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Sodium in PDB 6vf4: Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min), PDB code: 6vf4 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) 32.48 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.085, 68.757, 110.531, 90, 90, 90
R / Rfree (%) 16.8 / 19.2

Other elements in 6vf4:

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) also contains other interesting chemical elements:

Manganese (Mn) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) (pdb code 6vf4). 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-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min), PDB code: 6vf4:

Sodium binding site 1 out of 1 in 6vf4

Go back to Sodium Binding Sites List in 6vf4
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 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-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:27.1
occ:1.00
 O A:VAL246 2.2 28.2 1.0
O A:THR241 2.3 28.8 1.0
O A:ILE243 2.4 25.4 1.0
O A:HOH782 2.4 31.7 1.0
O P:HOH213 2.5 30.0 1.0
OP1 P:DT3 2.7 26.8 1.0
C A:VAL246 3.3 27.8 1.0
C A:ILE243 3.4 26.7 1.0
C A:THR241 3.4 27.6 1.0
N A:VAL246 3.7 26.7 1.0
O P:HOH212 3.7 42.7 1.0
P P:DT3 3.7 25.3 1.0
OP2 P:DT3 3.8 24.8 1.0
CA A:VAL246 4.0 28.4 1.0
N A:ILE243 4.0 27.1 1.0
C A:GLN242 4.1 28.2 0.7
N A:PHE244 4.1 27.7 1.0
N A:GLY245 4.2 25.2 1.0
CA A:THR241 4.2 27.0 1.0
CA A:PHE244 4.2 27.5 1.0
N A:GLN242 4.3 29.2 0.3
N A:GLN242 4.3 29.5 0.7
CA A:ILE243 4.3 26.4 1.0
C A:GLN242 4.3 28.7 0.3
CB A:VAL246 4.4 30.4 1.0
N A:GLY247 4.4 28.1 1.0
CA A:GLN242 4.4 30.3 0.3
CA A:GLN242 4.4 30.1 0.7
O A:GLN242 4.5 27.6 0.7
C A:PHE244 4.6 27.8 1.0
O3' P:DG2 4.7 25.0 1.0
CA A:GLY247 4.7 27.2 1.0
O A:PHE240 4.7 27.2 1.0
C A:GLY245 4.7 27.4 1.0
CB A:THR241 4.9 27.9 1.0
O5' P:DT3 4.9 24.5 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Reaction State Ternary Complex, 50 Mm MN2+ (30 Min) To Be Published.
Page generated: Tue Oct 8 14:22:02 2024

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