Chlorine in PDB 1rrv: X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin.

The structure of X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin., PDB code: 1rrv was solved by A.M.Mulichak, W.Lu, H.C.Losey, C.T.Walsh, R.M.Garavito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.670, 64.120, 144.080, 90.00, 91.73, 90.00
R / Rfree (%)	21 / 25.2

The structure of X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin. also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Chlorine atom in the X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin. (pdb code 1rrv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin., PDB code: 1rrv:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin. within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl2 b:24.8 occ:1.00 CL C:OMZ2 0.0 24.8 1.0 CE1 C:OMZ2 1.7 20.6 1.0 CD1 C:OMZ2 2.7 20.8 1.0 CZ C:OMZ2 2.7 23.1 1.0 O A:HOH2024 2.8 62.1 1.0 OH C:OMZ2 2.9 24.5 1.0 O A:GLY9 3.1 22.0 1.0 O A:HOH2056 3.4 40.9 1.0 C A:GLY9 3.4 19.4 1.0 CA A:GLY9 3.7 18.3 1.0 N A:GLY9 3.7 19.6 1.0 C5 C:GHP4 4.0 24.6 1.0 CG C:OMZ2 4.0 21.0 1.0 CE2 C:OMZ2 4.0 18.2 1.0 CG A:PRO36 4.2 23.6 1.0 C6 C:GHP4 4.2 25.4 1.0 N A:THR10 4.3 21.6 1.0 O A:HOH2020 4.3 36.7 1.0 SD A:MET60 4.4 35.1 1.0 CD2 C:OMZ2 4.5 21.2 1.0 C A:CYS8 4.6 21.6 1.0 O A:HOH2060 4.6 50.9 1.0 CB A:PRO36 4.8 21.8 1.0 CG2 A:THR10 4.8 23.8 1.0 O A:HOH2008 4.9 43.1 1.0 CA A:THR10 4.9 23.2 1.0 O C:OMZ2 5.0 26.8 1.0

Chlorine binding site 2 out of 4 in the X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin. within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl6 b:30.5 occ:1.00 CL C:OMY6 0.0 30.5 1.0 CE1 C:OMY6 1.8 25.0 1.0 CD1 C:OMY6 2.7 23.0 1.0 CZ C:OMY6 2.8 22.9 1.0 O C:HOH2011 2.9 29.9 1.0 OCZ C:OMY6 3.2 23.6 1.0 C3 C:GHP4 3.4 22.9 1.0 O A:HOH2135 3.5 29.0 1.0 CB A:ASP141 3.5 27.3 1.0 O5 C:BGC8 3.5 30.7 1.0 O C:HOH2004 3.7 44.9 1.0 C6 C:BGC8 3.8 32.1 1.0 C2 C:GHP4 3.9 22.1 1.0 CG C:OMY6 4.0 22.0 1.0 CE2 C:OMY6 4.1 23.3 1.0 C4 C:GHP4 4.1 25.1 1.0 O A:ASP141 4.1 31.4 1.0 O6 C:BGC8 4.2 34.4 1.0 C5 C:BGC8 4.4 32.5 1.0 CA A:ASP141 4.4 26.3 1.0 CG2 A:THR332 4.4 21.2 1.0 CG A:ASP141 4.5 28.6 1.0 O4 C:GHP4 4.5 27.6 1.0 CD2 C:OMY6 4.6 18.6 1.0 C1 C:BGC8 4.6 30.1 1.0 OD2 A:ASP141 4.6 26.8 1.0 C A:ASP141 4.7 27.6 1.0 O C:HOH2003 4.8 20.6 1.0 C1 C:GHP4 4.8 22.4 1.0 C5 C:GHP4 5.0 24.6 1.0

Chlorine binding site 3 out of 4 in the X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin. within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl2 b:40.1 occ:1.00 CL D:OMZ2 0.0 40.1 1.0 CE1 D:OMZ2 1.7 38.6 1.0 CD1 D:OMZ2 2.7 36.9 1.0 CZ D:OMZ2 2.7 38.5 1.0 OH D:OMZ2 3.0 35.0 1.0 O B:GLY9 3.1 35.9 1.0 C B:GLY9 3.4 35.9 1.0 CA B:GLY9 3.5 36.0 1.0 O B:HOH2020 3.5 47.0 1.0 N B:GLY9 3.6 37.7 1.0 CG D:OMZ2 4.0 37.7 1.0 CE2 D:OMZ2 4.1 37.4 1.0 C5 D:GHP4 4.2 32.9 1.0 CG B:PRO36 4.2 36.5 1.0 C B:CYS8 4.3 38.3 1.0 CE B:MET60 4.3 42.2 1.0 N B:THR10 4.3 35.0 1.0 C6 D:GHP4 4.4 33.2 1.0 SD B:MET60 4.5 46.7 1.0 CD2 D:OMZ2 4.6 37.0 1.0 O B:CYS8 4.7 39.2 1.0 SG B:CYS8 4.8 38.7 1.0 O B:HOH2001 4.9 41.8 1.0 O D:HOH2001 4.9 36.9 1.0 CB B:PRO36 4.9 38.6 1.0 O D:OMZ2 5.0 35.6 1.0 CA B:THR10 5.0 34.6 1.0

Chlorine binding site 4 out of 4 in the X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin.


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Crystal Structure of Tdp-Vancosaminyltransferase Gtfd As A Complex with Tdp and the Natural Substrate, Desvancosaminyl Vancomycin. within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl6 b:39.0 occ:1.00 CL D:OMY6 0.0 39.0 1.0 CE1 D:OMY6 1.8 33.4 1.0 CD1 D:OMY6 2.7 34.9 1.0 CZ D:OMY6 2.8 33.1 1.0 O D:HOH2004 3.0 60.3 1.0 OCZ D:OMY6 3.2 32.2 1.0 C3 D:GHP4 3.4 32.5 1.0 CB B:ASP141 3.7 44.0 1.0 O5 D:BGC8 3.7 42.3 1.0 O6 D:BGC8 3.8 51.3 1.0 C2 D:GHP4 3.8 31.4 1.0 O B:HOH2053 3.8 41.5 1.0 C6 D:BGC8 3.9 46.2 1.0 CG D:OMY6 4.0 34.3 1.0 CE2 D:OMY6 4.1 31.9 1.0 C4 D:GHP4 4.1 33.6 1.0 O D:HOH2007 4.2 41.3 1.0 O B:ASP141 4.3 48.1 1.0 C5 D:BGC8 4.5 45.0 1.0 O D:HOH2002 4.6 37.0 1.0 CD2 D:OMY6 4.6 33.8 1.0 CA B:ASP141 4.6 44.7 1.0 O4 D:GHP4 4.6 38.4 1.0 C1 D:GHP4 4.6 32.9 1.0 O D:GHP4 4.7 35.5 1.0 CG B:ASP141 4.7 42.9 1.0 CG2 B:THR332 4.7 33.9 1.0 C1 D:BGC8 4.8 41.9 1.0 OD2 B:ASP141 4.9 43.5 1.0 C B:ASP141 4.9 46.0 1.0 C5 D:GHP4 4.9 32.9 1.0 C D:GHP4 5.0 36.0 1.0

A.M.Mulichak, W.Lu, H.C.Losey, C.T.Walsh, R.M.Garavito. Crystal Structure of Vancosaminyltransferase Gtfd From the Vancomycin Biosynthetic Pathway: Interactions with Acceptor and Nucleotide Ligands Biochemistry V. 43 5170 2004.
ISSN: ISSN 0006-2960
PubMed: 15122882
DOI: 10.1021/BI036130C