Sodium in PDB 7rbf: Human Dna Polymerase Beta Crosslinked Binary Complex - B

All present enzymatic activity of Human Dna Polymerase Beta Crosslinked Binary Complex - B:
2.7.7.7;

The structure of Human Dna Polymerase Beta Crosslinked Binary Complex - B, PDB code: 7rbf was solved by A.J.Reed, A.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.13 / 1.84
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.68, 79.571, 54.828, 90, 91.68, 90
R / Rfree (%)	17.6 / 20.8

The binding sites of Sodium atom in the Human Dna Polymerase Beta Crosslinked Binary Complex - B (pdb code 7rbf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Dna Polymerase Beta Crosslinked Binary Complex - B, PDB code: 7rbf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Crosslinked Binary Complex - B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Dna Polymerase Beta Crosslinked Binary Complex - B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:17.0 occ:1.00 O A:THR101 2.3 13.9 1.0 O A:ILE106 2.4 15.2 1.0 O P:HOH116 2.4 15.3 1.0 OP1 P:DG9 2.4 13.2 1.0 O A:HOH740 2.5 17.2 1.0 O A:VAL103 2.6 15.7 1.0 C A:THR101 3.3 15.1 1.0 C A:ILE106 3.4 12.9 1.0 C A:VAL103 3.5 16.1 1.0 O A:HOH583 3.5 26.5 1.0 P P:DG9 3.5 14.8 1.0 OP2 P:DG9 3.7 15.4 1.0 CA A:THR101 3.8 14.7 1.0 N A:ILE106 3.8 13.1 1.0 CA A:SER104 4.0 15.7 1.0 N A:SER104 4.1 15.7 1.0 N A:GLY105 4.1 13.7 1.0 CA A:ILE106 4.1 13.6 1.0 O P:HOH132 4.2 41.9 1.0 N A:VAL103 4.2 16.5 1.0 CB A:THR101 4.3 15.9 1.0 N A:GLY107 4.3 13.2 1.0 C A:ARG102 4.3 16.2 1.0 N A:ARG102 4.4 15.6 1.0 C A:SER104 4.4 14.0 1.0 CA A:VAL103 4.5 17.0 1.0 CA A:GLY107 4.5 14.1 1.0 O3' P:DC8 4.6 14.5 1.0 CB A:ILE106 4.6 13.8 1.0 CA A:ARG102 4.7 16.7 1.0 O5' P:DG9 4.7 14.8 1.0 C A:GLY105 4.7 13.8 1.0 O A:ARG102 4.8 15.4 1.0 O A:HOH589 4.8 27.3 1.0 O A:LEU100 4.8 15.8 1.0

Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Crosslinked Binary Complex - B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Dna Polymerase Beta Crosslinked Binary Complex - B within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:28.1 occ:1.00 O A:VAL65 2.2 23.0 1.0 O A:HOH735 2.3 36.6 1.0 O A:LEU62 2.3 24.4 1.0 O A:LYS60 2.3 29.5 1.0 O D:HOH106 2.5 28.0 1.0 OP1 D:DC3 3.1 27.1 1.0 C A:LEU62 3.3 26.6 1.0 C A:VAL65 3.4 22.4 1.0 C A:LYS60 3.4 29.4 1.0 N A:VAL65 3.9 18.9 1.0 N A:LEU62 3.9 26.7 1.0 OP2 D:DC3 4.0 20.3 1.0 CA A:VAL65 4.0 21.4 1.0 P D:DC3 4.0 24.2 1.0 C A:LYS61 4.0 29.0 1.0 N A:PRO63 4.1 24.4 1.0 CA A:PRO63 4.1 27.3 1.0 CA A:LYS60 4.1 26.1 1.0 O D:HOH102 4.1 28.0 1.0 CA A:LEU62 4.3 25.8 1.0 CB A:VAL65 4.3 21.9 1.0 N A:LYS61 4.4 28.4 1.0 N A:GLY64 4.4 23.5 1.0 O A:LYS61 4.4 30.0 1.0 N A:GLY66 4.4 22.1 1.0 CG A:LYS60 4.4 33.6 1.0 CA A:LYS61 4.5 27.9 1.0 C A:PRO63 4.6 25.6 1.0 CA A:GLY66 4.7 21.3 1.0 O A:ALA59 4.8 25.5 1.0 NZ A:LYS60 4.8 34.9 1.0 O3' D:DT2 4.8 23.8 1.0 C A:GLY64 4.9 21.7 1.0 CB A:LYS60 5.0 25.7 1.0

A.Kumar, A.J.Reed, W.J.Zahurancik, S.M.Daskalova, S.M.Hecht, Z.Suo. Interlocking Activities of Dna Polymerase Beta in the Base Excision Repair Pathway. Proc.Natl.Acad.Sci.Usa V. 119 40119 2022.
ISSN: ESSN 1091-6490
PubMed: 35238634
DOI: 10.1073/PNAS.2118940119