:GLU238 4.8 47.8 1.0 NH1 B:ARG146 4.9 27.5 1.0 O B:VAL194 4.9 24.0 1.0 C B:VAL194 4.9 24.0 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