Potassium in PDB 8df8: Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric Dna Complex

The structure of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric Dna Complex, PDB code: 8df8 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)	58.76 / 2.92
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.941, 120.941, 497.569, 90, 90, 90
R / Rfree (%)	25.7 / 28.8

The binding sites of Potassium atom in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric Dna Complex (pdb code 8df8). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric Dna Complex, PDB code: 8df8:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric 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. 40 Base Pair Symmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:K901 b:95.2 occ:1.00 O A:ILE740 3.0 47.4 1.0 O A:VAL737 3.3 56.7 1.0 O A:LEU735 3.6 50.0 1.0 C A:ILE740 4.0 47.5 1.0 N A:GLY739 4.0 43.6 1.0 CA A:PRO738 4.1 44.1 1.0 N A:ILE740 4.1 40.7 1.0 C A:VAL737 4.2 49.2 1.0 O B:HIS373 4.2 47.6 1.0 N A:PRO738 4.5 42.7 1.0 C A:PRO738 4.5 46.2 1.0 CA A:ILE740 4.7 39.6 1.0 O A:GLU736 4.7 34.4 1.0 C A:LEU735 4.8 48.5 1.0 N A:GLY741 4.9 41.9 1.0 C A:GLY739 5.0 38.0 1.0 C B:HIS373 5.0 45.2 1.0 CA A:GLY739 5.0 42.1 1.0

Potassium binding site 2 out of 4 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric 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. 40 Base Pair Symmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:K902 b:109.3 occ:1.00 O A:ILE473 3.4 87.0 1.0 O A:ILE476 3.5 86.5 1.0 O A:ILE471 3.6 74.2 1.0 N A:GLY475 4.0 86.9 1.0 CA A:ARG474 4.2 79.6 1.0 C A:ILE473 4.2 75.5 1.0 C A:ILE476 4.3 79.0 1.0 O B:ASP303 4.4 78.1 1.0 C A:ARG474 4.5 81.2 1.0 N A:ILE476 4.6 79.0 1.0 N A:ARG474 4.6 68.3 1.0 C A:GLY475 4.8 91.4 1.0 C A:ILE471 4.8 70.5 1.0 CA A:GLY475 4.8 93.8 1.0

Potassium binding site 3 out of 4 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K902 b:89.0 occ:1.00 O B:LEU735 2.8 58.7 1.0 O B:ILE740 3.0 55.4 1.0 O B:VAL737 3.3 59.4 1.0 C B:LEU735 4.0 59.4 1.0 C B:ILE740 4.1 55.7 1.0 C B:VAL737 4.2 39.3 1.0 O B:GLU736 4.3 56.5 1.0 CA B:PRO738 4.4 44.6 1.0 N B:ILE740 4.4 42.0 1.0 C B:GLU736 4.5 41.3 1.0 N B:GLY739 4.6 48.2 1.0 N B:PRO738 4.6 38.4 1.0 CA B:LEU735 4.7 56.1 1.0 CA B:ILE740 4.8 43.1 1.0 N B:VAL737 4.9 34.9 1.0 N B:GLU736 5.0 50.2 1.0 C B:PRO738 5.0 45.1 1.0

Potassium binding site 4 out of 4 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric Dna Complex


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 40 Base Pair Symmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K903 b:114.1 occ:1.00 O B:ILE471 3.3 48.7 1.0 O B:ILE476 3.7 92.3 1.0 O B:ILE473 3.7 90.8 1.0 O A:ASP303 4.0 101.8 1.0 C B:ILE473 4.5 76.2 1.0 CA B:ARG474 4.5 89.6 1.0 C B:ILE471 4.5 75.5 1.0 N B:GLY475 4.6 89.3 1.0 C B:ILE476 4.7 75.0 1.0 CD1 B:ILE471 4.7 81.4 1.0 N B:ARG474 4.9 72.3 1.0 C A:ASP303 4.9 81.9 1.0 CG1 B:ILE471 5.0 75.6 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