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Sodium in PDB 4pgx: Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese

Enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese:
2.7.7.7;

Protein crystallography data

The structure of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese, PDB code: 4pgx 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) 19.97 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.969, 79.796, 55.635, 90.00, 107.37, 90.00
R / Rfree (%) 18.3 / 22.7

Other elements in 4pgx:

The structure of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp 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 G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese (pdb code 4pgx). 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 G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese, PDB code: 4pgx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4pgx

Go back to Sodium Binding Sites List in 4pgx
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp 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 G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp and Manganese within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:19.9
occ:1.00
O A:ILE106 2.4 19.4 1.0
O A:THR101 2.4 21.6 1.0
O A:VAL103 2.4 19.0 1.0
O A:HOH550 2.5 24.5 1.0
OP1 P:DG9 2.5 19.1 1.0
O A:HOH567 2.6 23.4 1.0
C A:THR101 3.3 21.3 1.0
C A:VAL103 3.3 17.9 1.0
C A:ILE106 3.4 20.1 1.0
P P:DG9 3.5 21.7 1.0
OP2 P:DG9 3.7 21.6 1.0
N A:ILE106 3.7 19.3 1.0
CA A:SER104 3.9 21.2 1.0
N A:GLY105 4.0 17.8 1.0
N A:SER104 4.0 16.3 1.0
CA A:THR101 4.0 22.4 1.0
CA A:ILE106 4.0 17.7 1.0
N A:VAL103 4.1 19.1 1.0
C A:ARG102 4.3 20.7 1.0
C A:SER104 4.3 18.9 1.0
N A:ARG102 4.3 20.6 1.0
CA A:VAL103 4.3 19.7 1.0
O3' P:DC8 4.3 15.2 1.0
N A:GLY107 4.4 20.3 1.0
CB A:ILE106 4.4 18.1 1.0
CA A:ARG102 4.6 20.3 1.0
C A:GLY105 4.6 20.6 1.0
CB A:THR101 4.6 23.1 1.0
O A:ARG102 4.7 23.2 1.0
CA A:GLY107 4.7 19.1 1.0
O5' P:DG9 4.8 20.1 1.0
O A:LEU100 4.9 20.2 1.0
CA A:GLY105 4.9 21.2 1.0

Sodium binding site 2 out of 2 in 4pgx

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

b:26.7
occ:1.00
O A:LEU62 2.4 27.4 1.0
O A:LYS60 2.4 30.7 1.0
O A:VAL65 2.4 27.2 1.0
O A:HOH562 2.5 29.4 1.0
OP1 D:DC3 2.6 24.6 1.0
C A:LEU62 3.4 30.7 1.0
C A:LYS60 3.5 28.8 1.0
C A:VAL65 3.5 26.9 1.0
P D:DC3 3.7 26.3 1.0
N A:VAL65 3.8 24.8 1.0
OP2 D:DC3 3.9 28.1 1.0
N A:LEU62 4.0 27.4 1.0
C A:LYS61 4.1 29.9 1.0
CA A:VAL65 4.1 25.6 1.0
N A:GLY64 4.1 25.7 1.0
CA A:PRO63 4.2 25.9 1.0
N A:PRO63 4.2 29.7 1.0
CA A:LYS60 4.2 25.5 1.0
O A:LYS61 4.3 28.9 1.0
CB A:VAL65 4.4 25.6 1.0
CA A:LEU62 4.4 27.5 1.0
N A:LYS61 4.4 27.6 1.0
CG A:LYS60 4.4 29.6 1.0
CA A:LYS61 4.5 28.4 1.0
N A:GLY66 4.6 25.4 1.0
C A:PRO63 4.6 27.7 1.0
O3' D:DT2 4.7 26.8 1.0
C A:GLY64 4.8 26.0 1.0
O5' D:DC3 4.8 36.0 1.0
CA A:GLY66 4.9 25.1 1.0
CB A:LYS60 4.9 29.0 1.0
O A:ALA59 5.0 24.1 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 06:58:12 2020

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