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Sodium in PDB 7kt5: Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN), PDB code: 7kt5 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) 34.93 / 1.46
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.996, 68.701, 110.125, 90, 90, 90
R / Rfree (%) 16.2 / 18.3

Other elements in 7kt5:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) also contains other interesting chemical elements:

Manganese (Mn) 7 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) (pdb code 7kt5). 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 Product State Ternary Complex, 10 Mm MN2+ (120MIN), PDB code: 7kt5:

Sodium binding site 1 out of 1 in 7kt5

Go back to Sodium Binding Sites List in 7kt5
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN)


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 Product State Ternary Complex, 10 Mm MN2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:22.4
occ:1.00
 O A:VAL246 2.3 21.9 1.0
O A:THR241 2.3 21.7 1.0
O A:HOH835 2.4 27.7 1.0
O P:HOH116 2.4 24.9 1.0
O A:ILE243 2.4 21.5 1.0
OP1 P:DT3 2.7 20.9 1.0
C A:VAL246 3.4 23.1 1.0
C A:THR241 3.4 21.5 1.0
C A:ILE243 3.4 23.7 1.0
O P:HOH115 3.8 27.4 1.0
N A:VAL246 3.8 21.6 1.0
P P:DT3 3.8 20.4 1.0
OP2 P:DT3 3.9 19.4 1.0
N A:ILE243 4.0 21.1 1.0
CA A:VAL246 4.1 22.4 1.0
O A:HOH812 4.1 41.5 1.0
C A:GLN242 4.2 23.5 1.0
CA A:THR241 4.2 22.0 1.0
N A:PHE244 4.2 21.8 1.0
N A:GLY245 4.3 21.2 1.0
CA A:PHE244 4.3 21.8 1.0
N A:GLN242 4.4 24.4 1.0
CA A:ILE243 4.4 22.8 1.0
CA A:GLN242 4.4 26.5 1.0
O A:HOH853 4.4 43.5 1.0
CB A:VAL246 4.4 24.2 1.0
N A:GLY247 4.5 24.4 1.0
O A:GLN242 4.6 26.3 1.0
C A:PHE244 4.7 21.6 1.0
O3' P:DG2 4.7 20.4 1.0
O A:PHE240 4.7 23.6 1.0
CA A:GLY247 4.8 24.1 1.0
C A:GLY245 4.9 21.6 1.0
CB A:THR241 4.9 24.7 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Product State Ternary Complex, 10 Mm MN2+ (120MIN) To Be Published.
Page generated: Tue Oct 8 17:28:17 2024

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