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

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8-Clg in the Template Base Paired with Incoming Non-Hydrolyzable Gtp 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 Gtp 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 Gtp and Manganese, PDB code: 6cua 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) 19.91 / 2.17
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.713, 79.620, 55.262, 90.00, 108.78, 90.00
R / Rfree (%) 20.9 / 25.9

Other elements in 6cua:

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

Sodium binding site 1 out of 2 in 6cua

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

b:16.5
occ:1.00
OP1 P:DG9 2.3 19.8 1.0
O A:THR101 2.3 20.6 1.0
O A:ILE106 2.4 17.4 1.0
O A:VAL103 2.5 15.9 1.0
O P:HOH102 2.6 17.8 1.0
O A:HOH581 2.7 17.4 1.0
C A:THR101 3.3 19.6 1.0
C A:ILE106 3.4 14.7 1.0
C A:VAL103 3.4 19.4 1.0
P P:DG9 3.4 21.5 1.0
O A:HOH504 3.4 28.2 1.0
OP2 P:DG9 3.7 19.6 1.0
N A:ILE106 3.8 18.6 1.0
CA A:THR101 3.9 16.0 1.0
CA A:SER104 3.9 18.2 1.0
N A:GLY105 3.9 20.0 1.0
N A:SER104 4.0 19.7 1.0
CA A:ILE106 4.1 15.7 1.0
N A:VAL103 4.2 17.6 1.0
N A:ARG102 4.3 18.7 1.0
C A:ARG102 4.3 22.7 1.0
C A:SER104 4.3 17.9 1.0
N A:GLY107 4.3 19.5 1.0
CA A:VAL103 4.4 18.7 1.0
CB A:THR101 4.4 17.2 1.0
O5' P:DG9 4.5 21.0 1.0
CB A:ILE106 4.5 14.9 1.0
O3' P:DC8 4.5 19.9 1.0
CA A:ARG102 4.6 18.2 1.0
CA A:GLY107 4.6 15.2 1.0
C A:GLY105 4.6 17.4 1.0
O A:ARG102 4.7 24.4 1.0
CA A:GLY105 4.9 19.6 1.0
O A:LEU100 4.9 17.5 1.0

Sodium binding site 2 out of 2 in 6cua

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

b:34.1
occ:1.00
O A:LYS60 2.4 27.8 1.0
O A:HOH556 2.5 30.7 1.0
O A:VAL65 2.5 25.3 1.0
OP1 D:DC3 2.7 26.1 1.0
O A:LEU62 2.9 23.5 1.0
C A:LYS60 3.6 27.1 1.0
C A:VAL65 3.6 25.9 1.0
P D:DC3 3.7 24.4 1.0
C A:LEU62 3.8 26.8 1.0
OP2 D:DC3 3.8 23.2 1.0
N A:VAL65 4.1 24.8 1.0
C A:LYS61 4.2 25.7 1.0
CG A:LYS60 4.3 25.9 1.0
CA A:VAL65 4.3 22.3 1.0
N A:LEU62 4.3 28.4 1.0
CA A:LYS60 4.3 25.5 1.0
O A:LYS61 4.3 29.8 1.0
CA A:PRO63 4.4 27.7 1.0
N A:PRO63 4.4 28.5 1.0
N A:GLY64 4.5 25.1 1.0
N A:LYS61 4.5 26.4 1.0
NZ A:LYS60 4.5 30.9 1.0
N A:GLY66 4.6 23.5 1.0
CB A:VAL65 4.6 25.7 1.0
CA A:LYS61 4.7 26.1 1.0
CA A:LEU62 4.7 26.0 1.0
O3' D:DT2 4.7 29.8 1.0
CA A:GLY66 4.8 20.0 1.0
C A:PRO63 4.8 29.0 1.0
O5' D:DC3 4.8 19.8 1.0
CB A:LYS60 4.9 27.9 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 Gtp and Manganese To Be Published.
Page generated: Tue Dec 15 12:06:29 2020

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