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Sodium in PDB 7ksz: Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN)

Enzymatic activity of Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN)

All present enzymatic activity of Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN), PDB code: 7ksz 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) 32.83 / 1.42
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.753, 68.778, 110.133, 90, 90, 90
R / Rfree (%) 15.7 / 17.5

Other elements in 7ksz:

The structure of Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN) also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN) (pdb code 7ksz). 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:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN), PDB code: 7ksz:

Sodium binding site 1 out of 1 in 7ksz

Go back to Sodium Binding Sites List in 7ksz
Sodium binding site 1 out of 1 in the Dna Polymerase Mu, Dgtp:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (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:at Pre-Catalytic Ground State Ternary Complex, 10 Mm CA2+ (960MIN) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na506

b:15.2
occ:1.00
 O A:VAL246 2.3 15.2 1.0
O A:THR241 2.3 17.6 1.0
O A:HOH645 2.4 32.4 1.0
O A:ILE243 2.4 16.4 1.0
O P:HOH212 2.4 25.1 1.0
OP1 P:DT3 2.6 14.8 1.0
C A:VAL246 3.4 15.1 1.0
C A:ILE243 3.4 18.4 1.0
C A:THR241 3.4 16.0 1.0
P P:DT3 3.6 14.5 1.0
N A:VAL246 3.8 14.7 1.0
OP2 P:DT3 3.9 15.0 1.0
O P:HOH210 4.1 33.1 1.0
CA A:VAL246 4.1 14.8 1.0
N A:ILE243 4.1 16.1 1.0
C A:GLN242 4.1 19.5 0.5
C A:GLN242 4.2 19.5 0.5
N A:PHE244 4.2 15.8 1.0
CA A:THR241 4.2 17.1 1.0
O A:HOH840 4.2 42.2 1.0
CA A:PHE244 4.2 15.4 1.0
N A:GLY245 4.2 14.7 1.0
CA A:ILE243 4.4 15.0 1.0
N A:GLN242 4.4 17.8 0.5
N A:GLN242 4.4 18.1 0.5
N A:GLY247 4.4 16.1 1.0
O A:GLN242 4.4 21.4 0.5
CA A:GLN242 4.4 19.6 0.5
CB A:VAL246 4.5 16.0 1.0
CA A:GLN242 4.5 19.1 0.5
O A:HOH878 4.5 37.8 1.0
O A:GLN242 4.5 22.3 0.5
N2 A:DGT511 4.6 49.0 0.6
C A:PHE244 4.6 14.7 1.0
O3' P:DG2 4.7 14.4 1.0
CA A:GLY247 4.7 15.0 1.0
O A:PHE240 4.8 15.8 1.0
C A:GLY245 4.8 12.8 1.0
O5' P:DT3 4.8 14.5 1.0
CB A:THR241 4.9 16.0 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 17:27:17 2024

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