Sodium in PDB 7ksx: Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN), PDB code: 7ksx 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)	41.83 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.011, 68.695, 110.522, 90, 90, 90
R / Rfree (%)	16.3 / 18.6

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN) also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN) (pdb code 7ksx). 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN), PDB code: 7ksx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN)


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, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:24.6 occ:1.00 O A:VAL246 2.3 24.5 1.0 O A:HOH815 2.3 33.4 1.0 O A:THR241 2.3 25.7 1.0 O A:ILE243 2.4 23.9 1.0 O P:HOH117 2.4 27.2 1.0 OP1 P:DT3 2.7 23.0 1.0 C A:VAL246 3.4 25.0 1.0 C A:ILE243 3.4 28.2 1.0 C A:THR241 3.4 26.8 1.0 P P:DT3 3.7 23.0 1.0 N A:VAL246 3.7 22.8 1.0 OP2 P:DT3 3.9 21.2 1.0 CA A:VAL246 4.0 24.6 1.0 N A:ILE243 4.0 25.7 1.0 O P:HOH105 4.1 40.1 1.0 CA A:THR241 4.1 26.3 1.0 O A:HOH760 4.1 45.8 1.0 C A:GLN242 4.1 26.9 1.0 N A:PHE244 4.2 25.0 1.0 N A:GLY245 4.2 21.6 1.0 CA A:PHE244 4.3 25.9 1.0 CA A:ILE243 4.3 21.8 1.0 N A:GLN242 4.4 28.2 1.0 CB A:VAL246 4.4 25.1 1.0 N A:GLY247 4.4 24.2 1.0 O A:GLN242 4.5 33.0 1.0 CA A:GLN242 4.6 31.9 1.0 O A:HOH832 4.6 45.4 1.0 C A:PHE244 4.6 26.1 1.0 O3' P:DG2 4.7 22.9 1.0 O A:PHE240 4.7 25.2 1.0 CA A:GLY247 4.7 24.2 1.0 CB A:THR241 4.8 26.3 1.0 C A:GLY245 4.8 21.6 1.0 O5' P:DT3 4.9 21.4 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN)


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, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:18.6 occ:1.00 OD2 A:ASP418 2.1 23.9 1.0 OD1 A:ASP332 2.2 18.4 1.0 OP1 P:DG5 2.4 17.9 1.0 O P:HOH106 2.4 27.0 1.0 O3' P:DA4 2.7 18.8 1.0 OD1 A:ASP330 2.7 19.7 1.0 P P:DG5 3.1 19.1 1.0 CG A:ASP332 3.2 19.1 1.0 CG A:ASP418 3.2 21.2 1.0 CG A:ASP330 3.3 29.0 1.0 MG A:MG509 3.5 17.3 1.0 OD2 A:ASP332 3.5 17.8 1.0 C3' P:DA4 3.9 17.3 1.0 CB A:ASP418 3.9 17.9 1.0 OD2 A:ASP330 4.0 33.4 1.0 C5' P:DA4 4.0 19.1 1.0 C4' P:DA4 4.0 18.0 1.0 CB A:ASP330 4.0 21.1 1.0 OP2 P:DG5 4.1 19.7 1.0 OD1 A:ASP418 4.2 21.6 1.0 O5' P:DG5 4.3 16.4 1.0 C5' P:DG5 4.4 17.2 1.0 NH2 A:ARG416 4.5 20.2 1.0 CB A:ASP332 4.5 16.2 1.0 O32 A:PPV508 4.7 24.9 1.0 OP1 P:DA4 4.7 21.0 1.0 O A:VAL331 4.8 17.8 1.0 O5' P:DA4 4.8 18.8 1.0 CZ3 A:TRP434 4.9 21.8 1.0 C A:VAL331 5.0 17.0 1.0 CA A:ASP332 5.0 15.9 1.0

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (30MIN) To Be Published.