Chlorine in PDB 2dxd: Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Atp Analog

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

The structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Atp Analog, PDB code: 2dxd 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)	37.15 / 1.77
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	115.622, 115.622, 194.171, 90.00, 90.00, 120.00
R / Rfree (%)	16.9 / 19.3

The binding sites of Chlorine atom in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Atp Analog (pdb code 2dxd). 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 Nucleoside Diphosphate Kinase in Complex with Atp Analog, PDB code: 2dxd:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Atp 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 Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl701 b:23.8 occ:1.00 O A:HOH877 2.8 26.1 1.0 O A:HOH923 3.1 44.1 1.0 N A:ALA96 3.1 12.7 1.0 N A:ALA103 3.1 13.1 1.0 CA A:GLY95 3.6 12.5 1.0 CA A:ALA102 3.6 13.8 1.0 C A:GLY95 3.8 13.1 1.0 C A:ALA102 3.9 14.3 1.0 CB A:ALA103 3.9 14.5 1.0 CB A:ALA96 4.0 13.1 1.0 O A:HOH728 4.0 20.1 1.0 CA A:ALA96 4.1 13.3 1.0 O A:HOH913 4.1 42.4 1.0 CA A:ALA103 4.1 12.9 1.0 CG2 A:THR106 4.2 11.5 1.0 CB A:ALA102 4.2 12.6 1.0 O A:ASP101 4.3 13.6 1.0 O A:HOH864 4.4 28.9 1.0 OG1 A:THR106 4.5 11.8 1.0 N A:ALA102 4.7 13.8 1.0 CB A:THR106 4.9 12.0 1.0 C A:ASP101 4.9 14.3 1.0 N A:GLY95 4.9 12.6 1.0 O A:GLY95 5.0 13.6 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Atp 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 Atp Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl702 b:25.0 occ:1.00 O B:HOH884 2.8 32.9 1.0 N B:ALA96 3.2 15.6 1.0 N B:ALA103 3.2 14.1 1.0 CA B:GLY95 3.6 14.4 1.0 CA B:ALA102 3.7 14.2 1.0 C B:GLY95 3.8 14.8 1.0 O B:HOH749 3.9 21.8 1.0 CB B:ALA103 3.9 15.8 1.0 C B:ALA102 4.0 14.7 1.0 CB B:ALA96 4.0 15.4 1.0 CG2 B:THR106 4.1 12.4 1.0 O B:HOH820 4.1 49.4 1.0 CA B:ALA96 4.1 16.1 1.0 O B:HOH852 4.2 36.4 1.0 CA B:ALA103 4.2 14.9 1.0 CB B:ALA102 4.2 12.9 1.0 O B:ASP101 4.4 18.3 1.0 OG1 B:THR106 4.5 13.1 1.0 N B:ALA102 4.8 15.9 1.0 CB B:THR106 4.8 13.5 1.0 N B:GLY95 4.9 14.8 1.0 C B:ASP101 5.0 17.8 1.0

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