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Sodium in PDB 7kta: Dna Polymerase Mu, 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)

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

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7kta 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) 32.44 / 1.84
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.905, 68.718, 110.398, 90, 90, 90
R / Rfree (%) 16.7 / 19.8

Other elements in 7kta:

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

Calcium (Ca) 2 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) (pdb code 7kta). 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-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN), PDB code: 7kta:

Sodium binding site 1 out of 1 in 7kta

Go back to Sodium Binding Sites List in 7kta
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN)


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-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:28.2
occ:1.00
 O A:VAL246 2.3 29.3 1.0
O P:HOH210 2.3 37.5 1.0
O A:THR241 2.4 30.9 1.0
O A:ILE243 2.4 29.1 1.0
O A:HOH737 2.5 37.3 1.0
OP1 P:DT3 2.6 26.4 1.0
C A:VAL246 3.4 29.8 1.0
C A:ILE243 3.4 33.1 1.0
C A:THR241 3.4 40.1 1.0
P P:DT3 3.7 30.7 1.0
N A:VAL246 3.7 30.1 1.0
OP2 P:DT3 3.9 30.7 1.0
CA A:VAL246 4.1 30.4 1.0
N A:ILE243 4.1 34.5 1.0
CA A:THR241 4.2 34.0 1.0
C A:GLN242 4.2 37.7 1.0
N A:PHE244 4.2 32.8 1.0
N A:GLY245 4.2 30.5 1.0
CA A:PHE244 4.3 30.8 1.0
CA A:ILE243 4.4 29.7 1.0
N A:GLN242 4.4 32.5 1.0
CB A:VAL246 4.4 30.8 1.0
N A:GLY247 4.4 34.2 1.0
CA A:GLN242 4.5 38.4 1.0
O A:GLN242 4.6 34.3 1.0
C A:PHE244 4.6 31.8 1.0
O3' P:DG2 4.7 29.5 1.0
CA A:GLY247 4.7 39.6 1.0
O A:PHE240 4.8 30.5 1.0
C A:GLY245 4.8 30.2 1.0
CB A:THR241 4.8 30.8 1.0
O5' P:DT3 4.9 28.5 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:Ct Pre-Catalytic Ground State Ternary Complex, 20 Mm CA2+ (120MIN) To Be Published.
Page generated: Mon Aug 18 10:34:54 2025

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