Potassium 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:

Chlorine

(Cl)

4 atoms

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium 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 Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 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 Potassium with other atoms in the K 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 A:K417 b:26.0 occ:1.00 O3 A:GOL1006 2.7 32.9 1.0 OD1 A:ASP333 2.7 26.2 1.0 OG1 A:THR332 2.8 19.1 1.0 O A:HOH2122 2.9 30.9 1.0 O2 A:GOL1006 2.9 45.6 1.0 O A:HOH2266 2.9 28.8 1.0 OG A:SER311 3.0 27.2 1.0 C3 A:GOL1006 3.2 40.4 1.0 C2 A:GOL1006 3.6 43.9 1.0 CG A:ASP333 3.7 25.1 1.0 CB A:THR332 3.9 18.8 1.0 CB A:SER311 3.9 26.3 1.0 O C:HOH2013 4.0 46.9 1.0 OD2 A:ASP333 4.0 24.4 1.0 CA A:SER311 4.1 24.2 1.0 NE2 A:GLN334 4.1 19.7 1.0 CG A:GLN334 4.3 20.6 1.0 O3B A:TYD1003 4.3 21.2 1.0 N A:ASP333 4.4 19.3 1.0 CG2 A:THR332 4.5 21.2 1.0 ND2 A:ASN331 4.5 17.0 1.0 CD A:GLN334 4.6 23.2 1.0 O A:HOH2300 4.7 48.2 1.0 C1 A:GOL1006 4.8 45.4 1.0 N A:ALA312 4.8 26.6 1.0 CB A:ASP333 4.9 21.1 1.0

Potassium binding site 2 out of 2 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 Potassium with other atoms in the K 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 B:K417 b:38.2 occ:1.00 O3 B:GOL1007 2.6 37.7 1.0 O B:HOH2044 2.7 38.3 1.0 O2 B:GOL1007 2.9 44.6 1.0 OG1 B:THR332 2.9 34.8 1.0 OD1 B:ASP333 2.9 35.1 1.0 O B:HOH2151 2.9 38.7 1.0 OG B:SER311 3.2 34.5 1.0 C3 B:GOL1007 3.4 41.6 1.0 C2 B:GOL1007 3.7 45.3 1.0 CG B:ASP333 3.8 33.8 1.0 CB B:THR332 3.9 34.0 1.0 CB B:SER311 4.0 34.5 1.0 NE2 B:GLN334 4.1 26.4 1.0 OD2 B:ASP333 4.1 32.7 1.0 CG B:GLN334 4.1 27.5 1.0 CA B:SER311 4.2 33.3 1.0 O3B B:TYD1004 4.2 33.0 1.0 O D:HOH2005 4.3 46.5 1.0 ND2 B:ASN331 4.4 28.0 1.0 N B:ASP333 4.5 34.2 1.0 CG2 B:THR332 4.5 33.9 1.0 CD B:GLN334 4.5 22.6 1.0 C1 B:GOL1007 5.0 46.5 1.0 N B:ALA312 5.0 32.4 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