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

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with G in the Template Base Paired with Incoming Non-Hydrolyzable Ttp:
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, PDB code: 4pgq 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) 19.27 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.898, 80.087, 55.077, 90.00, 106.15, 90.00
R / Rfree (%) 20.3 / 26

Other elements in 4pgq:

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

Sodium binding site 1 out of 2 in 4pgq

Go back to Sodium Binding Sites List in 4pgq
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:40.8
occ:1.00
 O A:LYS60 2.8 40.4 1.0
O A:VAL65 2.9 38.9 1.0
OP1 D:DC3 3.1 33.3 1.0
OP2 D:DC3 3.2 22.6 1.0
P D:DC3 3.6 31.7 1.0
NZ A:LYS60 3.6 37.6 1.0
CG A:LYS60 3.9 37.6 1.0
C A:LYS60 4.0 37.8 1.0
C A:VAL65 4.1 31.5 1.0
O A:LEU62 4.1 38.4 1.0
CE A:LYS60 4.6 36.7 1.0
CA A:GLY66 4.6 26.0 1.0
O3' D:DT2 4.8 33.9 1.0
CA A:LYS60 4.8 35.3 1.0
O5' D:DC3 4.8 28.0 1.0
N A:GLY66 4.8 30.5 1.0
O A:HOH522 4.8 36.0 1.0
CB A:LYS60 4.9 39.7 1.0
CD A:LYS60 4.9 41.9 1.0

Sodium binding site 2 out of 2 in 4pgq

Go back to Sodium Binding Sites List in 4pgq
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


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

b:18.3
occ:1.00
 O A:THR101 2.3 23.6 1.0
O A:ILE106 2.4 19.1 1.0
OP1 P:DG9 2.4 17.3 1.0
O A:VAL103 2.4 19.0 1.0
O P:HOH102 2.5 20.9 1.0
C A:VAL103 3.2 23.6 1.0
C A:THR101 3.3 23.9 1.0
C A:ILE106 3.4 19.1 1.0
O A:HOH527 3.6 21.3 1.0
P P:DG9 3.6 20.1 1.0
N A:ILE106 3.7 16.0 1.0
CA A:SER104 3.8 17.7 1.0
OP2 P:DG9 3.8 22.2 1.0
N A:SER104 3.8 18.6 1.0
N A:GLY105 3.9 20.0 1.0
CA A:THR101 3.9 19.1 1.0
N A:VAL103 4.0 23.2 1.0
CA A:ILE106 4.0 16.0 1.0
C A:ARG102 4.2 26.7 1.0
C A:SER104 4.2 20.3 1.0
CA A:VAL103 4.2 21.4 1.0
N A:ARG102 4.3 24.9 1.0
N A:GLY107 4.3 20.6 1.0
CB A:ILE106 4.4 18.9 1.0
CB A:THR101 4.5 21.4 1.0
O3' P:DC8 4.6 19.9 1.0
CA A:ARG102 4.6 23.4 1.0
C A:GLY105 4.6 17.1 1.0
O A:ARG102 4.6 29.2 1.0
O5' P:DG9 4.7 23.8 1.0
CA A:GLY107 4.7 21.3 1.0
CA A:GLY105 4.8 17.2 1.0
O A:LEU100 4.9 21.2 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 06:58:11 2020

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