Sodium in PDB 7k97: Human Dna Polymerase Beta Dgdp Product Complex with MN2+

All present enzymatic activity of Human Dna Polymerase Beta Dgdp Product Complex with MN2+:
2.7.7.7;

The structure of Human Dna Polymerase Beta Dgdp Product Complex with MN2+, PDB code: 7k97 was solved by F.A.Varela, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.58 / 2.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.102, 77.309, 55.111, 90, 114.85, 90
R / Rfree (%)	18.5 / 24

The structure of Human Dna Polymerase Beta Dgdp Product Complex with MN2+ also contains other interesting chemical elements:

Manganese

(Mn)

8 atoms

The binding sites of Sodium atom in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+ (pdb code 7k97). 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 Dgdp Product Complex with MN2+, PDB code: 7k97:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


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 Dgdp Product Complex with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:29.3 occ:1.00 O A:HOH532 2.3 29.6 1.0 O A:THR101 2.5 32.6 1.0 OP1 P:DG9 2.5 24.6 1.0 O A:ILE106 2.6 23.6 1.0 O A:VAL103 2.8 30.2 1.0 OP2 P:DG9 3.3 27.6 1.0 P P:DG9 3.3 26.8 1.0 C A:THR101 3.5 29.9 1.0 C A:VAL103 3.6 30.2 1.0 C A:ILE106 3.7 25.0 1.0 CA A:SER104 4.0 22.7 1.0 CA A:THR101 4.1 30.5 1.0 N A:ILE106 4.1 29.3 1.0 N A:SER104 4.1 27.5 1.0 N A:GLY105 4.2 25.2 1.0 O3' P:DC8 4.4 22.2 1.0 N A:VAL103 4.5 26.4 1.0 CA A:ILE106 4.5 29.2 1.0 C A:ARG102 4.5 33.2 1.0 C A:SER104 4.5 27.4 1.0 O5' P:DG9 4.5 29.8 1.0 N A:ARG102 4.5 32.0 1.0 CB A:THR101 4.6 28.2 1.0 N A:GLY107 4.6 26.3 1.0 CA A:VAL103 4.7 29.3 1.0 CA A:ARG102 4.7 30.0 1.0 O A:ARG102 4.8 40.6 1.0 CA A:GLY107 4.8 23.5 1.0 CB A:ILE106 4.9 27.9 1.0 C A:GLY105 5.0 33.4 1.0

Sodium binding site 2 out of 2 in the Human Dna Polymerase Beta Dgdp Product Complex with MN2+


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 Dgdp Product Complex with MN2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:46.1 occ:1.00 O A:LEU62 2.2 48.2 1.0 O A:VAL65 2.3 45.8 1.0 O A:LYS60 2.4 49.6 1.0 OP1 D:DC3 2.4 45.7 1.0 O A:HOH524 2.8 44.3 1.0 C A:LEU62 3.3 45.6 1.0 C A:VAL65 3.3 40.6 1.0 C A:LYS60 3.4 47.5 1.0 N A:VAL65 3.5 36.9 1.0 P D:DC3 3.5 40.3 1.0 OP2 D:DC3 3.8 42.8 1.0 CA A:VAL65 3.9 38.5 1.0 N A:LEU62 3.9 45.5 1.0 N A:GLY64 4.0 48.3 1.0 C A:LYS61 4.1 52.0 1.0 CA A:LYS60 4.1 50.0 1.0 N A:PRO63 4.1 45.1 1.0 CA A:PRO63 4.1 40.9 1.0 CB A:VAL65 4.2 46.5 1.0 CA A:LEU62 4.2 45.6 1.0 N A:GLY66 4.4 42.7 1.0 N A:LYS61 4.4 47.5 1.0 O A:LYS61 4.4 53.7 1.0 CG A:LYS60 4.5 52.5 1.0 C A:PRO63 4.5 49.7 1.0 C A:GLY64 4.6 45.1 1.0 CA A:LYS61 4.6 52.6 1.0 O3' D:DT2 4.6 40.0 1.0 O A:ALA59 4.6 48.3 1.0 O5' D:DC3 4.6 39.8 1.0 CA A:GLY66 4.8 38.9 1.0 CA A:GLY64 4.9 35.9 1.0 CB A:LYS60 4.9 49.3 1.0 CG1 A:VAL65 5.0 45.0 1.0

F.A.Varela, B.D.Freudenthal. Mechanism of Deoxyguanosine Diphosphate Insertion By Human Dna Polymerase Beta. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33475337
DOI: 10.1021/ACS.BIOCHEM.0C00847