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Sodium in PDB 6vez: Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min), PDB code: 6vez 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) 24.58 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.966, 68.481, 110.194, 90, 90, 90
R / Rfree (%) 16.6 / 20.5

Other elements in 6vez:

The structure of Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) (pdb code 6vez). 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 Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min), PDB code: 6vez:

Sodium binding site 1 out of 1 in 6vez

Go back to Sodium Binding Sites List in 6vez
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 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 Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na505

b:18.0
occ:1.00
 O A:VAL246 2.3 22.5 1.0
O A:THR241 2.3 24.2 1.0
O P:HOH114 2.3 30.4 1.0
O A:HOH816 2.3 27.4 1.0
O A:ILE243 2.4 22.0 1.0
OP1 P:DT3 2.7 19.3 1.0
C A:VAL246 3.4 22.2 1.0
C A:ILE243 3.4 23.7 1.0
C A:THR241 3.4 29.2 1.0
P P:DT3 3.6 20.8 1.0
N A:VAL246 3.8 21.9 1.0
OP2 P:DT3 3.9 19.7 1.0
O P:HOH107 3.9 47.1 1.0
CA A:VAL246 4.1 21.5 1.0
N A:ILE243 4.1 20.9 1.0
O A:HOH782 4.1 41.5 1.0
CA A:THR241 4.2 24.7 1.0
C A:GLN242 4.2 23.3 1.0
N A:PHE244 4.2 23.2 1.0
N A:GLY245 4.2 19.4 1.0
CA A:PHE244 4.2 22.0 1.0
CA A:ILE243 4.4 21.3 1.0
N A:GLN242 4.4 23.9 1.0
N A:GLY247 4.4 24.1 1.0
CB A:VAL246 4.5 20.0 1.0
O A:GLN242 4.6 22.7 1.0
CA A:GLN242 4.6 24.5 1.0
O3' P:DG2 4.6 20.2 1.0
C A:PHE244 4.6 20.8 1.0
O A:HOH825 4.6 45.0 1.0
O A:PHE240 4.7 21.1 1.0
CA A:GLY247 4.7 25.0 1.0
CB A:THR241 4.8 20.9 1.0
C A:GLY245 4.8 21.6 1.0
O5' P:DT3 4.8 23.0 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:at Pre-Catalytic Ternary Complex, 20 Mm CA2+ (60 Min) To Be Published.
Page generated: Mon Aug 18 07:53:27 2025

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