Atomistry » Chlorine » PDB 4f1b-4fbx » 4f96
Atomistry »
  Chlorine »
    PDB 4f1b-4fbx »
      4f96 »

Chlorine in PDB 4f96: Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp

Protein crystallography data

The structure of Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp, PDB code: 4f96 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) 37.52 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.821, 121.151, 84.333, 90.00, 91.74, 90.00
R / Rfree (%) 19 / 20.9

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp (pdb code 4f96). 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, PDB code: 4f96:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 4f96

Go back to Chlorine Binding Sites List in 4f96
Chlorine binding site 1 out of 2 in the Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:32.7
occ:1.00
OG B:SER187 3.0 29.2 1.0
CL A:CL502 3.0 35.5 1.0
NH2 A:ARG114 3.1 22.6 1.0
NH1 A:ARG114 3.1 24.4 1.0
CE2 B:TYR110 3.3 22.0 1.0
CZ A:ARG114 3.5 29.0 1.0
CB B:SER187 3.5 22.8 1.0
OH B:TYR110 3.6 25.3 1.0
CZ B:TYR110 3.6 26.6 1.0
CB A:TYR190 3.7 24.6 1.0
N A:TYR190 3.8 17.2 1.0
CB A:ASP189 3.9 26.2 1.0
CD2 B:TYR110 4.1 20.6 1.0
CB A:SER187 4.1 23.3 1.0
CB B:TYR190 4.1 23.1 1.0
CA A:TYR190 4.2 19.3 1.0
C A:ASP189 4.3 25.7 1.0
OG A:SER187 4.4 27.4 1.0
NH2 B:ARG114 4.5 26.7 1.0
N B:SER187 4.6 20.6 1.0
CD1 A:TYR190 4.6 20.3 1.0
CE1 B:TYR110 4.6 26.8 1.0
CA A:ASP189 4.6 25.3 1.0
CG A:TYR190 4.6 20.1 1.0
CG B:TYR190 4.6 18.6 1.0
CA B:SER187 4.7 23.8 1.0
CD1 B:TYR190 4.7 22.4 1.0
NE A:ARG114 4.9 22.7 1.0
N A:ASP189 4.9 20.5 1.0
CG A:ASP189 5.0 27.2 1.0
CG B:TYR110 5.0 27.7 1.0

Chlorine binding site 2 out of 2 in 4f96

Go back to Chlorine Binding Sites List in 4f96
Chlorine binding site 2 out of 2 in the Crystal Structure of Vlde, the Pseudo-Glycosyltransferase, in Complex with Gdp


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:35.5
occ:1.00
OG A:SER187 2.8 27.4 1.0
CL B:CL502 3.0 32.7 1.0
NH1 B:ARG114 3.1 27.0 1.0
NH2 B:ARG114 3.1 26.7 1.0
CE2 A:TYR110 3.2 22.2 1.0
OH A:TYR110 3.5 22.8 1.0
CZ A:TYR110 3.5 28.5 1.0
CB A:SER187 3.5 23.3 1.0
CZ B:ARG114 3.5 29.7 1.0
CB B:ASP189 3.7 23.4 1.0
N B:TYR190 3.8 21.7 1.0
CB B:TYR190 3.8 23.1 1.0
CB B:SER187 4.1 22.8 1.0
CD2 A:TYR110 4.1 20.7 1.0
CB A:TYR190 4.2 24.6 1.0
CA B:TYR190 4.2 21.2 1.0
C B:ASP189 4.3 25.6 1.0
OG B:SER187 4.4 29.2 1.0
N A:SER187 4.5 19.8 1.0
CA B:ASP189 4.5 24.3 1.0
CE1 A:TYR110 4.5 25.4 1.0
CA A:SER187 4.6 25.2 1.0
NH2 A:ARG114 4.6 22.6 1.0
CD1 B:TYR190 4.7 22.4 1.0
CG A:TYR190 4.7 20.1 1.0
CG B:TYR190 4.7 18.6 1.0
CD1 A:TYR190 4.8 20.3 1.0
N B:ASP189 4.8 20.4 1.0
CG B:ASP189 4.9 30.6 1.0
NE B:ARG114 4.9 25.4 1.0
CG A:TYR110 5.0 28.3 1.0
O B:ASP189 5.0 24.9 1.0
OD2 B:ASP189 5.0 28.1 1.0

Reference:

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
Page generated: Fri Jul 11 15:09:02 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy