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Sodium in PDB 6vf8: Dna Polymerase Mu, 8-Oxorgtp:Ct Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 Min)

Enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 Min)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxorgtp:Ct Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 Min):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 Min), PDB code: 6vf8 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) 34.94 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.101, 62.271, 118.637, 90, 90, 90
R / Rfree (%) 16.8 / 19.2

Other elements in 6vf8:

The structure of Dna Polymerase Mu, 8-Oxorgtp:Ct Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 Min) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxorgtp:Ct Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 Min) (pdb code 6vf8). 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 Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 Min), PDB code: 6vf8:

Sodium binding site 1 out of 1 in 6vf8

Go back to Sodium Binding Sites List in 6vf8
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxorgtp:Ct Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 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 Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 Min) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:13.4
occ:1.00
 O A:THR241 2.3 20.2 1.0
O P:HOH112 2.3 24.8 1.0
O A:VAL246 2.4 17.6 1.0
O A:ILE243 2.5 18.1 1.0
OP1 P:DT3 2.5 18.0 1.0
O P:HOH104 2.6 24.7 1.0
C A:VAL246 3.4 18.0 1.0
C A:THR241 3.5 18.4 1.0
C A:ILE243 3.5 22.0 1.0
P P:DT3 3.6 17.5 1.0
N A:VAL246 3.8 18.2 1.0
OP2 P:DT3 3.9 19.1 1.0
N A:ILE243 4.1 20.3 1.0
CA A:VAL246 4.2 18.6 1.0
C A:GLN242 4.2 25.5 1.0
N A:GLY245 4.2 17.6 1.0
CA A:THR241 4.2 18.2 1.0
N A:PHE244 4.3 18.5 1.0
CA A:PHE244 4.3 19.6 1.0
N A:GLN242 4.4 20.9 1.0
CA A:ILE243 4.4 19.8 1.0
N A:GLY247 4.5 18.1 1.0
CA A:GLN242 4.5 26.5 1.0
O A:GLN242 4.5 23.4 1.0
CB A:VAL246 4.6 19.1 1.0
O3' P:DG2 4.6 17.2 1.0
C A:PHE244 4.7 19.6 1.0
O P:HOH115 4.7 39.1 1.0
OP2 P:DA4 4.7 24.8 1.0
O5' P:DT3 4.7 19.2 1.0
CA A:GLY247 4.8 17.8 1.0
C3' P:DA4 4.8 38.4 1.0
O3' P:DA4 4.8 35.5 1.0
C A:GLY245 4.8 18.4 1.0
O A:PHE240 4.9 21.4 1.0
CB A:THR241 4.9 21.4 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxorgtp:Ct Pre-Catalytic Ternary Complex, 20 Mm CA2+ (120 Min) To Be Published.
Page generated: Tue Oct 8 14:22:54 2024

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