Sodium in PDB 6vf9: Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min):
2.7.7.7;

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min), PDB code: 6vf9 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)	34.93 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.2, 62.13, 118.533, 90, 90, 90
R / Rfree (%)	16.5 / 18.2

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min) 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-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min) (pdb code 6vf9). 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-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min), PDB code: 6vf9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min)


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-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:18.3 occ:1.00 O A:HOH825 2.3 28.1 1.0 O A:VAL246 2.3 18.1 1.0 O P:HOH112 2.4 22.2 1.0 O A:THR241 2.4 19.5 1.0 O A:ILE243 2.4 19.1 1.0 OP1 P:DT3 2.7 19.2 1.0 C A:VAL246 3.4 17.0 1.0 C A:ILE243 3.4 18.6 1.0 C A:THR241 3.5 18.6 1.0 N A:VAL246 3.7 17.5 1.0 P P:DT3 3.8 17.5 1.0 OP2 P:DT3 4.0 19.0 1.0 O A:HOH719 4.0 42.2 1.0 N A:ILE243 4.0 19.5 1.0 CA A:VAL246 4.1 16.3 1.0 CA A:THR241 4.1 16.8 1.0 C A:GLN242 4.2 21.9 1.0 N A:PHE244 4.2 18.4 1.0 N A:GLY245 4.3 16.2 1.0 CA A:PHE244 4.3 17.9 1.0 CA A:ILE243 4.4 18.0 1.0 N A:GLY247 4.4 15.6 1.0 N A:GLN242 4.4 20.2 1.0 CB A:VAL246 4.4 18.4 1.0 O A:GLN242 4.5 23.5 1.0 CA A:GLN242 4.6 22.6 1.0 O A:HOH849 4.6 26.7 1.0 C A:PHE244 4.6 16.5 1.0 O3' P:DG2 4.7 17.2 1.0 CA A:GLY247 4.8 16.1 1.0 C A:GLY245 4.8 16.6 1.0 CB A:THR241 4.8 17.7 1.0 O A:PHE240 4.8 20.1 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min)


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-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:33.2 occ:0.71 O A:HOH708 2.0 34.6 1.0 OD1 A:ASP330 2.1 35.0 1.0 OD2 A:ASP332 2.3 35.3 1.0 O A:HOH628 2.5 29.7 1.0 O P:HOH101 2.7 33.7 1.0 CG A:ASP330 3.1 36.9 1.0 OD2 A:ASP330 3.4 42.8 1.0 CG A:ASP332 3.4 28.4 1.0 MG A:MG505 3.5 26.2 0.7 O A:HOH758 3.5 42.3 1.0 O A:ASP330 3.9 24.2 1.0 OD1 A:ASP332 3.9 37.7 1.0 N A:GLY320 4.0 16.8 1.0 O A:HOH606 4.0 19.4 1.0 C A:ASP330 4.1 22.6 1.0 CA A:GLY319 4.2 15.4 1.0 CB A:ASP330 4.4 27.8 1.0 CB A:ASP332 4.5 16.6 1.0 O A:HOH818 4.6 45.5 1.0 N A:VAL331 4.6 19.1 1.0 O A:HOH775 4.6 43.4 1.0 N A:ASP332 4.7 16.0 1.0 C A:GLY319 4.7 14.9 1.0 CA A:ASP330 4.7 21.7 1.0 O A:HOH803 4.8 38.7 1.0 CA A:VAL331 4.8 17.5 1.0 N A:ASP330 4.9 21.6 1.0 C A:VAL331 4.9 18.6 1.0 O3' P:DA4 4.9 35.9 1.0 CA A:GLY320 5.0 18.1 1.0

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:Ct Ternary Complex, 50 Mm MG2+ (2160 Min) To Be Published.