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Sodium in PDB 7kt4: Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)

Enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)

All present enzymatic activity of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN), PDB code: 7kt4 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) 21.43 / 1.92
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.119, 68.819, 110.296, 90, 90, 90
R / Rfree (%) 16.6 / 20.4

Other elements in 7kt4:

The structure of Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) also contains other interesting chemical elements:

Manganese (Mn) 4 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) (pdb code 7kt4). 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:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN), PDB code: 7kt4:

Sodium binding site 1 out of 1 in 7kt4

Go back to Sodium Binding Sites List in 7kt4
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN)


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:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:22.6
occ:1.00
 O A:VAL246 2.3 24.5 1.0
O A:ILE243 2.3 17.9 1.0
O A:HOH804 2.4 26.5 1.0
O A:THR241 2.4 23.6 1.0
O P:HOH215 2.5 25.5 1.0
OP1 P:DT3 2.7 22.1 1.0
C A:ILE243 3.3 26.2 1.0
C A:VAL246 3.4 21.2 1.0
C A:THR241 3.5 25.3 1.0
O P:HOH211 3.6 30.5 1.0
N A:VAL246 3.7 23.6 1.0
P P:DT3 3.7 22.0 1.0
OP2 P:DT3 3.8 19.2 1.0
N A:ILE243 3.9 21.1 1.0
CA A:VAL246 4.0 25.2 1.0
N A:PHE244 4.1 24.6 1.0
C A:GLN242 4.1 25.8 1.0
N A:GLY245 4.2 20.6 1.0
CA A:PHE244 4.2 22.8 1.0
CA A:THR241 4.3 23.5 1.0
CA A:ILE243 4.3 24.5 1.0
N A:GLN242 4.4 24.1 1.0
O A:HOH827 4.4 36.4 1.0
N A:GLY247 4.4 24.2 1.0
CB A:VAL246 4.4 27.8 1.0
CA A:GLN242 4.5 23.3 1.0
C A:PHE244 4.6 21.4 1.0
O A:GLN242 4.6 21.2 1.0
O3' P:DG2 4.6 21.3 1.0
C A:GLY245 4.7 30.3 1.0
O A:PHE240 4.7 23.8 1.0
CA A:GLY247 4.8 19.5 1.0
O5' P:DT3 4.9 18.1 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, 8-Oxodgtp:at Reaction State Ternary Complex, 10 Mm MN2+ (30MIN) To Be Published.
Page generated: Tue Oct 8 17:28:15 2024

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