Potassium in PDB 8df9: Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Asymmetric Dna Complex

The structure of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Asymmetric Dna Complex, PDB code: 8df9 was solved by A.Osterman, A.Mondragon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.28 / 3.24
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	193.751, 193.751, 245.979, 90, 90, 90
R / Rfree (%)	23.5 / 26.6

The structure of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Asymmetric Dna Complex also contains other interesting chemical elements:

Magnesium

(Mg)

12 atoms

The binding sites of Potassium atom in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Asymmetric Dna Complex (pdb code 8df9). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Asymmetric Dna Complex, PDB code: 8df9:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Asymmetric Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Asymmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ S:K101 b:132.0 occ:1.00 O4' T:DT20 3.2 136.8 1.0 O4' S:DT22 3.2 123.3 1.0 C4' S:DT22 3.4 123.7 1.0 O2 T:DT19 3.4 132.9 1.0 O2 S:DT21 3.4 136.6 1.0 C5' S:DT22 3.7 126.3 1.0 C4' T:DT20 3.7 136.3 1.0 C5' T:DT20 4.2 135.1 1.0 C1' S:DT22 4.3 124.0 1.0 C1' T:DT20 4.3 137.3 1.0 C1' S:DT21 4.5 135.4 1.0 O2 T:DT20 4.5 139.6 1.0 C2 T:DT19 4.5 133.4 1.0 C2 S:DT21 4.5 135.8 1.0 C1' T:DT19 4.8 133.4 1.0 C3' S:DT22 4.8 121.4 1.0 N1 T:DT20 4.8 137.9 1.0 C2 T:DT20 4.9 138.9 1.0

Potassium binding site 2 out of 2 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Asymmetric Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Asymmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ T:K101 b:118.7 occ:1.00 O4' T:DT13 2.9 114.8 1.0 O2 T:DT12 2.9 124.7 1.0 O2 S:DT28 3.0 134.9 1.0 O4' S:DC29 3.2 129.5 1.0 C1' T:DT13 3.4 115.3 1.0 C4' T:DT13 3.6 113.8 1.0 N1 T:DT13 3.9 116.9 1.0 O2 T:DT13 4.0 117.2 1.0 C4' S:DC29 4.0 128.6 1.0 C2 S:DT28 4.1 134.7 1.0 C2 T:DT12 4.1 124.3 1.0 C1' S:DC29 4.2 130.0 1.0 C2 T:DT13 4.2 117.4 1.0 C1' S:DT28 4.3 133.4 1.0 C2 S:DA27 4.3 131.2 1.0 C5' S:DC29 4.5 129.0 1.0 N1 S:DC29 4.5 131.4 1.0 O3' T:DT13 4.6 113.7 1.0 C3' T:DT13 4.6 114.1 1.0 O4' S:DT28 4.6 133.2 1.0 N1 S:DT28 4.6 134.5 1.0 C1' T:DT12 4.6 121.2 1.0 C5' T:DT13 4.7 112.4 1.0 C2' T:DT13 4.7 114.5 1.0 O2 S:DC29 4.7 133.1 1.0 C2 T:DA11 4.7 134.1 1.0 C2 S:DC29 4.8 132.3 1.0 C6 T:DT13 4.8 118.6 1.0 N3 S:DA27 4.9 131.7 1.0 N1 T:DT12 4.9 123.1 1.0

A.Osterman, A.Mondragon. Structures of Topoisomerase V in Complex with Dna Reveal Unusual Dna Binding Mode and Novel Relaxation Mechanism. Elife V. 11 2022.
ISSN: ESSN 2050-084X
PubMed: 35969036
DOI: 10.7554/ELIFE.72702