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Sodium in PDB 6cub: Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Atp and Manganese:
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 Atp and Manganese, PDB code: 6cub 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) 19.75 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.786, 78.993, 54.771, 90.00, 105.91, 90.00
R / Rfree (%) 19.7 / 25.4

Other elements in 6cub:

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

Manganese (Mn) 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 Atp and Manganese (pdb code 6cub). 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 Atp and Manganese, PDB code: 6cub:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6cub

Go back to Sodium Binding Sites List in 6cub
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 Atp and Manganese


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 Atp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:12.3
occ:1.00
 O A:THR101 2.3 14.1 1.0
O A:ILE106 2.3 12.5 1.0
O A:VAL103 2.4 13.0 1.0
OP1 P:DG9 2.4 10.2 1.0
O P:HOH111 2.5 15.3 1.0
O A:HOH610 2.6 16.5 1.0
C A:THR101 3.3 14.1 1.0
C A:ILE106 3.3 11.1 1.0
C A:VAL103 3.3 14.8 1.0
P P:DG9 3.5 15.4 1.0
N A:ILE106 3.7 11.1 1.0
OP2 P:DG9 3.8 15.9 1.0
CA A:THR101 3.8 12.5 1.0
N A:GLY105 4.0 12.2 1.0
CA A:SER104 4.0 10.6 1.0
N A:SER104 4.0 13.7 1.0
CA A:ILE106 4.0 10.0 1.0
N A:VAL103 4.1 12.2 1.0
N A:GLY107 4.3 12.6 1.0
C A:ARG102 4.3 15.5 1.0
N A:ARG102 4.3 13.1 1.0
CB A:THR101 4.3 13.8 1.0
CA A:VAL103 4.3 12.3 1.0
C A:SER104 4.4 12.0 1.0
CB A:ILE106 4.5 11.1 1.0
CA A:GLY107 4.5 12.2 1.0
O3' P:DC8 4.6 13.4 1.0
CA A:ARG102 4.6 15.2 1.0
C A:GLY105 4.6 10.4 1.0
O5' P:DG9 4.6 15.7 1.0
O A:ARG102 4.8 15.4 1.0
O A:LEU100 4.8 12.6 1.0
CA A:GLY105 4.9 9.9 1.0

Sodium binding site 2 out of 2 in 6cub

Go back to Sodium Binding Sites List in 6cub
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 Atp and Manganese


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 Atp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:25.7
occ:1.00
 O D:HOH102 2.2 27.6 1.0
O A:VAL65 2.4 23.2 1.0
O A:LYS60 2.4 29.7 1.0
O A:HOH604 2.5 30.9 1.0
O A:LEU62 2.6 27.3 1.0
OP1 D:DC3 2.7 22.6 1.0
C A:VAL65 3.4 22.7 1.0
C A:LYS60 3.5 31.5 1.0
C A:LEU62 3.6 25.9 1.0
P D:DC3 3.6 22.3 1.0
OP2 D:DC3 3.7 17.8 1.0
N A:VAL65 3.9 19.2 1.0
CA A:VAL65 4.1 18.4 1.0
N A:LEU62 4.2 28.9 1.0
N A:GLY64 4.2 20.5 1.0
C A:LYS61 4.2 28.1 1.0
CA A:PRO63 4.3 27.7 1.0
CA A:LYS60 4.3 25.2 1.0
N A:PRO63 4.3 26.8 1.0
CG A:LYS60 4.3 27.2 1.0
N A:GLY66 4.4 16.6 1.0
CB A:VAL65 4.5 20.6 1.0
N A:LYS61 4.5 27.1 1.0
O3' D:DT2 4.5 20.6 1.0
CA A:LEU62 4.5 26.4 1.0
O A:LYS61 4.6 33.4 1.0
CA A:LYS61 4.6 30.9 1.0
CA A:GLY66 4.6 15.7 1.0
C A:PRO63 4.7 24.6 1.0
NZ A:LYS60 4.8 24.2 1.0
C A:GLY64 4.9 21.1 1.0
O5' D:DC3 4.9 21.3 1.0
CB A:LYS60 5.0 25.0 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 Atp and Manganese To Be Published.
Page generated: Tue Oct 8 06:47:24 2024

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