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

Protein crystallography data

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

Other elements in 8df9:

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:

Potassium (K) 2 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 12 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 8df9

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Magnesium binding site 1 out of 12 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 Magnesium with other atoms in the Mg 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
A:Mg901

b:120.2
occ:1.00
 O A:ALA450 2.4 120.5 1.0
O A:VAL455 3.0 114.5 1.0
O A:VAL452 3.4 113.4 1.0
C A:ALA450 3.5 120.5 1.0
C A:VAL455 4.0 114.5 1.0
CA A:ALA450 4.2 120.5 1.0
N A:VAL455 4.2 114.5 1.0
C A:VAL452 4.5 113.4 1.0
CA A:VAL455 4.5 114.5 1.0
CB A:ALA450 4.5 121.3 1.0
N A:SER451 4.6 116.2 1.0
N A:GLY454 4.7 118.6 1.0
CB A:VAL455 4.7 116.9 1.0
C A:SER451 4.7 116.2 1.0
CA A:SER451 4.8 116.2 1.0
N A:VAL452 4.9 113.4 1.0
N A:GLY456 5.0 121.0 1.0
O A:SER451 5.0 116.2 1.0

Magnesium binding site 2 out of 12 in 8df9

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Magnesium binding site 2 out of 12 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 Magnesium with other atoms in the Mg 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
A:Mg902

b:108.8
occ:1.00
 O A:THR414 2.6 97.1 1.0
O A:LYS416 2.8 105.3 1.0
O A:VAL419 3.5 103.4 1.0
C A:LYS416 3.7 105.3 1.0
C A:THR414 3.8 97.1 1.0
C A:LYS415 4.0 104.7 1.0
O A:LYS415 4.0 104.7 1.0
CA A:GLU417 4.3 115.2 1.0
N A:LYS416 4.3 105.3 1.0
CA A:LYS415 4.3 104.7 1.0
N A:GLY418 4.4 110.0 1.0
N A:GLU417 4.4 115.2 1.0
N A:LYS415 4.5 104.7 1.0
C A:VAL419 4.5 103.4 1.0
N A:VAL419 4.6 103.4 1.0
CA A:LYS416 4.7 105.3 1.0
C A:GLU417 4.8 115.2 1.0
CA A:THR414 4.8 97.1 1.0

Magnesium binding site 3 out of 12 in 8df9

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Magnesium binding site 3 out of 12 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 Magnesium with other atoms in the Mg binding site number 3 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
A:Mg903

b:150.2
occ:1.00
 O A:ILE476 2.2 151.8 1.0
O A:ILE471 2.7 140.0 1.0
O A:ILE473 2.9 155.3 1.0
C A:ILE476 3.3 151.8 1.0
C A:ILE471 3.7 140.0 1.0
N A:ILE476 3.8 151.8 1.0
CD1 A:ILE471 4.0 143.5 1.0
CA A:ILE476 4.0 151.8 1.0
C A:ILE473 4.0 155.3 1.0
CG1 A:ILE471 4.2 143.5 1.0
N A:ASP477 4.3 148.0 1.0
CA A:ILE471 4.3 140.0 1.0
N A:GLY475 4.3 161.6 1.0
CB A:ILE476 4.4 154.3 1.0
CA A:ASP477 4.5 148.0 1.0
CA A:ARG474 4.6 166.0 1.0
C A:GLY475 4.6 161.6 1.0
N A:ILE473 4.7 155.3 1.0
C A:ARG474 4.7 166.0 1.0
N A:ARG474 4.8 166.0 1.0
C A:SER472 4.8 146.1 1.0
N A:SER472 4.8 146.1 1.0
CB A:ILE471 4.9 143.5 1.0

Magnesium binding site 4 out of 12 in 8df9

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Magnesium binding site 4 out of 12 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 Magnesium with other atoms in the Mg binding site number 4 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
A:Mg904

b:105.7
occ:1.00
 O A:HOH1002 2.2 99.2 1.0
O A:HOH1004 2.2 107.3 1.0
O A:HOH1005 2.2 106.8 1.0
O A:HOH1010 2.2 108.8 1.0
O A:HOH1003 2.2 102.8 1.0
O A:HOH1007 2.2 107.4 1.0
OD2 A:ASP384 3.8 109.7 1.0
OD1 A:ASP384 4.0 109.7 1.0
OE1 A:GLU221 4.3 98.6 1.0
CG A:ASP384 4.3 109.7 1.0
O A:PHE431 4.4 106.0 1.0
OE2 A:GLU221 4.6 98.3 1.0
CD A:GLU221 4.9 97.9 1.0

Magnesium binding site 5 out of 12 in 8df9

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Magnesium binding site 5 out of 12 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 Magnesium with other atoms in the Mg binding site number 5 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
A:Mg905

b:141.1
occ:1.00
 O A:HOH1001 2.2 141.1 1.0
O A:HOH1011 2.2 141.1 1.0
O A:HOH1009 2.2 141.1 1.0
O A:HOH1008 2.2 141.1 1.0
O A:GLU393 4.1 129.6 1.0

Magnesium binding site 6 out of 12 in 8df9

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Magnesium binding site 6 out of 12 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 Magnesium with other atoms in the Mg binding site number 6 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
B:Mg901

b:154.8
occ:1.00
 O B:ILE473 2.2 155.1 1.0
OP1 S:DT14 2.6 196.1 1.0
O B:ILE471 2.6 141.1 1.0
O B:ILE476 2.9 153.3 1.0
C B:ILE473 3.1 155.1 1.0
C B:ILE471 3.7 141.1 1.0
P S:DT14 3.8 196.0 1.0
CA B:ARG474 3.8 174.7 1.0
N B:ILE476 3.8 153.3 1.0
N B:ARG474 3.8 174.7 1.0
C B:ILE476 3.9 153.3 1.0
N B:GLY475 3.9 166.3 1.0
N B:ILE473 4.0 155.1 1.0
C B:SER472 4.0 144.9 1.0
C B:ARG474 4.1 174.7 1.0
CA B:ILE473 4.2 155.1 1.0
O5' S:DT14 4.3 192.1 1.0
CA B:ILE476 4.3 153.3 1.0
O B:SER472 4.3 144.9 1.0
OP2 S:DT14 4.4 195.6 1.0
CA B:ILE471 4.5 141.1 1.0
N B:SER472 4.5 144.9 1.0
CA B:SER472 4.5 144.9 1.0
CB B:ILE476 4.6 156.2 1.0
C B:GLY475 4.6 166.3 1.0
O B:LEU470 4.8 143.6 1.0
C5' S:DT14 4.8 188.1 1.0
CA B:GLY475 4.8 166.3 1.0
CD1 B:ILE471 4.9 143.7 1.0
CG1 B:ILE471 4.9 143.7 1.0
N B:ASP477 5.0 149.9 1.0
O B:ARG474 5.0 174.7 1.0

Magnesium binding site 7 out of 12 in 8df9

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Magnesium binding site 7 out of 12 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 Magnesium with other atoms in the Mg binding site number 7 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
B:Mg902

b:118.0
occ:1.00
 O B:ALA450 2.2 122.2 1.0
O B:VAL452 3.3 118.1 1.0
OP1 T:DG21 3.3 139.8 1.0
C B:ALA450 3.4 122.2 1.0
OP2 T:DG21 3.4 140.3 1.0
P T:DG21 3.6 140.3 1.0
O5' T:DG21 3.9 143.4 1.0
O B:VAL455 3.9 116.4 1.0
C B:SER451 4.1 118.6 1.0
C B:VAL452 4.2 118.1 1.0
O B:SER451 4.2 118.6 1.0
CA B:SER451 4.3 118.6 1.0
N B:SER451 4.3 118.6 1.0
CA B:ALA450 4.3 122.2 1.0
N B:VAL452 4.5 118.1 1.0
CB B:ALA450 4.7 123.3 1.0
N B:VAL455 4.7 116.4 1.0
C B:VAL455 4.8 116.4 1.0
N B:GLY454 4.8 122.3 1.0
CA B:GLU453 4.9 125.5 1.0
N B:GLU453 4.9 125.5 1.0
C5' T:DG21 4.9 146.2 1.0

Magnesium binding site 8 out of 12 in 8df9

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Magnesium binding site 8 out of 12 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 Magnesium with other atoms in the Mg binding site number 8 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
B:Mg903

b:106.3
occ:1.00
 O B:THR414 2.4 103.7 1.0
O B:LYS416 2.7 110.4 1.0
OP2 S:DG24 2.8 115.5 1.0
O B:VAL419 3.5 109.8 1.0
C B:THR414 3.6 103.7 1.0
C B:LYS416 3.6 110.4 1.0
P S:DG24 3.7 115.6 1.0
OP1 S:DG24 3.7 115.4 1.0
C B:LYS415 3.9 106.6 1.0
O B:LYS415 4.0 106.6 1.0
N B:LYS416 4.2 110.4 1.0
CA B:LYS415 4.3 106.6 1.0
CA B:GLU417 4.3 116.4 1.0
N B:LYS415 4.4 106.6 1.0
O5' S:DG24 4.4 116.6 1.0
N B:GLU417 4.4 116.4 1.0
N B:GLY418 4.4 115.2 1.0
C B:VAL419 4.5 109.8 1.0
CA B:THR414 4.5 103.7 1.0
N B:VAL419 4.6 109.8 1.0
CA B:LYS416 4.6 110.4 1.0
C B:GLU417 4.8 116.4 1.0

Magnesium binding site 9 out of 12 in 8df9

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Magnesium binding site 9 out of 12 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 Magnesium with other atoms in the Mg binding site number 9 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
B:Mg904

b:160.5
occ:1.00
 OP1 S:DG17 2.0 167.1 1.0
O B:ILE740 2.6 177.8 1.0
O B:VAL737 2.9 184.3 1.0
O B:LEU735 3.0 182.0 1.0
P S:DG17 3.2 167.1 1.0
OP2 S:DG17 3.4 167.1 1.0
C B:ILE740 3.6 177.8 1.0
N B:ILE740 3.8 177.8 1.0
C B:VAL737 3.9 184.3 1.0
C B:LEU735 4.1 182.0 1.0
O3' S:DA16 4.1 171.0 1.0
CA B:PRO738 4.1 183.0 1.0
N B:GLY739 4.1 179.2 1.0
CA B:ILE740 4.2 177.8 1.0
O5' S:DG17 4.4 166.9 1.0
N B:PRO738 4.4 183.0 1.0
C B:PRO738 4.6 183.0 1.0
CB B:ILE740 4.6 180.7 1.0
CA B:LEU735 4.7 182.0 1.0
N B:GLY741 4.7 176.9 1.0
C B:GLU736 4.7 184.5 1.0
N B:VAL737 4.7 184.3 1.0
O B:GLU736 4.8 184.5 1.0
C B:GLY739 4.8 179.2 1.0
CA B:VAL737 4.9 184.3 1.0
CA B:GLY741 5.0 176.9 1.0

Magnesium binding site 10 out of 12 in 8df9

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Magnesium binding site 10 out of 12 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 Magnesium with other atoms in the Mg binding site number 10 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
B:Mg905

b:107.2
occ:1.00
 O B:HOH1004 2.2 106.7 1.0
O B:HOH1014 2.2 108.0 1.0
O B:HOH1005 2.2 104.8 1.0
O B:HOH1001 2.2 110.7 1.0
O B:HOH1008 2.2 109.1 1.0
O B:HOH1003 2.2 106.2 1.0
OE1 B:GLU221 4.2 101.4 1.0
OE2 B:GLU221 4.2 101.1 1.0
O B:PHE431 4.3 112.1 1.0
OD1 B:ASP384 4.4 116.8 1.0
OD2 B:ASP384 4.5 116.8 1.0
CD B:GLU221 4.6 100.7 1.0
CG B:ASP384 4.9 116.8 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: Fri Apr 7 08:54:59 2023

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