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Sodium in PDB 6e3v: Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA 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 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 6e3v 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) 19.71 / 1.96
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.134, 80.381, 55.674, 90.00, 107.41, 90.00
R / Rfree (%) 19.5 / 24

Other elements in 6e3v:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA 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 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp (pdb code 6e3v). 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 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp, PDB code: 6e3v:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6e3v

Go back to Sodium Binding Sites List in 6e3v
Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA 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 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:24.3
occ:1.00
 OP1 P:DG9 2.3 23.7 1.0
O A:THR101 2.4 22.5 1.0
O A:HOH630 2.4 26.6 1.0
O A:ILE106 2.4 20.5 1.0
O P:HOH102 2.4 27.1 1.0
O A:VAL103 2.6 19.9 1.0
C A:THR101 3.3 20.8 1.0
C A:ILE106 3.4 21.2 1.0
P P:DG9 3.4 24.4 1.0
C A:VAL103 3.5 19.1 1.0
OP2 P:DG9 3.6 24.5 1.0
N A:ILE106 3.8 22.9 1.0
CA A:THR101 3.8 22.1 1.0
CA A:ILE106 4.0 21.3 1.0
CA A:SER104 4.0 19.2 1.0
N A:GLY105 4.0 21.9 1.0
N A:SER104 4.1 16.8 1.0
N A:VAL103 4.2 21.8 1.0
N A:GLY107 4.3 22.1 1.0
N A:ARG102 4.3 22.1 1.0
CB A:THR101 4.3 20.0 1.0
C A:ARG102 4.4 24.6 1.0
C A:SER104 4.4 19.9 1.0
CA A:VAL103 4.4 21.8 1.0
CB A:ILE106 4.4 22.5 1.0
O5' P:DG9 4.5 25.2 1.0
O3' P:DC8 4.5 20.4 1.0
CA A:GLY107 4.6 22.6 1.0
C A:GLY105 4.6 23.3 1.0
CA A:ARG102 4.7 24.2 1.0
O A:LEU100 4.8 20.4 1.0
O A:ARG102 4.9 23.8 1.0
O P:HOH110 4.9 39.9 1.0
CA A:GLY105 4.9 23.1 1.0

Sodium binding site 2 out of 2 in 6e3v

Go back to Sodium Binding Sites List in 6e3v
Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with 8OA 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 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Ttp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:34.1
occ:1.00
 O A:VAL65 2.4 32.6 1.0
O A:LYS60 2.4 31.8 1.0
O A:LEU62 2.4 31.3 1.0
O A:HOH619 2.5 35.0 1.0
OP1 D:DC3 2.7 32.4 1.0
C A:VAL65 3.4 33.5 1.0
C A:LEU62 3.4 30.3 1.0
C A:LYS60 3.5 29.1 1.0
P D:DC3 3.7 36.2 1.0
OP2 D:DC3 3.7 34.5 1.0
N A:VAL65 3.8 28.3 1.0
CA A:VAL65 4.0 27.0 1.0
N A:GLY64 4.0 31.1 1.0
CA A:PRO63 4.1 32.5 1.0
N A:LEU62 4.1 29.6 1.0
N A:PRO63 4.2 29.5 1.0
C A:LYS61 4.2 31.3 1.0
CA A:LYS60 4.3 28.9 1.0
CB A:VAL65 4.3 26.8 1.0
O A:LYS61 4.4 31.7 1.0
CA A:LEU62 4.4 28.3 1.0
N A:GLY66 4.4 32.8 1.0
CG A:LYS60 4.4 31.2 1.0
C A:PRO63 4.5 29.9 1.0
N A:LYS61 4.5 28.1 1.0
O3' D:DT2 4.6 38.8 1.0
CA A:LYS61 4.7 27.3 1.0
CA A:GLY66 4.7 34.5 1.0
C A:GLY64 4.7 30.1 1.0
O5' D:DC3 4.9 40.3 1.0
CB A:LYS60 5.0 31.3 1.0
O A:ALA59 5.0 25.4 1.0
NZ A:LYS60 5.0 41.8 1.0

Reference:

M.C.Koag, H.Jung, S.Lee. Mutagenic Replication of the Major Oxidative Adenine Lesion 7,8-Dihydro-8-Oxoadenine By Human Dna Polymerases. J. Am. Chem. Soc. V. 141 4584 2019.
ISSN: ESSN 1520-5126
PubMed: 30817143
DOI: 10.1021/JACS.8B08551
Page generated: Mon Aug 18 04:27:53 2025

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