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Sodium in PDB 6cu9: Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp 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 Ctp 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 Ctp and Manganese, PDB code: 6cu9 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) 19.82 / 2.04
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.707, 80.049, 55.602, 90.00, 107.70, 90.00
R / Rfree (%) 19.4 / 24.1

Other elements in 6cu9:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Ctp 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 Ctp and Manganese (pdb code 6cu9). 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 and Manganese, PDB code: 6cu9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6cu9

Go back to Sodium Binding Sites List in 6cu9
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 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 Ctp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:21.4
occ:1.00
 O A:THR101 2.3 22.6 1.0
O A:ILE106 2.3 18.7 1.0
OP1 P:DG9 2.4 21.3 1.0
O A:VAL103 2.5 17.9 1.0
O P:HOH109 2.5 23.6 1.0
O A:HOH611 2.8 23.2 1.0
C A:ILE106 3.3 20.4 1.0
C A:THR101 3.3 20.9 1.0
C A:VAL103 3.4 17.4 1.0
P P:DG9 3.5 21.2 1.0
N A:ILE106 3.7 20.0 1.0
OP2 P:DG9 3.7 20.1 1.0
O A:HOH586 3.7 31.4 1.0
CA A:THR101 4.0 21.1 1.0
CA A:ILE106 4.0 17.1 1.0
CA A:SER104 4.0 19.7 1.0
N A:GLY105 4.0 18.6 1.0
N A:SER104 4.1 18.1 1.0
N A:VAL103 4.2 18.5 1.0
C A:ARG102 4.3 21.1 1.0
C A:SER104 4.3 21.6 1.0
O3' P:DC8 4.3 18.7 1.0
N A:GLY107 4.3 19.4 1.0
N A:ARG102 4.4 20.3 1.0
CA A:VAL103 4.4 20.9 1.0
CB A:ILE106 4.4 18.8 1.0
CB A:THR101 4.5 25.2 1.0
O A:ARG102 4.6 23.2 1.0
C A:GLY105 4.6 21.8 1.0
CA A:ARG102 4.6 21.4 1.0
CA A:GLY107 4.6 20.4 1.0
O5' P:DG9 4.7 20.0 1.0
CA A:GLY105 4.9 20.0 1.0
O A:LEU100 4.9 20.5 1.0

Sodium binding site 2 out of 2 in 6cu9

Go back to Sodium Binding Sites List in 6cu9
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 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 Ctp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:33.6
occ:1.00
 O A:VAL65 2.4 33.2 1.0
OP1 D:DC3 2.4 37.8 1.0
O A:HOH569 2.4 38.1 1.0
O A:LYS60 2.5 39.9 1.0
O A:LEU62 2.5 33.8 1.0
C A:LEU62 3.4 30.9 1.0
C A:VAL65 3.5 36.7 1.0
P D:DC3 3.6 37.3 1.0
C A:LYS60 3.6 31.7 1.0
OP2 D:DC3 3.8 37.0 1.0
CA A:PRO63 3.9 32.1 1.0
N A:VAL65 4.0 34.3 1.0
N A:PRO63 4.1 35.9 1.0
N A:GLY64 4.1 36.3 1.0
C A:LYS61 4.1 34.1 1.0
N A:LEU62 4.2 34.6 1.0
O A:LYS61 4.2 32.2 1.0
CA A:VAL65 4.2 28.8 1.0
CG A:LYS60 4.3 32.8 1.0
CA A:LYS60 4.3 32.2 1.0
CA A:LEU62 4.4 32.5 1.0
C A:PRO63 4.4 36.1 1.0
N A:GLY66 4.5 32.9 1.0
CB A:VAL65 4.5 30.7 1.0
N A:LYS61 4.6 34.1 1.0
O3' D:DT2 4.6 39.7 1.0
O5' D:DC3 4.7 43.1 1.0
CA A:LYS61 4.7 33.8 1.0
CA A:GLY66 4.7 32.7 1.0
NZ A:LYS60 4.8 39.6 1.0
C A:GLY64 4.9 32.5 1.0
CB A:LYS60 5.0 33.4 1.0
O A:ALA59 5.0 31.3 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 and Manganese To Be Published.
Page generated: Tue Dec 15 12:06:29 2020

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