Sodium in PDB 6vf1: Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min):
2.7.7.7;

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min), PDB code: 6vf1 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)	35.02 / 1.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.044, 68.415, 111.07, 90, 90, 90
R / Rfree (%)	16.3 / 18.8

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Chlorine	(Cl)	1 atom

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) (pdb code 6vf1). 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:at Product State Ternary Complex, 50 Mm MG2+ (120 Min), PDB code: 6vf1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 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:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:15.9 occ:1.00 O A:VAL246 2.3 16.4 1.0 O A:HOH822 2.3 27.4 1.0 O P:HOH115 2.3 20.8 1.0 O A:THR241 2.4 18.9 1.0 O A:ILE243 2.4 18.0 1.0 OP1 P:DT3 2.7 15.6 1.0 C A:VAL246 3.4 16.3 1.0 C A:THR241 3.4 18.2 1.0 C A:ILE243 3.5 19.1 1.0 P P:DT3 3.7 15.9 1.0 O P:HOH114 3.7 40.0 1.0 N A:VAL246 3.8 17.1 1.0 OP2 P:DT3 3.9 14.7 1.0 CA A:VAL246 4.1 17.4 1.0 N A:ILE243 4.1 16.5 1.0 CA A:THR241 4.1 16.8 1.0 C A:GLN242 4.2 18.7 1.0 N A:PHE244 4.2 18.6 1.0 N A:GLY245 4.3 16.1 1.0 CA A:PHE244 4.3 18.4 1.0 N A:GLN242 4.4 18.8 1.0 CA A:ILE243 4.4 16.1 1.0 N A:GLY247 4.4 17.1 1.0 O A:HOH849 4.5 35.0 1.0 CB A:VAL246 4.5 16.9 1.0 O A:GLN242 4.5 22.4 1.0 CA A:GLN242 4.5 21.2 1.0 O3' P:DG2 4.7 15.3 1.0 C A:PHE244 4.7 17.9 1.0 CA A:GLY247 4.7 18.3 1.0 O A:PHE240 4.8 16.6 1.0 CB A:THR241 4.8 17.3 1.0 C A:GLY245 4.8 17.6 1.0 O5' P:DT3 4.9 15.4 1.0 O P:HOH119 4.9 60.7 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 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:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) within 5.0Å range: probe atom residue distance (Å) B Occ T:Na101 b:55.0 occ:1.00 O T:HOH205 2.2 33.7 1.0 O T:HOH213 2.2 41.1 1.0 O T:HOH237 2.2 54.8 1.0 O T:HOH206 2.2 27.3 1.0 O D:HOH110 3.6 41.5 1.0 O D:HOH113 3.9 58.9 1.0 N7 T:DG2 4.2 20.7 1.0 O6 T:DG3 4.3 18.6 1.0 O T:HOH201 4.4 39.3 1.0 O T:HOH207 4.4 28.0 1.0 O6 T:DG2 4.5 17.7 1.0 N4 D:DC2 4.5 18.6 1.0

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (120 Min) To Be Published.