Sodium in PDB 7rbe: Human Dna Polymerase Beta Crosslinked Binary Complex - A

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

The structure of Human Dna Polymerase Beta Crosslinked Binary Complex - A, PDB code: 7rbe 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)	44.18 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.585, 79.48, 54.906, 90, 104.55, 90
R / Rfree (%)	21.6 / 26.8

The binding sites of Sodium atom in the Human Dna Polymerase Beta Crosslinked Binary Complex - A (pdb code 7rbe). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Human Dna Polymerase Beta Crosslinked Binary Complex - A, PDB code: 7rbe:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Human Dna Polymerase Beta Crosslinked Binary Complex - A


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 - A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:15.4 occ:1.00 O A:THR101 2.3 15.8 1.0 OP1 P:DG9 2.3 13.7 1.0 O A:HOH716 2.3 17.3 1.0 O A:ILE106 2.4 13.7 1.0 O P:HOH115 2.4 16.0 1.0 O A:VAL103 2.6 11.3 1.0 C A:THR101 3.3 15.4 1.0 P P:DG9 3.4 14.0 1.0 C A:ILE106 3.5 12.9 1.0 C A:VAL103 3.5 12.0 1.0 O A:HOH549 3.5 27.0 1.0 OP2 P:DG9 3.6 14.8 1.0 N A:ILE106 3.9 10.6 1.0 CA A:THR101 3.9 14.9 1.0 CA A:SER104 4.0 11.5 1.0 N A:SER104 4.1 11.7 1.0 N A:GLY105 4.1 11.3 1.0 CA A:ILE106 4.2 11.0 1.0 N A:VAL103 4.2 13.5 1.0 O3' P:DC8 4.4 14.7 1.0 C A:ARG102 4.4 15.3 1.0 CB A:THR101 4.4 16.0 1.0 N A:ARG102 4.4 15.8 1.0 N A:GLY107 4.4 11.8 1.0 C A:SER104 4.4 11.4 1.0 CA A:VAL103 4.5 14.2 1.0 O5' P:DG9 4.6 13.6 1.0 CB A:ILE106 4.6 11.4 1.0 C A:GLY105 4.7 10.7 1.0 CA A:GLY107 4.7 14.7 1.0 CA A:ARG102 4.7 16.4 1.0 O A:ARG102 4.8 14.0 1.0 CA A:GLY105 5.0 10.8 1.0

Sodium binding site 2 out of 4 in the Human Dna Polymerase Beta Crosslinked Binary Complex - A


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 - A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:28.4 occ:1.00 O A:PRO108 2.6 14.7 1.0 O A:ASN28 2.6 16.6 1.0 NE2 A:GLN31 2.8 33.0 1.0 NE A:ARG112 3.3 31.0 1.0 C A:PRO108 3.4 15.8 1.0 NH2 A:ARG112 3.5 30.7 1.0 CD A:GLN31 3.6 26.6 1.0 CB A:PRO108 3.7 15.4 1.0 CB A:ARG112 3.7 19.9 1.0 CA A:PRO108 3.7 15.6 1.0 CG A:GLN31 3.7 23.4 1.0 O A:VAL29 3.7 19.6 1.0 CZ A:ARG112 3.7 33.3 1.0 CG2 A:ILE97 3.7 16.3 1.0 C A:ASN28 3.8 16.8 1.0 CA A:VAL29 4.1 20.2 1.0 CD A:ARG112 4.3 26.9 1.0 C A:VAL29 4.3 20.2 1.0 N A:SER109 4.4 15.3 1.0 N A:ARG112 4.4 15.8 1.0 N A:VAL29 4.4 18.0 1.0 CA A:ARG112 4.5 17.1 1.0 CG A:ARG112 4.6 22.3 1.0 O A:HOH681 4.7 28.8 1.0 CD1 A:ILE97 4.7 19.3 1.0 O A:HOH650 4.8 33.5 1.0 OE1 A:GLN31 4.8 30.5 1.0 CA A:SER109 4.9 17.4 1.0 NH1 A:ARG112 5.0 36.6 1.0 CA A:ASN28 5.0 17.2 1.0

Sodium binding site 3 out of 4 in the Human Dna Polymerase Beta Crosslinked Binary Complex - A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Human Dna Polymerase Beta Crosslinked Binary Complex - A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:29.6 occ:1.00 O A:LYS60 2.2 26.5 1.0 O A:VAL65 2.2 24.9 1.0 O D:HOH109 2.4 30.7 1.0 O A:LEU62 2.6 24.9 1.0 OP1 D:DC3 3.1 23.3 1.0 C A:LYS60 3.4 29.1 1.0 C A:VAL65 3.4 22.5 1.0 C A:LEU62 3.6 26.9 1.0 N A:VAL65 3.9 20.6 1.0 OP2 D:DC3 3.9 21.2 1.0 P D:DC3 4.0 23.5 1.0 CA A:LYS60 4.1 25.6 1.0 N A:LEU62 4.1 25.7 1.0 CA A:VAL65 4.1 23.4 1.0 C A:LYS61 4.2 27.8 1.0 CA A:PRO63 4.3 26.7 1.0 N A:GLY64 4.3 23.4 1.0 N A:PRO63 4.3 28.0 1.0 CG A:LYS60 4.4 33.2 1.0 N A:LYS61 4.4 26.9 1.0 CB A:VAL65 4.4 22.6 1.0 N A:GLY66 4.5 22.5 1.0 CA A:LEU62 4.5 25.9 0.5 CA A:LEU62 4.5 26.8 0.5 O A:LYS61 4.5 32.1 1.0 CA A:LYS61 4.6 28.7 1.0 C A:PRO63 4.7 26.0 1.0 CA A:GLY66 4.7 21.7 1.0 O3' D:DT2 4.8 20.0 1.0 CB A:LYS60 4.9 27.5 1.0 O A:ALA59 4.9 18.9 1.0 NZ A:LYS60 4.9 35.8 1.0 C A:GLY64 4.9 22.8 1.0

Sodium binding site 4 out of 4 in the Human Dna Polymerase Beta Crosslinked Binary Complex - A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Human Dna Polymerase Beta Crosslinked Binary Complex - A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na405 b:33.9 occ:1.00 OE1 A:GLU154 2.7 27.4 1.0 NE A:ARG253 3.0 20.7 1.0 O A:HOH644 3.1 20.1 1.0 SD A:MET158 3.3 23.1 1.0 CG A:ARG253 3.4 19.6 1.0 CG2 A:ILE150 3.6 25.7 1.0 CD1 A:LEU241 3.7 29.6 1.0 CB A:GLU154 3.7 28.1 1.0 CD A:ARG253 3.7 22.1 1.0 CD A:GLU154 3.8 32.0 1.0 CZ A:ARG253 3.9 25.6 1.0 NH2 A:ARG253 3.9 25.4 1.0 CG A:GLU154 4.1 28.4 1.0 CG A:LEU241 4.1 28.1 1.0 CG A:MET158 4.2 22.2 1.0 CE A:MET158 4.2 25.4 1.0 O A:PRO251 4.7 27.4 1.0 CB A:ARG253 4.7 19.8 1.0 O A:GLU154 4.8 26.8 1.0 CA A:GLU154 4.8 28.6 1.0 CB A:LEU241 4.8 27.6 1.0 C A:GLU154 4.8 26.2 1.0 CB A:ILE150 4.8 25.7 1.0 OE2 A:GLU154 4.9 28.0 1.0 CD1 A:TYR250 5.0 32.8 1.0 CG1 A:ILE150 5.0 25.2 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