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Sodium in PDB 6e3w: Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp

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

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp:
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 Gtp, PDB code: 6e3w 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) 19.90 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.588, 79.594, 55.718, 90.00, 107.54, 90.00
R / Rfree (%) 19.3 / 24.5

Other elements in 6e3w:

The structure of Structure of Human Dna Polymerase Beta Complexed with 8OA in the Template Base Paired with Incoming Non-Hydrolyzable Gtp 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 Gtp (pdb code 6e3w). 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 Gtp, PDB code: 6e3w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 6e3w

Go back to Sodium Binding Sites List in 6e3w
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 Gtp


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

b:18.5
occ:1.00
OP1 P:DG9 2.3 19.1 1.0
O A:THR101 2.3 18.0 1.0
O A:ILE106 2.4 16.8 1.0
O A:VAL103 2.5 15.2 1.0
O A:HOH633 2.5 22.1 1.0
C A:THR101 3.3 16.8 1.0
P P:DG9 3.4 20.7 1.0
C A:ILE106 3.4 16.5 1.0
C A:VAL103 3.4 14.0 1.0
OP2 P:DG9 3.6 22.0 1.0
N A:ILE106 3.8 15.6 1.0
CA A:THR101 3.9 18.3 1.0
N A:GLY105 4.0 16.5 1.0
CA A:SER104 4.0 16.7 1.0
CA A:ILE106 4.1 14.3 1.0
N A:SER104 4.1 12.3 1.0
N A:VAL103 4.2 14.7 1.0
N A:ARG102 4.3 16.5 1.0
C A:SER104 4.3 17.2 1.0
C A:ARG102 4.3 18.0 1.0
N A:GLY107 4.4 14.7 1.0
CB A:THR101 4.4 16.6 1.0
CA A:VAL103 4.4 15.2 1.0
O3' P:DC8 4.4 17.0 1.0
O5' P:DG9 4.5 18.4 1.0
CB A:ILE106 4.5 17.0 1.0
C A:GLY105 4.6 19.0 1.0
CA A:ARG102 4.6 19.7 1.0
CA A:GLY107 4.6 16.7 1.0
O A:LEU100 4.8 16.6 1.0
CA A:GLY105 4.8 16.0 1.0
O A:ARG102 4.8 21.1 1.0

Sodium binding site 2 out of 2 in 6e3w

Go back to Sodium Binding Sites List in 6e3w
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 Gtp


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 Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:26.1
occ:1.00
O A:VAL65 2.3 25.7 1.0
O A:HOH588 2.4 25.1 1.0
O A:LYS60 2.4 26.1 1.0
O A:LEU62 2.5 27.4 1.0
OP1 D:DC3 2.6 27.0 1.0
C A:VAL65 3.4 27.0 1.0
C A:LEU62 3.4 27.3 1.0
C A:LYS60 3.5 25.4 1.0
P D:DC3 3.6 28.3 1.0
OP2 D:DC3 3.7 27.0 1.0
N A:VAL65 3.9 23.0 1.0
CA A:PRO63 4.0 24.8 1.0
CA A:VAL65 4.0 24.8 1.0
N A:PRO63 4.1 23.9 1.0
N A:GLY64 4.1 26.8 1.0
C A:LYS61 4.1 23.8 1.0
N A:LEU62 4.1 20.9 1.0
CA A:LYS60 4.3 22.7 1.0
O A:LYS61 4.3 21.9 1.0
CB A:VAL65 4.3 23.5 1.0
CA A:LEU62 4.4 24.2 1.0
N A:GLY66 4.4 25.2 1.0
CG A:LYS60 4.5 27.6 1.0
N A:LYS61 4.5 24.7 1.0
C A:PRO63 4.5 26.6 1.0
O3' D:DT2 4.6 29.5 1.0
CA A:LYS61 4.7 22.6 1.0
CA A:GLY66 4.7 25.4 1.0
O5' D:DC3 4.8 34.6 1.0
C A:GLY64 4.8 25.9 1.0
O A:ALA59 4.9 22.3 1.0
NZ A:LYS60 5.0 34.2 1.0
CB A:LYS60 5.0 26.4 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: Tue Dec 15 12:09:19 2020

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