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Chlorine in PDB 2dy9: Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp

Enzymatic activity of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp

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

Protein crystallography data

The structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp, PDB code: 2dy9 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) 34.92 / 2.01
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 69.835, 69.835, 106.897, 90.00, 90.00, 120.00
R / Rfree (%) 12.2 / 16.8

Other elements in 2dy9:

The structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp (pdb code 2dy9). 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 Adp, PDB code: 2dy9:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2dy9

Go back to Chlorine Binding Sites List in 2dy9
Chlorine binding site 1 out of 4 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:22.8
occ:1.00
 N A:ALA103 3.2 13.7 1.0
N A:ALA96 3.4 12.8 1.0
CA A:ALA102 3.6 14.7 1.0
CA A:GLY95 3.7 12.8 1.0
O A:HOH724 3.8 10.0 1.0
CB A:ALA103 3.9 9.6 1.0
C A:ALA102 3.9 14.3 1.0
C A:GLY95 4.0 12.9 1.0
CA A:ALA103 4.1 12.3 1.0
CB A:ALA96 4.2 15.6 1.0
O A:ASP101 4.3 15.0 1.0
CG2 A:THR106 4.3 11.3 1.0
CB A:ALA102 4.3 15.3 1.0
CA A:ALA96 4.4 14.4 1.0
OG1 A:THR106 4.6 12.7 1.0
N A:ALA102 4.7 15.6 1.0
O A:HOH784 4.9 29.1 1.0
C A:ASP101 4.9 16.1 1.0
CB A:THR106 5.0 12.8 1.0

Chlorine binding site 2 out of 4 in 2dy9

Go back to Chlorine Binding Sites List in 2dy9
Chlorine binding site 2 out of 4 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:27.4
occ:1.00
 N A:ALA152 3.1 14.2 1.0
NE A:ARG150 3.3 14.0 1.0
N A:ALA151 3.5 13.1 1.0
O A:HOH768 3.6 35.2 1.0
NH2 A:ARG150 3.6 16.8 1.0
CB A:ALA151 3.8 12.8 1.0
CB A:ARG150 3.8 12.7 1.0
CB A:ALA152 3.8 13.4 1.0
CZ A:ARG150 3.9 16.6 1.0
CA A:ALA151 3.9 13.2 1.0
O B:VAL20 4.0 14.8 1.0
C A:ALA151 4.0 13.5 1.0
C A:ARG150 4.0 12.4 1.0
CA A:ALA152 4.0 14.0 1.0
CD A:ARG150 4.2 12.6 1.0
CA A:ARG150 4.5 11.6 1.0
CG A:ARG150 4.5 12.6 1.0
O A:ARG150 4.6 12.8 1.0
O A:HOH806 4.8 35.3 1.0
C A:ALA152 4.8 13.9 1.0
N A:ASP153 4.9 13.4 1.0

Chlorine binding site 3 out of 4 in 2dy9

Go back to Chlorine Binding Sites List in 2dy9
Chlorine binding site 3 out of 4 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl703

b:24.6
occ:1.00
 N B:ALA96 3.3 11.2 1.0
O B:HOH793 3.3 15.7 1.0
N B:ALA103 3.3 13.6 1.0
O B:HOH783 3.4 22.3 1.0
CA B:GLY95 3.6 12.2 1.0
CA B:ALA102 3.8 11.5 1.0
C B:GLY95 3.9 12.2 1.0
CB B:ALA103 4.0 12.8 1.0
C B:ALA102 4.1 12.5 1.0
CB B:ALA96 4.2 12.9 1.0
CA B:ALA103 4.3 13.1 1.0
CA B:ALA96 4.3 13.0 1.0
CG2 B:THR106 4.3 9.2 1.0
O B:HOH777 4.4 20.2 1.0
CB B:ALA102 4.4 10.4 1.0
O B:ASP101 4.5 13.8 1.0
OG1 B:THR106 4.6 11.6 1.0
N B:GLY95 4.9 12.3 1.0
N B:ALA102 4.9 13.3 1.0
O B:GLY95 5.0 12.2 1.0
CB B:THR106 5.0 9.4 1.0

Chlorine binding site 4 out of 4 in 2dy9

Go back to Chlorine Binding Sites List in 2dy9
Chlorine binding site 4 out of 4 in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp


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 Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl704

b:35.5
occ:1.00
 O B:HOH761 3.2 29.1 1.0
NE B:ARG150 3.3 12.1 1.0
N B:ALA152 3.3 13.8 1.0
N B:ALA151 3.5 13.1 1.0
NH2 B:ARG150 3.6 10.6 1.0
CB B:ALA151 3.7 11.6 1.0
O A:VAL20 3.7 12.3 1.0
CB B:ARG150 3.8 12.3 1.0
CZ B:ARG150 3.9 12.1 1.0
CA B:ALA151 3.9 12.5 1.0
CB B:ALA152 4.1 15.7 1.0
C B:ALA151 4.1 13.1 1.0
C B:ARG150 4.1 13.6 1.0
CA B:ALA152 4.3 15.2 1.0
CD B:ARG150 4.3 12.0 1.0
CA B:ARG150 4.5 13.5 1.0
CG B:ARG150 4.5 10.5 1.0
O B:ARG150 4.9 14.6 1.0
C A:VAL20 4.9 13.6 1.0

Reference:

M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama. Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp To Be Published.
Page generated: Sat Jul 20 06:42:33 2024

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