Sodium in PDB 7ksv: Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)

Enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7ksv 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) 34.95 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.002, 68.825, 110.101, 90, 90, 90
R / Rfree (%) 16.2 / 18.8

Other elements in 7ksv:

The structure of Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) (pdb code 7ksv). 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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN), PDB code: 7ksv:

Sodium binding site 1 out of 1 in 7ksv

Go back to Sodium Binding Sites List in 7ksv
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN)


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, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:24.9
occ:1.00
 O A:VAL246 2.3 24.4 1.0
O A:THR241 2.3 25.2 1.0
O A:ILE243 2.4 25.4 1.0
O P:HOH116 2.4 26.5 1.0
O A:HOH812 2.4 29.0 1.0
OP1 P:DT3 2.6 23.5 1.0
C A:VAL246 3.4 29.4 1.0
C A:THR241 3.4 29.8 1.0
C A:ILE243 3.4 23.4 1.0
P P:DT3 3.7 22.7 1.0
N A:VAL246 3.7 24.1 1.0
O P:HOH115 3.8 31.5 1.0
OP2 P:DT3 3.9 20.9 1.0
CA A:VAL246 4.0 25.5 1.0
N A:ILE243 4.0 24.2 1.0
O A:HOH763 4.1 40.6 1.0
C A:GLN242 4.2 28.1 1.0
CA A:THR241 4.2 25.2 1.0
N A:PHE244 4.2 26.5 1.0
CA A:PHE244 4.3 26.7 1.0
N A:GLY245 4.3 24.4 1.0
N A:GLN242 4.3 24.7 1.0
CA A:ILE243 4.3 24.5 1.0
CB A:VAL246 4.4 26.2 1.0
N A:GLY247 4.4 25.1 1.0
CA A:GLN242 4.4 27.8 1.0
O A:GLN242 4.6 32.5 1.0
C A:PHE244 4.6 24.7 1.0
O3' P:DG2 4.7 22.4 1.0
O A:PHE240 4.7 26.0 1.0
CA A:GLY247 4.7 26.8 1.0
C A:GLY245 4.8 26.1 1.0
CB A:THR241 4.9 22.9 1.0
O5' P:DT3 4.9 21.3 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Mu, Dgtp:Ct Product State Ternary Complex, 10 Mm MN2+ (960MIN) To Be Published.
Page generated: Tue Oct 8 17:26:40 2024

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