Sodium in PDB 7ksy: Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN):
2.7.7.7;

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN), PDB code: 7ksy 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)	35.04 / 1.58
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.316, 62.323, 119.043, 90, 90, 90
R / Rfree (%)	15.6 / 17

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN) 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+ (960MIN) (pdb code 7ksy). 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+ (960MIN), PDB code: 7ksy:
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+ (960MIN)


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+ (960MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:21.9 occ:0.99 OD2 A:ASP418 2.1 28.5 1.0 OD1 A:ASP332 2.2 20.3 1.0 OP1 P:DG5 2.3 19.1 1.0 O P:HOH107 2.5 26.9 1.0 OD1 A:ASP330 2.7 22.1 1.0 O3' P:DA4 2.9 18.3 1.0 P P:DG5 3.1 18.1 1.0 CG A:ASP332 3.2 19.7 1.0 CG A:ASP418 3.2 28.8 1.0 CG A:ASP330 3.3 38.5 1.0 MG A:MG501 3.4 20.5 1.0 OD2 A:ASP332 3.5 18.7 1.0 CB A:ASP418 3.9 18.7 1.0 CB A:ASP330 3.9 20.6 1.0 OD2 A:ASP330 4.0 54.2 1.0 C3' P:DA4 4.0 18.0 1.0 C5' P:DA4 4.1 16.6 1.0 OD1 A:ASP418 4.1 23.6 1.0 C4' P:DA4 4.1 16.3 1.0 OP2 P:DG5 4.2 19.8 1.0 O5' P:DG5 4.3 18.8 1.0 NH2 A:ARG416 4.4 20.1 1.0 C5' P:DG5 4.5 17.3 1.0 CB A:ASP332 4.5 17.1 1.0 O2 A:GOA506 4.6 35.8 1.0 O A:VAL331 4.7 19.9 1.0 O P:HOH104 4.7 35.2 1.0 OP1 P:DA4 4.8 18.4 1.0 CZ3 A:TRP434 4.9 21.4 1.0 O5' P:DA4 4.9 17.2 1.0 C A:VAL331 4.9 18.6 1.0 N A:ASP418 4.9 17.7 1.0 CA A:ASP332 5.0 16.4 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MG2+ (960MIN)


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+ (960MIN) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:20.8 occ:1.00 O A:VAL246 2.3 18.6 1.0 O P:HOH116 2.4 23.5 1.0 O A:THR241 2.4 22.4 1.0 O A:ILE243 2.4 19.9 1.0 O A:HOH809 2.4 27.9 1.0 OP1 P:DT3 2.7 18.1 1.0 C A:VAL246 3.4 19.3 1.0 C A:THR241 3.4 20.9 1.0 C A:ILE243 3.5 22.0 1.0 O P:HOH110 3.6 38.1 1.0 N A:VAL246 3.7 19.2 1.0 P P:DT3 3.8 18.9 1.0 OP2 P:DT3 4.0 19.8 1.0 O A:HOH698 4.0 41.9 1.0 CA A:VAL246 4.0 18.8 1.0 N A:ILE243 4.1 20.7 1.0 CA A:THR241 4.1 18.9 1.0 C A:GLN242 4.2 23.6 1.0 N A:PHE244 4.3 21.8 1.0 N A:GLY245 4.3 17.8 1.0 CA A:PHE244 4.3 20.0 1.0 CA A:ILE243 4.4 19.9 1.0 N A:GLN242 4.4 23.2 1.0 N A:GLY247 4.4 18.2 1.0 CB A:VAL246 4.5 19.3 1.0 CA A:GLN242 4.5 25.3 1.0 O A:HOH831 4.5 32.9 1.0 O A:HOH817 4.6 48.8 1.0 O A:GLN242 4.6 25.9 1.0 C A:PHE244 4.7 21.7 1.0 O3' P:DG2 4.7 17.9 1.0 CA A:GLY247 4.7 18.1 1.0 CB A:THR241 4.8 20.3 1.0 C A:GLY245 4.8 18.5 1.0 O A:PHE240 4.8 21.4 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+ (960MIN) To Be Published.