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

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

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MG2+ (2160MIN), PDB code: 7ktn 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)	35.09 / 1.33
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.229, 68.293, 111.412, 90, 90, 90
R / Rfree (%)	14.1 / 16.3

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

Sodium binding site 1 out of 2 in the Dna Polymerase Mu, 8-Oxodgtp:at 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:at Product State Ternary Complex, 10 Mm MG2+ (2160MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:17.3 occ:1.00 O A:VAL246 2.3 15.9 1.0 O A:HOH855 2.4 26.0 1.0 O A:THR241 2.4 19.9 1.0 O P:HOH216 2.4 20.5 1.0 O A:ILE243 2.4 17.5 1.0 OP1 P:DT3 2.6 15.6 1.0 C A:ILE243 3.4 19.3 1.0 C A:VAL246 3.4 15.6 1.0 C A:THR241 3.4 20.1 1.0 O P:HOH217 3.6 30.4 1.0 P P:DT3 3.7 15.0 1.0 N A:VAL246 3.8 16.1 1.0 OP2 P:DT3 3.9 15.2 1.0 N A:ILE243 4.0 20.9 1.0 CA A:VAL246 4.0 16.5 1.0 C A:GLN242 4.1 21.9 1.0 CA A:THR241 4.1 18.5 1.0 N A:PHE244 4.2 19.7 1.0 O A:HOH792 4.2 35.1 1.0 CA A:PHE244 4.2 19.0 1.0 N A:GLY245 4.2 17.2 1.0 CA A:ILE243 4.3 20.3 1.0 N A:GLN242 4.4 21.2 1.0 CB A:VAL246 4.4 17.4 1.0 O A:GLN242 4.4 26.7 1.0 N A:GLY247 4.5 15.8 1.0 CA A:GLN242 4.5 23.1 1.0 O A:HOH908 4.5 31.6 1.0 C A:PHE244 4.6 18.0 1.0 O3' P:DG2 4.6 15.4 1.0 O A:HOH949 4.7 23.4 0.5 O A:PHE240 4.8 18.0 1.0 CA A:GLY247 4.8 16.6 1.0 CB A:THR241 4.8 20.1 1.0 C A:GLY245 4.8 16.8 1.0 O5' P:DT3 4.9 13.7 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxodgtp:at 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:at Product State Ternary Complex, 10 Mm MG2+ (2160MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:15.0 occ:1.00 OD2 A:ASP418 2.2 16.1 1.0 O A:HOH806 2.3 21.6 1.0 OD1 A:ASP332 2.3 13.1 0.6 OP1 P:8OG5 2.4 13.3 1.0 OD1 A:ASP332 2.4 13.9 0.4 O P:HOH211 2.4 15.9 1.0 O3' P:DA4 3.2 12.6 1.0 CG A:ASP418 3.2 13.7 1.0 CG A:ASP332 3.2 12.0 0.6 P P:8OG5 3.3 12.5 1.0 CG A:ASP332 3.4 12.8 0.4 OD2 A:ASP332 3.5 11.5 0.6 MG A:MG501 3.6 12.8 0.4 OD2 A:ASP332 3.7 12.6 0.4 CB A:ASP418 3.8 13.6 1.0 OP2 P:8OG5 3.9 13.0 1.0 OD1 A:ASP418 4.0 14.4 1.0 C5' P:DA4 4.1 12.5 1.0 CA A:ASP330 4.1 18.8 0.6 NH2 A:ARG416 4.2 13.9 1.0 CB A:ASP330 4.2 19.4 0.6 O A:VAL331 4.3 13.6 0.6 C3' P:DA4 4.3 11.9 1.0 C4' P:DA4 4.3 11.4 1.0 C A:ASP330 4.4 16.9 0.6 N A:VAL331 4.6 18.3 0.6 CB A:ASP332 4.6 11.4 0.6 N A:ASP418 4.6 11.9 1.0 O5' P:8OG5 4.7 11.2 1.0 O A:VAL331 4.7 12.6 0.4 C A:VAL331 4.7 13.7 0.6 CB A:ASP332 4.7 11.9 0.4 OP1 P:DA4 4.7 13.6 1.0 CZ3 A:TRP434 4.8 12.2 1.0 N A:VAL331 4.9 11.3 0.4 CA A:ASP418 4.9 11.7 1.0 C A:VAL331 4.9 11.9 0.4 CZ A:ARG416 4.9 12.9 1.0 O A:ASP330 5.0 21.5 0.6 CA A:ASP330 5.0 14.0 0.4 O5' P:DA4 5.0 12.3 1.0

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MG2+ (2160MIN) To Be Published.