Chlorine in PDB 4f97: Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp and Validoxylamine A 7'-Phosphate

The structure of Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp and Validoxylamine A 7'-Phosphate, PDB code: 4f97 was solved by M.C.Cavalier, Y.-S.Yim, S.Asamizu, D.Neau, K.H.Almabruk, T.Mahmud, Y.-H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.94 / 2.11
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.959, 120.714, 84.236, 90.00, 91.63, 90.00
R / Rfree (%)	19.1 / 22.2

The binding sites of Chlorine atom in the Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp and Validoxylamine A 7'-Phosphate (pdb code 4f97). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp and Validoxylamine A 7'-Phosphate, PDB code: 4f97:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp and Validoxylamine A 7'-Phosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp and Validoxylamine A 7'-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl504 b:26.3 occ:1.00 CL B:CL504 2.9 29.8 1.0 OG A:SER187 2.9 28.7 1.0 CE1 A:TYR110 3.2 21.6 1.0 NH2 B:ARG114 3.2 22.5 1.0 NH1 B:ARG114 3.3 22.1 1.0 CB A:SER187 3.5 22.4 1.0 OH A:TYR110 3.5 23.5 1.0 CZ A:TYR110 3.6 27.9 1.0 CZ B:ARG114 3.7 27.2 1.0 CB B:TYR190 3.9 24.8 1.0 N B:TYR190 3.9 21.8 1.0 CB A:TYR190 3.9 23.8 1.0 CB B:ASP189 4.0 25.3 1.0 CD1 A:TYR110 4.1 20.6 1.0 CB B:SER187 4.1 22.4 1.0 OG B:SER187 4.3 28.7 1.0 CA B:TYR190 4.3 16.3 1.0 NH2 A:ARG114 4.5 25.2 1.0 C B:ASP189 4.5 27.8 1.0 CG A:TYR190 4.5 18.6 1.0 N A:SER187 4.5 23.4 1.0 CD2 A:TYR190 4.6 21.8 1.0 CA A:SER187 4.6 23.9 1.0 CD2 B:TYR190 4.7 21.2 1.0 CE2 A:TYR110 4.7 26.6 1.0 CA B:ASP189 4.7 27.1 1.0 CG B:TYR190 4.8 18.1 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp and Validoxylamine A 7'-Phosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp and Validoxylamine A 7'-Phosphate within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl504 b:29.8 occ:1.00 OG B:SER187 2.9 28.7 1.0 CL A:CL504 2.9 26.3 1.0 NH1 A:ARG114 3.1 22.2 1.0 CE1 B:TYR110 3.1 22.8 1.0 NH2 A:ARG114 3.2 25.2 1.0 OH B:TYR110 3.4 23.2 1.0 CZ B:TYR110 3.4 25.8 1.0 CB B:SER187 3.6 22.4 1.0 CZ A:ARG114 3.6 27.1 1.0 CB A:ASP189 3.8 24.8 1.0 N A:TYR190 3.9 21.9 1.0 CB A:TYR190 3.9 23.8 1.0 CD1 B:TYR110 4.0 18.6 1.0 CB B:TYR190 4.1 24.8 1.0 CB A:SER187 4.1 22.4 1.0 CA A:TYR190 4.3 17.8 1.0 C A:ASP189 4.3 26.3 1.0 OG A:SER187 4.4 28.7 1.0 N B:SER187 4.5 22.2 1.0 CE2 B:TYR110 4.5 25.2 1.0 CA A:ASP189 4.5 23.9 1.0 CG B:TYR190 4.6 18.1 1.0 NH2 B:ARG114 4.6 22.5 1.0 CD2 B:TYR190 4.7 21.2 1.0 CA B:SER187 4.7 24.4 1.0 CD2 A:TYR190 4.7 21.8 1.0 CG A:TYR190 4.8 18.6 1.0 CG A:ASP189 4.9 25.2 1.0 N A:ASP189 4.9 21.1 1.0 NE A:ARG114 4.9 22.6 1.0 CG B:TYR110 5.0 24.8 1.0 OD2 A:ASP189 5.0 23.3 1.0

M.C.Cavalier, Y.S.Yim, S.Asamizu, D.Neau, K.H.Almabruk, T.Mahmud, Y.H.Lee. Mechanistic Insights Into Validoxylamine A 7'-Phosphate Synthesis By Vlde Using the Structure of the Entire Product Complex. Plos One V. 7 44934 2012.
ISSN: ESSN 1932-6203
PubMed: 23028689
DOI: 10.1371/JOURNAL.PONE.0044934