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Sodium in PDB 6vfb: Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min), PDB code: 6vfb 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) 34.99 / 1.55
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.198, 62.334, 118.756, 90, 90, 90
R / Rfree (%) 16.7 / 18.2

Other elements in 6vfb:

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) also contains other interesting chemical elements:

Manganese (Mn) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) (pdb code 6vfb). 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:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min), PDB code: 6vfb:

Sodium binding site 1 out of 1 in 6vfb

Go back to Sodium Binding Sites List in 6vfb
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 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:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na508

b:18.0
occ:1.00
 O A:VAL246 2.3 20.1 1.0
O A:HOH617 2.3 26.8 1.0
O P:HOH202 2.4 30.4 1.0
O A:THR241 2.4 22.9 1.0
O A:ILE243 2.4 20.2 1.0
OP1 P:DT3 2.5 19.2 1.0
C A:VAL246 3.4 20.4 1.0
C A:ILE243 3.5 22.4 1.0
C A:THR241 3.5 21.7 1.0
P P:DT3 3.6 21.1 1.0
N A:VAL246 3.7 20.2 1.0
OP2 P:DT3 3.9 20.8 1.0
O A:HOH651 4.0 53.8 1.0
CA A:VAL246 4.1 19.9 1.0
N A:ILE243 4.1 21.5 1.0
CA A:THR241 4.2 21.6 1.0
C A:GLN242 4.2 26.2 1.0
N A:GLY245 4.2 20.8 1.0
N A:PHE244 4.2 21.3 1.0
CA A:PHE244 4.3 20.2 1.0
O8 A:8GT510 4.4 38.0 0.5
N A:GLY247 4.4 19.1 1.0
CA A:ILE243 4.4 21.0 1.0
N A:GLN242 4.5 23.4 1.0
CA A:GLN242 4.5 25.1 1.0
CB A:VAL246 4.5 21.1 1.0
O P:HOH213 4.6 43.2 1.0
O3' P:DG2 4.6 20.9 1.0
O3' P:DA4 4.6 30.2 0.5
C A:PHE244 4.6 20.5 1.0
C3' P:DA4 4.7 21.3 0.5
O A:GLN242 4.7 28.5 1.0
OP2 P:DA4 4.7 21.9 0.5
CA A:GLY247 4.7 21.2 1.0
O5' P:DT3 4.8 21.7 1.0
C A:GLY245 4.8 19.4 1.0
O A:PHE240 4.8 22.1 1.0
CB A:THR241 4.8 23.1 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:Ct Reaction State Ternary Complex, 50 Mm MN2+ (960 Min) To Be Published.
Page generated: Tue Oct 8 14:22:54 2024

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