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Chlorine in PDB 2dya: Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase

Enzymatic activity of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase

All present enzymatic activity of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase, PDB code: 2dya 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) 40.06 / 1.77
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 69.707, 69.707, 107.117, 90.00, 90.00, 120.00
R / Rfree (%) 11.4 / 16.9

Other elements in 2dya:

The structure of Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase (pdb code 2dya). 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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase, PDB code: 2dya:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2dya

Go back to Chlorine Binding Sites List in 2dya
Chlorine binding site 1 out of 4 in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase


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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:18.5
occ:1.00
 O A:HOH793 3.1 22.0 1.0
N A:ALA103 3.2 11.0 1.0
N A:ALA96 3.3 10.9 1.0
CA A:GLY95 3.6 10.9 1.0
O A:HOH731 3.6 11.1 1.0
CA A:ALA102 3.7 11.6 1.0
CB A:ALA103 3.9 11.7 1.0
C A:GLY95 3.9 11.7 1.0
C A:ALA102 4.0 11.1 1.0
CG2 A:THR106 4.1 8.4 1.0
CA A:ALA103 4.2 11.0 1.0
CB A:ALA96 4.2 13.8 1.0
CB A:ALA102 4.3 12.6 1.0
CA A:ALA96 4.3 12.2 1.0
O A:ASP101 4.4 15.1 1.0
OG1 A:THR106 4.5 10.1 1.0
N A:ALA102 4.8 13.4 1.0
CB A:THR106 4.9 10.1 1.0
N A:GLY95 4.9 10.7 1.0

Chlorine binding site 2 out of 4 in 2dya

Go back to Chlorine Binding Sites List in 2dya
Chlorine binding site 2 out of 4 in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase


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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl703

b:22.4
occ:1.00
 O A:HOH827 3.0 14.2 1.0
N A:ALA152 3.2 10.3 1.0
O A:HOH813 3.2 28.6 1.0
NE A:ARG150 3.4 13.2 1.0
N A:ALA151 3.6 12.1 1.0
NH2 A:ARG150 3.7 15.9 1.0
CB A:ALA152 3.7 8.6 1.0
CB A:ALA151 3.8 8.8 1.0
CZ A:ARG150 3.9 15.1 1.0
CB A:ARG150 3.9 11.0 1.0
CA A:ALA151 3.9 10.6 1.0
O B:VAL20 4.0 12.6 1.0
CA A:ALA152 4.0 10.5 1.0
C A:ALA151 4.0 10.5 1.0
C A:ARG150 4.2 11.8 1.0
CD A:ARG150 4.4 11.3 1.0
CA A:ARG150 4.6 11.5 1.0
CG A:ARG150 4.6 11.8 1.0
O A:HOH821 4.7 21.1 1.0
O A:ARG150 4.8 12.6 1.0
C A:ALA152 4.9 10.9 1.0

Chlorine binding site 3 out of 4 in 2dya

Go back to Chlorine Binding Sites List in 2dya
Chlorine binding site 3 out of 4 in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase


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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:18.2
occ:1.00
 O B:HOH829 3.2 23.5 1.0
N B:ALA103 3.2 12.3 1.0
N B:ALA96 3.2 11.3 1.0
O B:HOH736 3.5 11.0 1.0
CA B:GLY95 3.6 10.3 1.0
CA B:ALA102 3.7 11.0 1.0
C B:GLY95 3.8 10.9 1.0
CB B:ALA103 3.9 12.7 1.0
C B:ALA102 3.9 11.7 1.0
CB B:ALA96 4.0 13.4 1.0
CG2 B:THR106 4.1 6.2 1.0
CA B:ALA103 4.1 11.9 1.0
O B:HOH847 4.2 17.5 1.0
CA B:ALA96 4.2 10.8 1.0
CB B:ALA102 4.3 11.7 1.0
O B:ASP101 4.4 11.1 1.0
OG1 B:THR106 4.5 8.7 1.0
N B:ALA102 4.8 11.8 1.0
CB B:THR106 4.9 8.5 1.0
N B:GLY95 4.9 10.5 1.0

Chlorine binding site 4 out of 4 in 2dya

Go back to Chlorine Binding Sites List in 2dya
Chlorine binding site 4 out of 4 in the Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase


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 Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl704

b:26.6
occ:1.00
 O B:HOH815 3.1 21.1 1.0
NE B:ARG150 3.1 12.8 1.0
O B:HOH780 3.2 54.3 1.0
N B:ALA152 3.4 8.4 1.0
NH2 B:ARG150 3.5 12.8 1.0
N B:ALA151 3.6 11.1 1.0
CB B:ALA151 3.6 9.1 1.0
CZ B:ARG150 3.8 12.4 1.0
CB B:ARG150 3.8 11.1 1.0
O A:VAL20 3.9 10.1 1.0
CA B:ALA151 3.9 10.0 1.0
CB B:ALA152 4.1 9.5 1.0
CD B:ARG150 4.1 12.6 1.0
C B:ARG150 4.2 11.1 1.0
C B:ALA151 4.2 9.2 1.0
CA B:ALA152 4.3 10.4 1.0
O B:HOH808 4.4 24.6 1.0
CG B:ARG150 4.5 11.0 1.0
CA B:ARG150 4.6 11.1 1.0
O B:ARG150 4.9 10.2 1.0

Reference:

M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama. Crystal Structure of Complex Between Adenine Nucleotide and Nucleoside Diphosphate Kinase To Be Published.
Page generated: Thu Jul 10 21:56:51 2025

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