Chlorine in PDB 2dxf: Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog

All present enzymatic activity of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog:
2.7.4.6;

The structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog, PDB code: 2dxf was solved by M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.13 / 1.70
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	69.891, 69.891, 107.184, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 21.5

The binding sites of Chlorine atom in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog (pdb code 2dxf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog, PDB code: 2dxf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog


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 Nucleoside Diphosphate Kinase in Complex with Gtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl701 b:23.4 occ:1.00 O A:HOH858 2.7 37.8 1.0 O A:HOH818 3.1 41.8 1.0 N A:ALA96 3.2 15.1 1.0 N A:ALA103 3.2 13.2 1.0 CA A:GLY95 3.6 15.4 1.0 CA A:ALA102 3.7 13.2 1.0 O A:HOH742 3.8 22.3 1.0 C A:GLY95 3.9 15.2 1.0 CB A:ALA103 3.9 13.4 1.0 C A:ALA102 4.0 13.4 1.0 CB A:ALA96 4.0 14.2 1.0 CA A:ALA96 4.1 16.0 1.0 CA A:ALA103 4.1 11.4 1.0 CG2 A:THR106 4.2 9.9 1.0 CB A:ALA102 4.3 13.0 1.0 O A:ASP101 4.4 14.1 1.0 OG1 A:THR106 4.5 10.6 1.0 N A:ALA102 4.8 14.9 1.0 CB A:THR106 4.9 9.4 1.0 N A:GLY95 4.9 13.8 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog


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 Nucleoside Diphosphate Kinase in Complex with Gtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl703 b:20.3 occ:1.00 O A:HOH723 3.0 17.9 1.0

Chlorine binding site 3 out of 4 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl702 b:21.1 occ:1.00 O B:HOH901 2.8 42.7 1.0 O B:HOH826 3.0 30.0 1.0 N B:ALA96 3.2 13.6 1.0 N B:ALA103 3.2 11.4 1.0 CA B:GLY95 3.6 11.9 1.0 CA B:ALA102 3.7 11.3 1.0 O B:HOH730 3.7 16.4 1.0 C B:GLY95 3.9 13.1 1.0 CB B:ALA103 3.9 14.3 1.0 C B:ALA102 4.0 10.8 1.0 CB B:ALA96 4.1 13.7 1.0 CA B:ALA96 4.2 13.9 1.0 CA B:ALA103 4.2 11.0 1.0 CG2 B:THR106 4.2 9.8 1.0 CB B:ALA102 4.3 12.7 1.0 O B:ASP101 4.5 13.3 1.0 O B:HOH782 4.5 32.3 1.0 OG1 B:THR106 4.6 10.3 1.0 N B:ALA102 4.8 11.6 1.0 CB B:THR106 4.9 10.3 1.0 N B:GLY95 5.0 11.8 1.0

Chlorine binding site 4 out of 4 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl704 b:23.1 occ:1.00 O B:HOH833 2.9 25.9 1.0 N B:ALA152 3.3 12.2 1.0 NE B:ARG150 3.4 13.3 1.0 O B:HOH864 3.4 26.8 1.0 N B:ALA151 3.6 12.3 1.0 NH2 B:ARG150 3.7 13.0 1.0 CB B:ALA151 3.8 12.5 1.0 CB B:ALA152 3.9 12.9 1.0 CB B:ARG150 3.9 13.8 1.0 CZ B:ARG150 3.9 13.1 1.0 CA B:ALA151 4.0 11.3 1.0 O A:VAL20 4.0 11.6 1.0 C B:ALA151 4.1 12.7 1.0 CA B:ALA152 4.2 12.1 1.0 C B:ARG150 4.2 12.0 1.0 CD B:ARG150 4.4 12.9 1.0 O B:HOH749 4.5 23.1 1.0 CA B:ARG150 4.6 12.1 1.0 CG B:ARG150 4.6 13.0 1.0 O B:HOH858 4.8 41.9 1.0 O B:ARG150 4.9 12.6 1.0

M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama. Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Gtp Analog To Be Published.