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Sodium in PDB 7kt7: Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN), PDB code: 7kt7 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) 34.95 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.908, 68.531, 110.589, 90, 90, 90
R / Rfree (%) 16.1 / 18.7

Other elements in 7kt7:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN) also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN) (pdb code 7kt7). 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:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN), PDB code: 7kt7:

Sodium binding site 1 out of 1 in 7kt7

Go back to Sodium Binding Sites List in 7kt7
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN)


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:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:19.0
occ:1.00
O A:VAL246 2.3 18.8 1.0
O A:ILE243 2.4 19.3 1.0
O A:THR241 2.4 23.4 1.0
O P:HOH216 2.4 22.1 1.0
O A:HOH826 2.4 26.3 1.0
OP1 P:DT3 2.8 17.9 1.0
C A:ILE243 3.4 21.6 1.0
C A:VAL246 3.4 19.1 1.0
C A:THR241 3.4 24.5 1.0
O P:HOH215 3.6 33.1 1.0
N A:VAL246 3.7 17.1 1.0
P P:DT3 3.8 17.5 1.0
OP2 P:DT3 3.9 16.4 1.0
N A:ILE243 4.0 21.9 1.0
CA A:VAL246 4.1 18.7 1.0
O A:HOH762 4.1 48.8 1.0
C A:GLN242 4.2 25.1 0.4
N A:PHE244 4.2 20.5 1.0
CA A:THR241 4.2 21.0 1.0
C A:GLN242 4.2 25.1 0.6
N A:GLY245 4.2 18.8 1.0
CA A:PHE244 4.2 18.4 1.0
CA A:ILE243 4.3 18.8 1.0
N A:GLN242 4.3 26.5 0.6
N A:GLN242 4.3 26.5 0.4
CA A:GLN242 4.4 27.9 0.6
CB A:VAL246 4.4 18.1 1.0
CA A:GLN242 4.5 27.5 0.4
N A:GLY247 4.5 21.5 1.0
O A:HOH841 4.5 53.8 1.0
O A:GLN242 4.5 25.1 0.4
C A:PHE244 4.6 19.1 1.0
O A:GLN242 4.7 25.4 0.6
O A:PHE240 4.7 19.3 1.0
O3' P:DG2 4.8 17.7 1.0
CA A:GLY247 4.8 20.8 1.0
C A:GLY245 4.8 19.6 1.0
CB A:THR241 4.9 20.0 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 50 Mm MG2+ (60MIN) To Be Published.
Page generated: Fri Dec 17 11:18:27 2021

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