Sodium in PDB 7kth: Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN), PDB code: 7kth 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)	41.82 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.089, 68.373, 111.095, 90, 90, 90
R / Rfree (%)	16.6 / 19

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN) also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN) (pdb code 7kth). 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, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN), PDB code: 7kth:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN)


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, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:22.3 occ:1.00 OD2 A:ASP418 2.1 23.3 1.0 OP1 P:8OG5 2.1 23.2 1.0 OD1 A:ASP332 2.3 20.0 1.0 O A:HOH787 2.3 28.8 1.0 O A:HOH607 2.4 25.0 1.0 CG A:ASP418 3.1 17.8 1.0 P P:8OG5 3.2 20.1 1.0 CG A:ASP332 3.2 20.0 1.0 O3' P:DA4 3.2 20.6 1.0 CG A:ASP330 3.3 57.4 1.0 OD2 A:ASP332 3.4 26.0 1.0 OD2 A:ASP330 3.4 69.8 1.0 OD1 A:ASP330 3.5 41.8 1.0 CB A:ASP330 3.7 43.5 1.0 MG A:MG502 3.7 26.4 0.6 CB A:ASP418 3.8 16.5 1.0 OP2 P:8OG5 3.9 21.8 1.0 OD1 A:ASP418 4.0 20.0 1.0 C5' P:DA4 4.2 18.3 1.0 NH2 A:ARG416 4.3 18.5 1.0 O A:VAL331 4.3 16.4 1.0 C3' P:DA4 4.3 17.1 1.0 C4' P:DA4 4.4 15.4 1.0 O5' P:8OG5 4.5 18.5 1.0 CB A:ASP332 4.6 14.9 1.0 N A:ASP418 4.6 14.1 1.0 C A:VAL331 4.7 14.4 1.0 N A:VAL331 4.7 26.3 1.0 OP1 P:DA4 4.7 17.8 1.0 C5' P:8OG5 4.8 19.3 1.0 CA A:ASP418 4.8 13.5 1.0 CZ3 A:TRP434 4.9 17.7 1.0 CA A:ASP330 5.0 25.7 1.0 O5' P:DA4 5.0 16.8 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN)


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, 8-Oxodgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (2160MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:19.7 occ:0.99 O A:VAL246 2.3 18.8 1.0 O A:THR241 2.4 20.5 1.0 O P:HOH115 2.4 21.2 1.0 O A:ILE243 2.4 19.2 1.0 O A:HOH863 2.4 32.0 1.0 OP1 P:DT3 2.6 18.4 1.0 C A:VAL246 3.4 18.9 1.0 C A:ILE243 3.4 25.2 1.0 C A:THR241 3.5 20.3 1.0 P P:DT3 3.7 17.7 1.0 N A:VAL246 3.8 18.0 1.0 OP2 P:DT3 3.9 18.0 1.0 O P:HOH107 3.9 38.8 1.0 N A:ILE243 4.0 19.5 1.0 C A:GLN242 4.1 23.7 1.0 CA A:VAL246 4.1 18.9 1.0 N A:PHE244 4.1 19.7 1.0 CA A:THR241 4.2 19.5 1.0 N A:GLY245 4.2 18.1 1.0 CA A:PHE244 4.2 19.9 1.0 O A:HOH794 4.2 38.7 1.0 CA A:ILE243 4.3 21.1 1.0 O A:GLN242 4.4 28.3 1.0 CB A:VAL246 4.4 18.8 1.0 N A:GLN242 4.4 21.6 1.0 N A:GLY247 4.4 18.9 1.0 O A:HOH893 4.5 37.2 1.0 CA A:GLN242 4.5 20.8 1.0 C A:PHE244 4.6 21.4 1.0 O3' P:DG2 4.7 18.4 1.0 O A:PHE240 4.8 19.2 1.0 CA A:GLY247 4.8 18.6 1.0 C A:GLY245 4.8 17.1 1.0 CB A:THR241 4.8 18.4 1.0 O5' P:DT3 4.9 17.0 1.0

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