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Sodium in PDB 6vf7: Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf7 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 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.159, 68.927, 110.446, 90, 90, 90
R / Rfree (%) 16.6 / 19.7

Other elements in 6vf7:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) also contains other interesting chemical elements:

Manganese (Mn) 8 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) (pdb code 6vf7). 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 Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf7:

Sodium binding site 1 out of 1 in 6vf7

Go back to Sodium Binding Sites List in 6vf7
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)


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 Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na507

b:27.1
occ:1.00
 O A:VAL246 2.3 29.0 1.0
O A:THR241 2.3 30.4 1.0
O A:ILE243 2.3 27.1 1.0
O A:HOH814 2.4 27.2 1.0
O P:HOH111 2.6 29.4 1.0
OP1 P:DT3 2.8 24.6 1.0
C A:ILE243 3.3 21.3 1.0
C A:VAL246 3.4 22.1 1.0
C A:THR241 3.4 29.9 1.0
O P:HOH107 3.6 32.2 1.0
N A:VAL246 3.7 26.1 1.0
P P:DT3 3.8 25.2 1.0
OP2 P:DT3 3.9 24.7 1.0
N A:ILE243 4.0 26.1 1.0
CA A:VAL246 4.0 25.6 1.0
N A:PHE244 4.1 30.1 1.0
C A:GLN242 4.2 30.6 1.0
O A:HOH788 4.2 45.2 1.0
N A:GLY245 4.2 22.7 1.0
CA A:PHE244 4.2 28.6 1.0
CA A:THR241 4.2 29.1 1.0
CA A:ILE243 4.3 27.3 1.0
N A:GLN242 4.3 25.8 1.0
CA A:GLN242 4.3 27.5 1.0
CB A:VAL246 4.4 26.6 1.0
N A:GLY247 4.4 31.7 1.0
C A:PHE244 4.6 28.8 1.0
O3' P:DG2 4.7 24.2 1.0
O A:GLN242 4.7 28.6 1.0
C A:GLY245 4.7 27.1 1.0
O A:PHE240 4.7 26.4 1.0
CA A:GLY247 4.8 31.8 1.0
CB A:THR241 5.0 26.5 1.0

Reference:

J.A.Jamsen, A.Sassa, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) To Be Published.
Page generated: Tue Oct 8 14:22:54 2024

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