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Potassium in PDB 8df7: Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Symmetric Dna Complex

Protein crystallography data

The structure of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Symmetric Dna Complex, PDB code: 8df7 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) 59.10 / 3.52
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.665, 121.665, 498.82, 90, 90, 90
R / Rfree (%) 22.9 / 27.5

Potassium Binding Sites:

The binding sites of Potassium atom in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Symmetric Dna Complex (pdb code 8df7). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Symmetric Dna Complex, PDB code: 8df7:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 8df7

Go back to Potassium Binding Sites List in 8df7
Potassium binding site 1 out of 5 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 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. 38 Base Pair Symmetric Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K901

b:10.0
occ:1.00
 O A:ILE740 2.9 78.0 1.0
O A:VAL737 3.0 77.8 1.0
O A:LEU735 3.3 67.9 1.0
C A:ILE740 3.9 87.7 1.0
N A:GLY739 4.0 137.0 1.0
N A:ILE740 4.0 66.3 1.0
C A:VAL737 4.1 86.9 1.0
CA A:PRO738 4.2 79.5 1.0
O B:HIS373 4.4 77.6 1.0
C A:LEU735 4.5 95.8 1.0
C A:PRO738 4.5 70.6 1.0
CA A:ILE740 4.5 89.8 1.0
N A:PRO738 4.5 82.1 1.0
C A:GLY739 4.8 59.8 1.0
N A:GLY741 4.8 73.5 1.0
CA A:GLY739 4.9 84.9 1.0
CA A:GLY741 4.9 85.3 1.0
N A:VAL737 5.0 75.9 1.0

Potassium binding site 2 out of 5 in 8df7

Go back to Potassium Binding Sites List in 8df7
Potassium binding site 2 out of 5 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 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. 38 Base Pair Symmetric Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K902

b:39.7
occ:1.00
 O A:PHE576 3.4 104.6 1.0
C A:PHE576 4.1 85.5 1.0
O A:GLU574 4.4 132.8 1.0
O A:ALA575 4.5 109.0 1.0
N A:ASP577 4.7 98.1 1.0
O A:ARG573 4.8 98.9 1.0
C A:ALA575 4.8 82.7 1.0
C A:GLU574 4.8 124.5 1.0
CA A:ASP577 4.9 114.2 1.0
CA A:PHE576 4.9 94.6 1.0
N A:PHE576 5.0 92.8 1.0

Potassium binding site 3 out of 5 in 8df7

Go back to Potassium Binding Sites List in 8df7
Potassium binding site 3 out of 5 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 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. 38 Base Pair Symmetric Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K901

b:22.5
occ:1.00
 O B:LEU735 2.9 81.9 1.0
O B:ILE740 2.9 77.3 1.0
O B:VAL737 3.0 96.5 1.0
C B:VAL737 4.0 84.7 1.0
C B:ILE740 4.0 93.2 1.0
C B:LEU735 4.1 100.7 1.0
N B:ILE740 4.2 82.3 1.0
N B:GLY739 4.2 96.2 1.0
CA B:PRO738 4.2 92.2 1.0
N B:PRO738 4.5 78.7 1.0
CA B:ILE740 4.6 75.6 1.0
C B:PRO738 4.6 88.0 1.0
N B:VAL737 4.7 80.5 1.0
CA B:LEU735 4.8 105.1 1.0
C B:GLU736 4.8 74.3 1.0
N B:GLY741 4.9 75.4 1.0
C B:GLY739 5.0 75.5 1.0

Potassium binding site 4 out of 5 in 8df7

Go back to Potassium Binding Sites List in 8df7
Potassium binding site 4 out of 5 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 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. 38 Base Pair Symmetric Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K902

b:38.3
occ:1.00
 O B:ILE473 3.0 100.0 1.0
O B:ILE476 3.1 107.3 1.0
O B:ILE471 3.4 78.4 1.0
C B:ILE473 4.0 106.7 1.0
N B:GLY475 4.1 127.5 1.0
C B:ILE476 4.1 112.9 1.0
O A:ASP303 4.1 96.3 1.0
CA B:ARG474 4.2 140.6 1.0
N B:ILE476 4.3 125.0 1.0
C B:ARG474 4.5 105.0 1.0
N B:ARG474 4.5 123.7 1.0
C B:ILE471 4.5 102.7 1.0
CD1 B:ILE471 4.7 131.8 1.0
CA B:ILE476 4.7 98.4 1.0
C B:GLY475 4.8 112.1 1.0
N B:ILE473 4.8 167.3 1.0
CG1 B:ILE471 4.9 97.0 1.0
CA B:GLY475 4.9 122.3 1.0

Potassium binding site 5 out of 5 in 8df7

Go back to Potassium Binding Sites List in 8df7
Potassium binding site 5 out of 5 in the Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 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 5 of Structure of M. Kandleri Topoisomerase V in Complex with Dna. 38 Base Pair Symmetric Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K903

b:48.1
occ:1.00
 O B:PHE576 3.6 92.2 1.0
O B:GLU574 3.8 95.3 1.0
O B:ALA575 3.9 146.4 1.0
C B:PHE576 4.3 116.3 1.0
C B:ALA575 4.4 112.0 1.0
C B:GLU574 4.5 103.0 1.0
N B:PHE576 4.8 108.9 1.0
CA B:PHE576 4.8 128.8 1.0

Reference:

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
Page generated: Sat Aug 9 16:43:16 2025

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