Sodium in PDB 7kt9: Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 50 Mm MG2+ (960MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 50 Mm MG2+ (960MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 50 Mm MG2+ (960MIN), PDB code: 7kt9 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)	45.20 / 1.48
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.283, 68.316, 111.407, 90, 90, 90
R / Rfree (%)	15.5 / 17.6

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 50 Mm MG2+ (960MIN) 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, 50 Mm MG2+ (960MIN) (pdb code 7kt9). 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, 50 Mm MG2+ (960MIN), PDB code: 7kt9:
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, 50 Mm MG2+ (960MIN)


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, 50 Mm MG2+ (960MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na501 b:15.5 occ:1.00 OD2 A:ASP418 2.2 17.7 1.0 O A:HOH750 2.3 22.5 1.0 OD1 A:ASP332 2.3 14.1 0.4 OP1 P:8OG5 2.4 14.0 1.0 OD1 A:ASP332 2.4 12.3 0.6 O P:HOH609 2.4 17.9 1.0 O3' P:DA4 3.1 12.9 1.0 CG A:ASP418 3.2 15.6 1.0 P P:8OG5 3.2 12.0 1.0 CG A:ASP332 3.3 13.1 0.4 CG A:ASP332 3.3 13.1 0.6 OD2 A:ASP332 3.5 11.1 0.6 OD2 A:ASP332 3.6 14.2 0.4 MG A:MG509 3.6 18.5 0.5 CB A:ASP330 3.9 24.6 0.5 CB A:ASP418 3.9 13.9 1.0 OP2 P:8OG5 3.9 13.8 1.0 OD1 A:ASP418 4.0 14.9 1.0 C5' P:DA4 4.1 11.9 1.0 CA A:ASP330 4.1 19.7 0.6 O A:VAL331 4.1 12.6 0.6 NH2 A:ARG416 4.2 14.7 1.0 C3' P:DA4 4.3 12.0 1.0 CB A:ASP330 4.3 18.8 0.6 C4' P:DA4 4.3 11.2 1.0 C A:ASP330 4.4 17.9 0.6 N A:VAL331 4.5 16.0 0.6 CB A:ASP332 4.6 13.0 0.4 O5' P:8OG5 4.6 11.0 1.0 C A:VAL331 4.6 12.8 0.6 N A:ASP418 4.7 12.3 1.0 CB A:ASP332 4.7 12.8 0.6 OP1 P:DA4 4.7 14.1 1.0 O A:VAL331 4.7 11.6 0.5 CZ3 A:TRP434 4.9 11.7 1.0 CA A:ASP418 4.9 11.3 1.0 N A:VAL331 4.9 15.2 0.5 C A:VAL331 4.9 12.5 0.5 O5' P:DA4 5.0 12.7 1.0 CZ A:ARG416 5.0 14.9 1.0 O A:ASP330 5.0 20.6 0.6

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 50 Mm MG2+ (960MIN)


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, 50 Mm MG2+ (960MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:18.4 occ:1.00 O A:VAL246 2.3 18.4 1.0 O A:HOH853 2.4 28.4 1.0 O A:THR241 2.4 21.0 1.0 O A:ILE243 2.4 19.0 1.0 O P:HOH617 2.4 21.0 1.0 OP1 P:DT3 2.6 16.6 1.0 C A:ILE243 3.4 22.6 1.0 C A:VAL246 3.4 19.3 1.0 C A:THR241 3.4 19.8 1.0 O P:HOH616 3.6 25.8 0.5 O P:HOH616 3.6 20.1 0.5 P P:DT3 3.7 16.4 1.0 N A:VAL246 3.8 17.4 1.0 OP2 P:DT3 3.9 16.0 1.0 N A:ILE243 4.0 19.0 1.0 CA A:VAL246 4.1 18.7 1.0 C A:GLN242 4.1 21.6 1.0 N A:PHE244 4.1 20.0 1.0 CA A:THR241 4.2 17.7 1.0 N A:GLY245 4.2 18.8 1.0 CA A:PHE244 4.2 19.8 1.0 O A:HOH835 4.2 37.1 1.0 CA A:ILE243 4.3 20.2 1.0 N A:GLN242 4.4 21.6 1.0 CB A:VAL246 4.4 19.1 1.0 O A:GLN242 4.4 25.6 1.0 N A:GLY247 4.5 18.7 1.0 O A:HOH890 4.5 35.0 1.0 CA A:GLN242 4.5 23.1 1.0 C A:PHE244 4.6 19.2 1.0 O3' P:DG2 4.7 17.1 1.0 O A:HOH855 4.7 23.7 0.5 O A:PHE240 4.7 18.8 1.0 CA A:GLY247 4.8 18.5 1.0 C A:GLY245 4.8 16.4 1.0 CB A:THR241 4.8 19.5 1.0 O5' P:DT3 4.9 14.9 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, 50 Mm MG2+ (960MIN) To Be Published.