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Manganese in PDB 8s84: Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate

Enzymatic activity of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate

All present enzymatic activity of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate:
2.7.7.7;

Protein crystallography data

The structure of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate, PDB code: 8s84 was solved by C.Gutfreund, K.Betz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.58 / 2.35
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 110.97, 152.462, 70.125, 90, 90, 90
R / Rfree (%) 23.7 / 27.6

Other elements in 8s84:

The structure of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate (pdb code 8s84). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate, PDB code: 8s84:

Manganese binding site 1 out of 1 in 8s84

Go back to Manganese Binding Sites List in 8s84
Manganese binding site 1 out of 1 in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Kod-H4 Dna Polymerase Mutant in A Ternary Complex with Dna/Dna and Non-Hydrolyzable Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn807

b:75.6
occ:1.00
 OE2 A:GLU500 2.1 60.9 1.0
OP1 T:DT4 2.1 49.3 1.0
CD A:GLU500 2.8 80.3 1.0
OE1 A:GLU500 3.0 69.0 1.0
P T:DT4 3.3 56.5 1.0
O5' T:DT4 3.7 66.1 1.0
OP2 T:DG5 3.8 66.5 1.0
O T:HOH202 3.8 60.0 1.0
OP2 T:DT4 3.9 63.5 1.0
C5' T:DT4 4.1 56.5 1.0
CG A:GLU500 4.2 83.0 1.0
O3' T:DC3 4.6 55.4 1.0
O A:GLY498 4.7 62.3 1.0
P T:DG5 4.7 58.8 1.0
O3' T:DT4 4.9 54.3 1.0
C3' T:DT4 4.9 49.6 1.0
N A:GLU500 5.0 59.2 1.0

Reference:

C.Gutfreund, K.Betz. Structural Insights Into A Dna Polymerase Reading the Xeno Nucleic Acid Hna Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
Page generated: Wed Nov 27 20:28:02 2024

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