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Sodium in PDB 7ktf: Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN), PDB code: 7ktf 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) 34.97 / 1.49
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.947, 68.515, 110.696, 90, 90, 90
R / Rfree (%) 16.7 / 18.7

Other elements in 7ktf:

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN) (pdb code 7ktf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN), PDB code: 7ktf:

Sodium binding site 1 out of 1 in 7ktf

Go back to Sodium Binding Sites List in 7ktf
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN)


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-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na503

b:18.4
occ:1.00
 O A:VAL246 2.3 17.7 1.0
O P:HOH112 2.3 22.3 1.0
O A:THR241 2.4 20.9 1.0
O A:HOH858 2.4 31.7 1.0
O A:ILE243 2.4 20.1 1.0
OP1 P:DT3 2.7 17.0 1.0
C A:VAL246 3.4 17.4 1.0
C A:ILE243 3.4 20.3 1.0
C A:THR241 3.5 18.6 1.0
P P:DT3 3.7 17.1 1.0
N A:VAL246 3.7 18.2 1.0
O P:HOH114 3.8 40.2 1.0
O P:HOH113 3.9 46.5 1.0
OP2 P:DT3 3.9 17.1 1.0
CA A:VAL246 4.0 18.8 1.0
N A:ILE243 4.0 19.9 1.0
C A:GLN242 4.1 21.7 1.0
CA A:THR241 4.2 21.4 1.0
O A:HOH810 4.2 42.4 1.0
N A:PHE244 4.2 18.8 1.0
N A:GLY245 4.2 17.9 1.0
CA A:PHE244 4.2 20.1 1.0
CA A:ILE243 4.4 18.2 1.0
O A:GLN242 4.4 28.2 1.0
CB A:VAL246 4.4 17.7 1.0
N A:GLY247 4.4 18.4 1.0
N A:GLN242 4.4 20.0 1.0
O A:HOH879 4.5 36.9 1.0
CA A:GLN242 4.5 21.3 1.0
C A:PHE244 4.6 19.7 1.0
O3' P:DG2 4.6 18.1 1.0
CA A:GLY247 4.8 20.4 1.0
O A:PHE240 4.8 18.4 1.0
C A:GLY245 4.8 18.5 1.0
CB A:THR241 4.8 18.5 1.0
O5' P:DT3 4.9 17.2 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:Ct Product State Ternary Complex, 50 Mm MG2+ (180MIN) To Be Published.
Page generated: Tue Oct 8 17:29:11 2024

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