Sodium in PDB 6vf0: Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min):
2.7.7.7;

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min), PDB code: 6vf0 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)	34.96 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.982, 68.437, 110.615, 90, 90, 90
R / Rfree (%)	16.4 / 18.7

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) (pdb code 6vf0). 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 Reaction State Ternary Complex, 50 Mm MG2+ (30 Min), PDB code: 6vf0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 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 Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:23.5 occ:1.00 O A:HOH824 2.3 35.2 1.0 O A:VAL246 2.3 24.6 1.0 O P:HOH216 2.4 26.8 1.0 O A:ILE243 2.4 24.6 1.0 O A:THR241 2.4 26.1 1.0 OP1 P:DT3 2.7 23.9 1.0 C A:VAL246 3.4 27.5 1.0 C A:ILE243 3.4 24.8 1.0 C A:THR241 3.5 21.9 1.0 O P:HOH215 3.7 40.7 1.0 N A:VAL246 3.7 23.5 1.0 P P:DT3 3.7 22.7 1.0 OP2 P:DT3 3.9 21.3 1.0 CA A:VAL246 4.0 23.3 1.0 N A:ILE243 4.1 22.7 1.0 O A:HOH769 4.1 46.9 1.0 C A:GLN242 4.2 24.5 1.0 CA A:THR241 4.2 22.5 1.0 N A:PHE244 4.2 21.4 1.0 N A:GLY245 4.2 21.2 1.0 CA A:PHE244 4.2 21.9 1.0 CA A:ILE243 4.4 20.6 1.0 CB A:VAL246 4.4 22.6 1.0 N A:GLN242 4.5 26.0 1.0 N A:GLY247 4.5 25.9 1.0 O A:GLN242 4.5 30.1 1.0 O A:HOH848 4.5 43.7 1.0 CA A:GLN242 4.6 29.1 1.0 C A:PHE244 4.6 28.4 1.0 O3' P:DG2 4.6 21.7 1.0 CA A:GLY247 4.8 28.0 1.0 C A:GLY245 4.8 22.6 1.0 O A:PHE240 4.8 23.8 1.0 CB A:THR241 4.9 24.8 1.0 O5' P:DT3 4.9 21.7 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 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 Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:49.7 occ:0.74 O A:HOH833 2.3 45.1 0.7 OE1 A:GLN281 2.3 48.3 1.0 O A:HOH689 2.6 40.0 1.0 CD A:GLN281 3.2 41.7 1.0 NE2 A:GLN281 3.3 51.9 1.0 CA A:ALA278 3.8 28.5 1.0 N A:ALA278 3.9 24.1 1.0 CB A:ALA278 4.0 30.6 1.0 C A:LYS277 4.4 24.8 1.0 O A:HOH673 4.4 27.0 1.0 O A:LYS277 4.6 29.2 1.0 CG A:GLN281 4.6 29.0 1.0 CB A:LYS277 4.7 31.4 1.0 O A:GLN274 4.9 34.3 1.0

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (30 Min) To Be Published.