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Sodium in PDB 7ktk: Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN)

Enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN)

All present enzymatic activity of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN), PDB code: 7ktk 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) 33.19 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.109, 61.775, 118.076, 90, 90, 90
R / Rfree (%) 14.3 / 16.8

Other elements in 7ktk:

The structure of Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN) (pdb code 7ktk). 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 (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN), PDB code: 7ktk:

Sodium binding site 1 out of 1 in 7ktk

Go back to Sodium Binding Sites List in 7ktk
Sodium binding site 1 out of 1 in the Dna Polymerase Mu (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN)


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 (K438D), 8-Oxodgtp:Ct Ground State Ternary Complex, 50 Mm MG2+ (90MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na504

b:15.7
occ:1.00
 O A:VAL246 2.3 15.5 1.0
O P:HOH111 2.4 22.3 1.0
O A:THR241 2.4 18.4 1.0
O A:ILE243 2.4 15.8 1.0
O P:HOH104 2.5 22.3 1.0
OP1 P:DT3 2.5 15.5 1.0
C A:VAL246 3.4 14.6 1.0
C A:ILE243 3.5 15.7 1.0
C A:THR241 3.5 17.0 1.0
P P:DT3 3.6 15.5 1.0
N A:VAL246 3.7 15.6 1.0
OP2 P:DT3 3.9 16.4 1.0
CA A:VAL246 4.1 15.8 1.0
N A:ILE243 4.1 16.6 1.0
N A:GLY245 4.1 15.0 1.0
CA A:THR241 4.2 16.7 1.0
N A:PHE244 4.2 15.1 1.0
CA A:PHE244 4.3 15.4 1.0
C A:GLN242 4.3 18.0 1.0
CA A:ILE243 4.4 16.3 1.0
N A:GLY247 4.5 15.3 1.0
N A:GLN242 4.5 18.2 1.0
CB A:VAL246 4.5 15.5 1.0
C A:PHE244 4.6 16.3 1.0
CA A:GLN242 4.6 19.4 1.0
O3' P:DG2 4.6 15.4 1.0
O3' P:DA4 4.6 23.5 0.8
O A:GLN242 4.7 19.5 1.0
C3' P:DA4 4.7 19.8 0.8
C A:GLY245 4.7 15.1 1.0
O P:HOH115 4.7 27.5 1.0
OP2 P:DA4 4.7 18.1 0.8
CA A:GLY247 4.8 16.0 1.0
O5' P:DT3 4.8 15.7 1.0
O A:PHE240 4.8 16.6 1.0
CB A:THR241 4.9 17.0 1.0

Reference:

J.A.Jamsen, A.Sassa, D.D.Shock, W.A.Beard, S.H.Wilson. Watching A Double Strand Break Repair Polymerase Insert A Pro-Mutagenic Oxidized Nucleotide. Nat Commun V. 12 2059 2021.
ISSN: ESSN 2041-1723
PubMed: 33824325
DOI: 10.1038/S41467-021-21354-6
Page generated: Tue Oct 8 17:30:10 2024

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