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

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with A 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 A 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 A in the Template Base Paired with Incoming Non-Hydrolyzable Ctp and Manganese, PDB code: 4phd 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 / 2.21
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.245, 79.954, 54.403, 90.00, 108.88, 90.00
R / Rfree (%) 24.3 / 29.5

Other elements in 4phd:

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

Manganese (Mn) 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 and Manganese (pdb code 4phd). 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 and Manganese, PDB code: 4phd:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4phd

Go back to Sodium Binding Sites List in 4phd
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 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 A 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:7.5
occ:1.00
 O A:ILE106 2.4 11.6 1.0
O A:THR101 2.4 11.0 1.0
O A:HOH581 2.5 12.8 1.0
OP1 P:DG9 2.5 13.4 1.0
O A:VAL103 2.5 13.8 1.0
C A:THR101 3.3 9.9 1.0
C A:ILE106 3.4 13.1 1.0
C A:VAL103 3.4 13.2 1.0
P P:DG9 3.5 14.9 1.0
O A:HOH582 3.5 13.6 1.0
OP2 P:DG9 3.6 15.8 1.0
N A:ILE106 3.8 11.3 1.0
CA A:THR101 3.9 11.0 1.0
CA A:ILE106 4.0 9.0 1.0
N A:GLY105 4.1 9.3 1.0
CA A:SER104 4.1 12.6 1.0
N A:VAL103 4.1 9.2 1.0
N A:SER104 4.1 10.2 1.0
N A:ARG102 4.3 12.8 1.0
C A:ARG102 4.4 12.8 1.0
CA A:VAL103 4.4 11.8 1.0
N A:GLY107 4.4 10.3 1.0
C A:SER104 4.4 12.0 1.0
O3' P:DC8 4.4 14.3 1.0
CB A:ILE106 4.4 10.1 1.0
CB A:THR101 4.5 13.2 1.0
C A:GLY105 4.6 9.2 1.0
CA A:ARG102 4.7 12.6 1.0
CA A:GLY107 4.7 8.8 1.0
O5' P:DG9 4.7 15.6 1.0
O A:HOH547 4.9 20.6 1.0
O A:ARG102 4.9 13.2 1.0
O A:LEU100 4.9 14.9 1.0
CA A:GLY105 5.0 13.9 1.0

Sodium binding site 2 out of 2 in 4phd

Go back to Sodium Binding Sites List in 4phd
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 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 A 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:37.0
occ:1.00
 O A:HOH568 2.5 29.3 1.0
O A:VAL65 2.6 34.5 1.0
O A:LYS60 2.7 34.5 1.0
OP1 D:DC3 2.7 32.5 1.0
O A:LEU62 2.8 23.8 1.0
C A:VAL65 3.6 32.4 1.0
OP2 D:DC3 3.7 20.8 1.0
P D:DC3 3.7 29.4 1.0
C A:LEU62 3.7 24.9 1.0
C A:LYS60 3.8 34.5 1.0
N A:VAL65 4.0 27.9 1.0
C A:LYS61 4.2 29.0 1.0
N A:GLY64 4.2 31.9 1.0
O A:LYS61 4.2 28.3 1.0
CA A:PRO63 4.2 25.0 1.0
CA A:VAL65 4.3 20.9 1.0
N A:PRO63 4.3 24.3 1.0
N A:LEU62 4.4 29.1 1.0
CB A:VAL65 4.6 28.6 1.0
N A:LYS61 4.6 33.7 1.0
N A:GLY66 4.7 28.6 1.0
CA A:LYS61 4.7 26.3 1.0
C A:PRO63 4.7 31.1 1.0
CA A:LEU62 4.7 26.2 1.0
CA A:LYS60 4.7 28.9 1.0
O5' D:DC3 4.8 24.3 1.0
O3' D:DT2 4.8 29.6 1.0
CA A:GLY66 4.9 26.8 1.0
C A:GLY64 5.0 29.4 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: Mon Oct 7 17:43:19 2024

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