Sodium in PDB 5eoz: Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta

All present enzymatic activity of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta:
2.7.7.7;

The structure of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta, PDB code: 5eoz 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)	19.82 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.754, 80.015, 55.589, 90.00, 107.76, 90.00
R / Rfree (%)	18.4 / 23.8

The structure of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta also contains other interesting chemical elements:

Fluorine	(F)	1 atom
Magnesium	(Mg)	2 atoms

The binding sites of Sodium atom in the Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta (pdb code 5eoz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta, PDB code: 5eoz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:21.0 occ:1.00 O A:THR101 2.3 19.7 1.0 OP1 P:DG9 2.4 21.4 1.0 O A:ILE106 2.4 14.7 1.0 O A:HOH646 2.6 25.6 1.0 O A:VAL103 2.7 16.9 1.0 C A:THR101 3.3 19.9 1.0 P P:DG9 3.4 21.9 1.0 C A:ILE106 3.4 16.8 1.0 C A:VAL103 3.6 15.6 1.0 OP2 P:DG9 3.6 22.0 1.0 N A:ILE106 3.8 16.7 1.0 CA A:THR101 3.9 21.0 1.0 N A:GLY105 4.0 19.1 1.0 CA A:SER104 4.1 19.9 1.0 CA A:ILE106 4.1 15.1 1.0 N A:SER104 4.2 16.2 1.0 N A:VAL103 4.3 19.5 1.0 N A:ARG102 4.4 20.1 1.0 CB A:THR101 4.4 17.9 1.0 C A:ARG102 4.4 22.1 1.0 N A:GLY107 4.4 15.6 1.0 C A:SER104 4.4 17.6 1.0 O3' P:DC8 4.4 17.4 1.0 O P:HOH111 4.5 37.8 1.0 CB A:ILE106 4.6 18.3 1.0 O5' P:DG9 4.6 21.6 1.0 CA A:VAL103 4.6 20.4 1.0 C A:GLY105 4.6 19.9 1.0 CA A:GLY107 4.6 16.4 1.0 CA A:ARG102 4.6 21.3 1.0 O A:ARG102 4.8 23.3 1.0 CA A:GLY105 4.9 19.6 1.0 O A:LEU100 4.9 18.4 1.0

Sodium binding site 2 out of 2 in the Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mutagenicity of 7-Benzyl Guanine Lesion and Replication By Human Dna Polymerase Beta within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:31.7 occ:1.00 O A:LYS60 2.3 30.8 1.0 O A:VAL65 2.4 28.8 1.0 O A:LEU62 2.4 27.6 1.0 O A:HOH628 2.5 30.3 1.0 O D:HOH102 2.7 39.0 1.0 OP1 D:DC3 2.8 30.7 1.0 C A:LYS60 3.4 27.1 1.0 C A:LEU62 3.5 25.1 1.0 C A:VAL65 3.5 27.6 1.0 P D:DC3 3.8 29.5 1.0 OP2 D:DC3 3.9 27.6 1.0 N A:VAL65 3.9 26.3 1.0 C A:LYS61 4.0 28.6 1.0 N A:LEU62 4.0 26.7 1.0 CA A:VAL65 4.1 25.6 1.0 CA A:LYS60 4.2 26.9 1.0 CA A:PRO63 4.2 27.6 1.0 O A:LYS61 4.3 29.4 1.0 N A:PRO63 4.3 29.7 1.0 N A:LYS61 4.3 23.1 1.0 N A:GLY64 4.3 28.4 1.0 CB A:VAL65 4.4 25.2 1.0 CG A:LYS60 4.4 28.0 1.0 CA A:LEU62 4.4 24.4 1.0 CA A:LYS61 4.4 25.1 1.0 N A:GLY66 4.5 25.8 1.0 C A:PRO63 4.7 30.5 1.0 O3' D:DT2 4.7 30.4 1.0 NZ A:LYS60 4.8 35.7 1.0 O A:ALA59 4.8 21.9 1.0 CA A:GLY66 4.9 26.8 1.0 C A:GLY64 4.9 27.4 1.0 CB A:LYS60 4.9 28.6 1.0

Y.Kou, M.C.Koag, S.Lee. Structural and Kinetic Studies of the Effect of Guanine-N7 Alkylation and Metal Cofactors on Dna Replication. Biochemistry 2018.
ISSN: ISSN 1520-4995
PubMed: 29957995
DOI: 10.1021/ACS.BIOCHEM.8B00331