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Sodium in PDB 6cpq: Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 6cpq was solved by M.-C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.85 / 1.93
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.829, 80.243, 55.836, 90.00, 107.80, 90.00
R / Rfree (%) 19.1 / 23.9

Other elements in 6cpq:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp (pdb code 6cpq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 6cpq:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6cpq

Go back to Sodium Binding Sites List in 6cpq
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:18.4
occ:1.00
 O A:THR101 2.3 18.0 1.0
O A:ILE106 2.4 17.9 1.0
O P:HOH101 2.4 24.5 1.0
OP1 P:DG9 2.4 19.4 1.0
O A:HOH733 2.4 20.1 1.0
O A:VAL103 2.5 14.7 1.0
C A:THR101 3.3 16.0 1.0
C A:ILE106 3.4 17.9 1.0
C A:VAL103 3.4 14.6 1.0
P P:DG9 3.5 21.0 1.0
OP2 P:DG9 3.7 18.5 1.0
N A:ILE106 3.8 16.1 1.0
O A:HOH673 3.8 34.0 1.0
CA A:THR101 3.9 16.1 1.0
CA A:SER104 4.0 17.5 1.0
N A:GLY105 4.0 17.5 1.0
CA A:ILE106 4.1 16.3 1.0
N A:SER104 4.1 15.2 1.0
N A:VAL103 4.2 14.8 1.0
N A:ARG102 4.3 15.2 1.0
C A:ARG102 4.3 18.3 1.0
C A:SER104 4.4 15.8 1.0
N A:GLY107 4.4 17.9 1.0
CB A:THR101 4.4 17.9 1.0
CA A:VAL103 4.4 15.2 1.0
O3' P:DC8 4.4 18.5 1.0
CB A:ILE106 4.5 18.6 1.0
O A:HOH709 4.6 32.9 1.0
CA A:ARG102 4.6 15.8 1.0
C A:GLY105 4.7 20.2 1.0
CA A:GLY107 4.7 19.1 1.0
O5' P:DG9 4.7 20.1 1.0
O A:ARG102 4.8 16.6 1.0
O A:LEU100 4.8 15.3 1.0
CA A:GLY105 5.0 19.4 1.0

Sodium binding site 2 out of 2 in 6cpq

Go back to Sodium Binding Sites List in 6cpq
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:29.1
occ:1.00
 O A:LYS60 2.4 27.6 1.0
O A:VAL65 2.4 30.4 1.0
O A:LEU62 2.4 26.4 1.0
O A:HOH748 2.4 32.4 1.0
OP1 D:DC3 2.5 32.7 1.0
O D:HOH101 2.8 37.7 1.0
C A:LEU62 3.3 26.3 1.0
C A:VAL65 3.4 29.4 1.0
C A:LYS60 3.5 25.8 1.0
P D:DC3 3.6 33.1 1.0
OP2 D:DC3 3.7 31.3 1.0
N A:VAL65 3.8 26.8 1.0
CA A:PRO63 4.0 26.4 1.0
N A:PRO63 4.0 29.6 1.0
CA A:VAL65 4.1 25.8 1.0
N A:LEU62 4.1 28.4 1.0
C A:LYS61 4.1 30.2 1.0
N A:GLY64 4.2 27.0 1.0
CA A:LYS60 4.2 24.2 1.0
O A:LYS61 4.3 27.0 1.0
CA A:LEU62 4.3 26.3 1.0
CB A:VAL65 4.3 26.9 1.0
CG A:LYS60 4.4 27.9 1.0
N A:LYS61 4.5 27.2 1.0
C A:PRO63 4.5 29.7 1.0
N A:GLY66 4.5 27.0 1.0
O3' D:DT2 4.6 35.0 1.0
CA A:LYS61 4.6 27.1 1.0
O5' D:DC3 4.7 36.6 1.0
CA A:GLY66 4.8 30.8 1.0
C A:GLY64 4.8 28.6 1.0
O A:ALA59 4.9 22.3 1.0
CB A:LYS60 5.0 25.8 1.0

Reference:

M.-C.Koag, S.Lee. Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp To Be Published.
Page generated: Mon Aug 18 04:05:21 2025

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