Sodium in PDB 7kss: Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN), PDB code: 7kss was solved by J.A.Jamsen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.84 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.023, 68.767, 110.27, 90, 90, 90
R / Rfree (%)	16 / 17.7

The structure of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN) also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN) (pdb code 7kss). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN), PDB code: 7kss:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:17.4 occ:1.00 O A:HOH857 2.3 29.1 1.0 O A:VAL246 2.3 18.4 1.0 O A:THR241 2.3 20.9 1.0 O P:HOH113 2.4 29.1 1.0 O A:ILE243 2.4 20.3 1.0 OP1 P:DT3 2.6 18.4 1.0 C A:ILE243 3.4 21.8 1.0 C A:VAL246 3.4 17.4 1.0 C A:THR241 3.4 21.9 1.0 P P:DT3 3.7 18.5 1.0 N A:VAL246 3.8 18.4 1.0 OP2 P:DT3 3.9 20.1 1.0 O P:HOH110 4.0 37.8 1.0 N A:ILE243 4.1 21.0 1.0 CA A:VAL246 4.1 19.1 1.0 C A:GLN242 4.1 24.3 1.0 O A:HOH822 4.1 39.2 1.0 N A:PHE244 4.1 20.7 1.0 CA A:THR241 4.2 21.2 1.0 CA A:PHE244 4.2 20.8 1.0 N A:GLY245 4.2 19.4 1.0 O P:HOH101 4.3 45.3 1.0 CA A:ILE243 4.4 19.8 1.0 O A:GLN242 4.4 26.9 1.0 N A:GLN242 4.4 22.7 1.0 N A:GLY247 4.5 20.4 1.0 CB A:VAL246 4.5 20.4 1.0 CA A:GLN242 4.5 24.9 1.0 O A:HOH866 4.6 50.4 1.0 C A:PHE244 4.6 21.4 1.0 O A:PHE240 4.7 19.7 1.0 O3' P:DG2 4.8 18.4 1.0 CA A:GLY247 4.8 19.7 1.0 CB A:THR241 4.8 19.7 1.0 C A:GLY245 4.9 18.1 1.0 O5' P:DT3 4.9 19.0 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Mu, Dgtp:Ct Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (20MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:42.1 occ:1.00 O A:PHE205 2.3 33.6 1.0 O D:HOH113 2.3 47.3 1.0 O A:HOH632 2.4 37.5 1.0 O A:HOH728 2.4 45.6 1.0 O A:HOH770 2.8 53.3 1.0 C A:PHE205 3.5 28.4 1.0 N A:GLY206 4.3 23.8 1.0 O A:LEU202 4.3 28.2 1.0 CA A:GLY206 4.3 25.2 1.0 O A:HOH748 4.5 43.9 1.0 CA A:PHE205 4.5 23.4 1.0 OP1 D:DC3 4.7 22.4 0.8 CB A:PHE205 4.7 22.0 1.0 OP2 D:DC3 4.7 24.2 0.2 N A:PHE205 4.7 22.4 1.0 OP1 D:DC3 4.8 23.0 0.2 OP2 D:DC3 4.9 24.3 0.8

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6