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Sodium in PDB 6vf3: Dna Polymerase Mu, 8-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min)

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

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

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf3 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) 33.39 / 1.52
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.198, 62.385, 118.58, 90, 90, 90
R / Rfree (%) 16.3 / 18

Other elements in 6vf3:

The structure of Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) (pdb code 6vf3). 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 Ground State Ternary Complex, 50 Mm MN2+ (15 Min), PDB code: 6vf3:

Sodium binding site 1 out of 1 in 6vf3

Go back to Sodium Binding Sites List in 6vf3
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxorgtp: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-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:17.4
occ:1.00
 O A:VAL246 2.3 18.3 1.0
O P:HOH113 2.4 24.7 1.0
O P:HOH104 2.4 27.6 1.0
O A:THR241 2.4 20.5 1.0
O A:ILE243 2.5 19.3 1.0
OP1 P:DT3 2.6 17.8 1.0
C A:VAL246 3.4 18.4 1.0
C A:ILE243 3.5 20.9 1.0
C A:THR241 3.5 18.4 1.0
P P:DT3 3.7 18.1 1.0
N A:VAL246 3.8 17.1 1.0
OP2 P:DT3 3.9 17.5 1.0
O A:HOH772 4.0 48.2 1.0
CA A:VAL246 4.1 18.5 1.0
N A:ILE243 4.1 19.2 1.0
CA A:THR241 4.2 19.0 1.0
C A:GLN242 4.2 22.0 1.0
N A:GLY245 4.3 18.5 1.0
N A:PHE244 4.3 19.5 1.0
CA A:PHE244 4.3 19.8 1.0
N A:GLY247 4.4 18.5 1.0
CA A:ILE243 4.4 19.7 1.0
N A:GLN242 4.5 23.3 1.0
O P:HOH115 4.5 37.1 1.0
CB A:VAL246 4.5 20.9 1.0
CA A:GLN242 4.6 25.0 1.0
O A:GLN242 4.6 24.6 1.0
C A:PHE244 4.6 17.8 1.0
O3' P:DG2 4.7 18.1 1.0
O3' P:DA4 4.7 28.1 0.5
C3' P:DA4 4.7 24.2 0.5
CA A:GLY247 4.7 19.3 1.0
C A:GLY245 4.8 16.3 1.0
CB A:THR241 4.8 19.4 1.0
O5' P:DT3 4.8 18.9 1.0
O A:PHE240 4.8 21.0 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Ground State Ternary Complex, 50 Mm MN2+ (15 Min) To Be Published.
Page generated: Tue Oct 8 14:22:01 2024

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