Potassium in PDB 8dfb: Structure of M. Kandleri Topoisomerase V in Complex with Dna. 39 Base Pair Symmetric Dna Complex

The structure of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 39 Base Pair Symmetric Dna Complex, PDB code: 8dfb 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)	59.04 / 3.17
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.56, 121.56, 497.191, 90, 90, 90
R / Rfree (%)	21.9 / 25.1

The binding sites of Potassium atom in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 39 Base Pair Symmetric Dna Complex (pdb code 8dfb). 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. 39 Base Pair Symmetric Dna Complex, PDB code: 8dfb:
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. 39 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. 39 Base Pair Symmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:K901 b:101.5 occ:1.00 O A:ILE740 3.0 65.2 1.0 O A:VAL737 3.1 93.3 1.0 O A:LEU735 3.3 70.0 1.0 CA A:PRO738 4.0 68.7 1.0 N A:GLY739 4.0 63.9 1.0 C A:ILE740 4.0 70.8 1.0 C A:VAL737 4.1 78.2 1.0 N A:ILE740 4.2 55.4 1.0 O B:HIS373 4.3 73.4 1.0 N A:PRO738 4.4 60.8 1.0 C A:PRO738 4.5 64.7 1.0 C A:LEU735 4.6 71.1 1.0 CA A:ILE740 4.7 67.3 1.0 C A:GLY739 4.9 59.9 1.0 N A:GLY741 5.0 62.0 1.0 CA A:GLY739 5.0 57.1 1.0 C A:GLU736 5.0 64.7 1.0

Potassium binding site 2 out of 4 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 39 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. 39 Base Pair Symmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:K902 b:137.4 occ:1.00 O A:ILE471 3.0 81.8 1.0 O A:ILE473 3.7 89.9 1.0 O B:ASP303 3.7 95.8 1.0 O A:ILE476 3.7 95.0 1.0 C A:ILE471 4.3 86.5 1.0 CD1 A:ILE471 4.5 91.8 1.0 C A:ILE473 4.6 90.0 1.0 N A:GLY475 4.7 83.5 1.0 C B:ASP303 4.7 81.6 1.0 CG1 A:ILE471 4.7 84.4 1.0 C A:ILE476 4.8 98.7 1.0 N A:ILE476 4.9 98.6 1.0 CA B:ASP303 4.9 73.2 1.0 CA A:ARG474 5.0 102.2 1.0

Potassium binding site 3 out of 4 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 39 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. 39 Base Pair Symmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K901 b:127.8 occ:1.00 O B:LEU735 2.8 77.2 1.0 O B:ILE740 3.2 71.2 1.0 O B:VAL737 3.3 84.8 1.0 C B:LEU735 4.0 82.2 1.0 C B:VAL737 4.2 72.0 1.0 CA B:PRO738 4.3 73.9 1.0 C B:ILE740 4.3 65.6 1.0 N B:PRO738 4.6 68.0 1.0 N B:GLY739 4.6 63.8 1.0 N B:ILE740 4.7 66.6 1.0 C B:GLU736 4.7 75.9 1.0 O B:GLU736 4.8 85.5 1.0 CA B:LEU735 4.8 75.2 1.0 N B:VAL737 4.9 62.4 1.0 CA B:GLU736 5.0 79.7 1.0 C B:PRO738 5.0 77.0 1.0 N B:GLU736 5.0 74.8 1.0

Potassium binding site 4 out of 4 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 39 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. 39 Base Pair Symmetric Dna Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:K902 b:118.9 occ:1.00 O B:ILE471 3.1 69.6 1.0 O B:ILE473 3.3 95.7 1.0 O B:ILE476 3.5 109.3 1.0 O A:ASP303 4.0 98.9 1.0 N B:GLY475 4.2 99.5 1.0 C B:ILE473 4.2 93.7 1.0 C B:ILE471 4.3 87.8 1.0 N B:ILE476 4.4 105.8 1.0 C B:ILE476 4.4 95.4 1.0 CA B:ARG474 4.6 94.4 1.0 CD1 B:ILE471 4.6 78.2 1.0 C B:ARG474 4.8 99.8 1.0 N B:ARG474 4.8 89.0 1.0 N B:ILE473 4.9 106.4 1.0 CG1 B:ILE471 4.9 74.8 1.0 C B:SER472 4.9 99.3 1.0 C A:ASP303 4.9 79.0 1.0 CA B:ILE476 4.9 91.5 1.0 C B:GLY475 5.0 103.2 1.0 CA B:GLY475 5.0 106.0 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