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Sodium in PDB 4pha: Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with A 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 A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4pha 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) 20.00 / 2.52
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.440, 80.710, 54.834, 90.00, 108.88, 90.00
R / Rfree (%) 21.6 / 27.8

Other elements in 4pha:

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

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp (pdb code 4pha). 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 A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp, PDB code: 4pha:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4pha

Go back to Sodium Binding Sites List in 4pha
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A 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 A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:20.0
occ:1.00
 OP1 P:DG9 2.3 18.8 1.0
O A:THR101 2.4 21.6 1.0
O A:VAL103 2.5 19.9 1.0
O P:HOH109 2.5 22.6 1.0
O A:ILE106 2.7 18.5 1.0
O A:HOH548 2.8 22.5 1.0
O A:HOH515 3.1 28.0 1.0
C A:VAL103 3.3 22.4 1.0
C A:THR101 3.4 21.0 1.0
P P:DG9 3.5 17.9 1.0
C A:ILE106 3.7 18.6 1.0
OP2 P:DG9 3.8 23.7 1.0
CA A:SER104 3.8 19.1 1.0
N A:SER104 3.9 21.6 1.0
N A:ILE106 4.0 21.4 1.0
N A:GLY105 4.1 20.5 1.0
N A:VAL103 4.1 14.6 1.0
CA A:THR101 4.1 22.3 1.0
C A:SER104 4.3 18.2 1.0
CA A:VAL103 4.3 16.4 1.0
CA A:ILE106 4.3 23.8 1.0
C A:ARG102 4.3 22.4 1.0
O5' P:DG9 4.4 18.4 1.0
N A:ARG102 4.4 18.5 1.0
N A:GLY107 4.6 17.9 1.0
CA A:ARG102 4.6 18.1 1.0
CB A:THR101 4.6 21.6 1.0
O3' P:DC8 4.7 21.5 1.0
CB A:ILE106 4.8 23.6 1.0
C A:GLY105 4.8 22.3 1.0
CA A:GLY107 4.8 19.6 1.0
O A:ARG102 4.9 16.1 1.0

Sodium binding site 2 out of 2 in 4pha

Go back to Sodium Binding Sites List in 4pha
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A 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 A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:39.1
occ:1.00
 O A:LYS60 2.6 35.4 1.0
O A:VAL65 2.6 30.2 1.0
OP1 D:DC3 2.9 31.8 1.0
O A:LEU62 3.0 31.8 1.0
OP2 D:DC3 3.5 30.4 1.0
P D:DC3 3.7 36.3 1.0
C A:LYS60 3.8 33.4 1.0
C A:VAL65 3.8 29.2 1.0
C A:LEU62 3.9 28.1 1.0
O A:LYS61 4.3 34.4 1.0
C A:LYS61 4.3 28.0 1.0
CA A:PRO63 4.4 26.9 1.0
N A:VAL65 4.5 31.1 1.0
N A:PRO63 4.5 25.7 1.0
N A:LEU62 4.6 29.1 1.0
CG A:LYS60 4.6 33.4 1.0
N A:GLY64 4.6 30.4 1.0
CA A:VAL65 4.7 26.8 1.0
CA A:LYS60 4.7 27.7 1.0
N A:LYS61 4.7 34.6 1.0
O5' D:DC3 4.7 27.1 1.0
N A:GLY66 4.7 26.4 1.0
CA A:LYS61 4.8 27.2 1.0
CA A:GLY66 4.8 23.9 1.0
CA A:LEU62 4.9 24.5 1.0
C A:PRO63 4.9 30.9 1.0
O3' D:DT2 4.9 33.5 1.0

Reference:

M.C.Koag, K.Nam, S.Lee. The Spontaneous Replication Error and the Mismatch Discrimination Mechanisms of Human Dna Polymerase Beta. Nucleic Acids Res. V. 42 11233 2015.
ISSN: ESSN 1362-4962
PubMed: 25200079
DOI: 10.1093/NAR/GKU789
Page generated: Tue Dec 15 06:58:14 2020

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