Sodium in PDB 6vf2: Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min)

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

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min), PDB code: 6vf2 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)	34.98 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.278, 62.297, 118.573, 90, 90, 90
R / Rfree (%)	16.8 / 19.3

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 Min) (pdb code 6vf2). 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+ (960 Min), PDB code: 6vf2:
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+ (960 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+ (960 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:19.2 occ:1.00 O A:VAL246 2.3 18.2 1.0 O A:HOH797 2.3 26.8 1.0 O A:ILE243 2.4 20.3 1.0 O A:THR241 2.4 21.3 1.0 O P:HOH209 2.5 25.6 1.0 OP1 P:DT3 2.8 18.8 1.0 C A:VAL246 3.4 18.4 1.0 C A:ILE243 3.4 20.9 1.0 C A:THR241 3.4 18.2 1.0 N A:VAL246 3.8 18.6 1.0 P P:DT3 3.8 19.7 1.0 N A:ILE243 4.0 20.6 1.0 OP2 P:DT3 4.0 19.6 1.0 O A:HOH722 4.0 37.7 1.0 CA A:VAL246 4.1 19.1 1.0 C A:GLN242 4.1 24.3 1.0 CA A:THR241 4.1 18.7 1.0 N A:PHE244 4.2 20.8 1.0 N A:GLY245 4.3 18.0 1.0 CA A:PHE244 4.3 21.4 1.0 CA A:ILE243 4.3 19.7 1.0 N A:GLN242 4.4 22.3 1.0 CB A:VAL246 4.4 20.0 1.0 N A:GLY247 4.4 19.2 1.0 CA A:GLN242 4.5 25.9 1.0 O A:HOH824 4.5 32.4 1.0 O A:GLN242 4.5 23.6 1.0 C A:PHE244 4.6 18.8 1.0 O3' P:DG2 4.7 18.0 1.0 CA A:GLY247 4.8 19.3 1.0 O A:PHE240 4.8 20.1 1.0 CB A:THR241 4.8 19.8 1.0 C A:GLY245 4.8 19.6 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, 8-Oxorgtp:at Product State Ternary Complex, 50 Mm MG2+ (960 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+ (960 Min) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:35.2 occ:0.54 O A:HOH690 2.0 37.6 1.0 OD1 A:ASP330 2.3 40.2 1.0 OP1 P:8GM5 2.4 34.4 1.0 OD2 A:ASP332 2.4 36.2 1.0 O A:HOH660 2.5 31.7 1.0 CG A:ASP330 3.2 43.3 1.0 CG A:ASP332 3.4 28.3 1.0 O A:HOH768 3.5 36.1 0.7 MG A:MG509 3.5 20.4 0.6 P P:8GM5 3.5 35.1 0.6 OD2 A:ASP330 3.6 57.1 1.0 O5' P:8GM5 3.6 36.6 0.3 OD1 A:ASP332 3.9 33.7 1.0 O A:ASP330 4.0 26.6 1.0 N A:GLY320 4.0 17.9 1.0 C5' P:8GM5 4.1 41.2 1.0 O A:HOH621 4.2 20.5 1.0 CA A:GLY319 4.2 17.8 1.0 C A:ASP330 4.3 25.2 1.0 OP2 P:8GM5 4.4 45.9 0.8 O A:HOH795 4.4 48.6 1.0 CB A:ASP332 4.6 18.9 1.0 CB A:ASP330 4.6 26.7 1.0 C A:GLY319 4.7 17.6 1.0 O3' P:DA4 4.7 44.5 1.0 N A:ASP332 4.8 16.8 1.0 N A:VAL331 4.8 20.1 1.0 CA A:ASP330 4.9 23.6 1.0 N A:ASP330 5.0 23.1 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+ (960 Min) To Be Published.