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

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

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:
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, PDB code: 6crh 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 / 2.33
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.985, 79.622, 55.179, 90.00, 107.88, 90.00
R / Rfree (%) 19.7 / 24.4

Other elements in 6crh:

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

Sodium binding site 1 out of 2 in 6crh

Go back to Sodium Binding Sites List in 6crh
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:27.4
occ:1.00
 OP1 P:DG9 2.3 29.2 1.0
O A:THR101 2.4 29.4 1.0
O A:VAL103 2.5 23.8 1.0
O A:ILE106 2.5 21.3 1.0
O A:HOH541 2.5 34.0 1.0
O A:HOH562 2.6 25.9 1.0
C A:THR101 3.3 29.4 1.0
C A:VAL103 3.3 25.1 1.0
C A:ILE106 3.4 24.5 1.0
P P:DG9 3.5 26.7 1.0
O A:HOH506 3.6 30.3 1.0
N A:ILE106 3.8 24.1 1.0
OP2 P:DG9 3.8 27.5 1.0
CA A:THR101 3.9 27.5 1.0
CA A:SER104 3.9 24.1 1.0
N A:GLY105 3.9 26.8 1.0
N A:SER104 3.9 26.0 1.0
N A:VAL103 4.0 24.2 1.0
CA A:ILE106 4.1 23.6 1.0
N A:ARG102 4.3 27.0 1.0
C A:ARG102 4.3 30.1 1.0
CA A:VAL103 4.3 26.2 1.0
C A:SER104 4.3 25.1 1.0
N A:GLY107 4.4 24.6 1.0
CB A:THR101 4.5 26.3 1.0
CB A:ILE106 4.5 21.2 1.0
O5' P:DG9 4.5 26.9 1.0
O3' P:DC8 4.6 28.9 1.0
CA A:ARG102 4.6 27.3 1.0
C A:GLY105 4.6 24.0 1.0
CA A:GLY107 4.7 26.3 1.0
O A:LEU100 4.8 24.7 1.0
CA A:GLY105 4.9 25.8 1.0
O A:ARG102 4.9 34.5 1.0

Sodium binding site 2 out of 2 in 6crh

Go back to Sodium Binding Sites List in 6crh
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


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

b:30.8
occ:1.00
 O A:LYS60 2.4 28.9 1.0
O A:VAL65 2.4 32.8 1.0
O A:HOH555 2.4 35.5 1.0
O D:HOH103 2.4 33.9 1.0
O A:LEU62 2.6 29.0 1.0
OP1 D:DC3 2.8 33.5 1.0
C A:LYS60 3.4 29.6 1.0
C A:VAL65 3.5 28.8 1.0
C A:LEU62 3.6 31.8 1.0
P D:DC3 3.9 30.7 1.0
N A:VAL65 3.9 29.1 1.0
OP2 D:DC3 4.0 28.8 1.0
CA A:VAL65 4.1 28.6 1.0
C A:LYS61 4.1 31.0 1.0
N A:LEU62 4.1 32.3 1.0
CA A:LYS60 4.2 30.4 1.0
O A:LYS61 4.3 34.5 1.0
CB A:VAL65 4.3 33.4 1.0
CG A:LYS60 4.3 34.9 1.0
N A:LYS61 4.4 32.5 1.0
N A:PRO63 4.4 30.6 1.0
N A:GLY64 4.4 31.0 1.0
CA A:PRO63 4.4 31.1 1.0
CA A:LEU62 4.5 32.8 1.0
N A:GLY66 4.5 28.7 1.0
CA A:LYS61 4.6 28.6 1.0
NZ A:LYS60 4.7 34.9 1.0
C A:PRO63 4.8 31.0 1.0
O3' D:DT2 4.8 33.4 1.0
CA A:GLY66 4.8 26.8 1.0
CB A:LYS60 4.8 34.4 1.0
C A:GLY64 5.0 30.6 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: Tue Oct 8 06:41:52 2024

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