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Bromine in PDB 1a35: Human Topoisomerase I/Dna Complex

Enzymatic activity of Human Topoisomerase I/Dna Complex

All present enzymatic activity of Human Topoisomerase I/Dna Complex:
5.99.1.2;

Protein crystallography data

The structure of Human Topoisomerase I/Dna Complex, PDB code: 1a35 was solved by M.R.Redinbo, L.Stewart, P.Kuhn, J.J.Champoux, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.800, 66.300, 71.800, 90.00, 98.40, 90.00
R / Rfree (%) 20.9 / 30.8

Bromine Binding Sites:

The binding sites of Bromine atom in the Human Topoisomerase I/Dna Complex (pdb code 1a35). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the Human Topoisomerase I/Dna Complex, PDB code: 1a35:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 1a35

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Bromine binding site 1 out of 8 in the Human Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br18

b:55.8
occ:0.25
 BR C:BRU18 0.0 55.8 0.2
C5 C:BRU18 2.1 43.9 1.0
C6 C:BRU18 3.0 43.0 1.0
C4 C:BRU18 3.1 41.9 1.0
O4 C:BRU18 3.3 38.0 1.0
C8 C:DA17 3.3 32.0 1.0
N7 C:DA17 3.6 27.3 1.0
C2' C:DA17 3.7 56.4 1.0
O C:HOH1214 3.7 60.0 1.0
N9 C:DA17 3.9 36.3 1.0
C5 C:DA17 4.3 21.1 1.0
N3 C:BRU18 4.3 39.4 1.0
N1 C:BRU18 4.4 51.5 1.0
C1' C:DA17 4.4 46.5 1.0
C4 C:DA17 4.5 26.5 1.0
C3' C:DA17 4.8 62.4 1.0
C2 C:BRU18 4.9 46.7 1.0

Bromine binding site 2 out of 8 in 1a35

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Bromine binding site 2 out of 8 in the Human Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br19

b:50.7
occ:0.29
 BR C:BRU19 0.0 50.7 0.3
C5 C:BRU19 2.1 35.9 1.0
O C:HOH1214 2.9 60.0 1.0
C6 C:BRU19 3.0 40.6 1.0
C4 C:BRU19 3.1 33.0 1.0
O4 C:BRU19 3.3 28.6 1.0
C2' C:BRU18 3.4 66.1 1.0
C6 C:BRU18 3.7 43.0 1.0
N1 C:BRU18 3.9 51.5 1.0
C1' C:BRU18 4.1 61.7 1.0
C5 C:BRU18 4.2 43.9 1.0
N3 C:BRU19 4.3 28.9 1.0
N1 C:BRU19 4.4 44.5 1.0
O4 C:DT20 4.4 49.0 1.0
C2 C:BRU18 4.5 46.7 1.0
OP2 C:BRU19 4.6 72.6 1.0
C3' C:BRU18 4.8 69.2 1.0
C4 C:BRU18 4.9 41.9 1.0
N3 C:BRU18 4.9 39.4 1.0
C2 C:BRU19 4.9 36.6 1.0

Bromine binding site 3 out of 8 in 1a35

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Bromine binding site 3 out of 8 in the Human Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br107

b:48.1
occ:0.27
 BR D:BRU107 0.0 48.1 0.3
C5 D:BRU107 2.1 37.0 1.0
C4 D:BRU107 3.0 36.8 1.0
C6 D:BRU107 3.0 42.3 1.0
O4 D:BRU107 3.2 32.0 1.0
C5 D:DT106 3.8 27.1 1.0
C6 D:DT106 3.8 30.7 1.0
C7 D:DT106 4.0 21.0 1.0
N3 D:BRU107 4.3 35.5 1.0
BR D:BRU108 4.3 46.8 0.2
N1 D:BRU107 4.4 45.7 1.0
N1 D:DT106 4.4 40.9 1.0
C4 D:DT106 4.4 28.7 1.0
C2' D:DT106 4.5 62.3 1.0
O4 D:BRU108 4.5 29.6 1.0
N3 D:DT106 4.8 25.6 1.0
C2 D:DT106 4.9 38.7 1.0
C2 D:BRU107 4.9 38.3 1.0
O4 D:DT106 5.0 32.5 1.0

Bromine binding site 4 out of 8 in 1a35

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Bromine binding site 4 out of 8 in the Human Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br108

b:46.8
occ:0.24
 BR D:BRU108 0.0 46.8 0.2
C5 D:BRU108 2.1 32.9 1.0
C4 D:BRU108 3.0 36.5 1.0
C6 D:BRU108 3.1 33.9 1.0
O4 D:BRU108 3.2 29.6 1.0
C6 D:BRU107 3.5 42.3 1.0
C5 D:BRU107 3.8 37.0 1.0
N1 D:BRU107 4.1 45.7 1.0
C2' D:BRU107 4.1 56.1 1.0
O C:HOH1226 4.2 60.3 1.0
BR D:BRU107 4.3 48.1 0.3
N3 D:BRU108 4.3 33.8 1.0
N1 D:BRU108 4.4 34.0 1.0
O4 D:BRU109 4.5 16.6 1.0
C4 D:BRU107 4.6 36.8 1.0
C1' D:BRU107 4.6 53.6 1.0
C2 D:BRU107 4.8 38.3 1.0
N3 D:BRU107 4.9 35.5 1.0
C2 D:BRU108 4.9 34.9 1.0

Bromine binding site 5 out of 8 in 1a35

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Bromine binding site 5 out of 8 in the Human Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br109

b:31.0
occ:0.18
 BR D:BRU109 0.0 31.0 0.2
C5 D:BRU109 2.1 21.5 1.0
C6 D:BRU109 3.0 27.1 1.0
C4 D:BRU109 3.1 21.8 1.0
O4 D:BRU109 3.3 16.6 1.0
C2' D:BRU108 3.6 35.6 1.0
C6 D:BRU108 3.8 33.9 1.0
N1 D:BRU108 4.0 34.0 1.0
C1' D:BRU108 4.3 34.1 1.0
C5 D:BRU108 4.3 32.9 1.0
N3 D:BRU109 4.3 23.1 1.0
N1 D:BRU109 4.4 35.3 1.0
C2 D:BRU108 4.6 34.9 1.0
C2 D:BRU109 4.9 33.2 1.0
C3' D:BRU108 4.9 39.2 1.0
OP2 D:BRU109 5.0 46.2 1.0
C4 D:BRU108 5.0 36.5 1.0

Bromine binding site 6 out of 8 in 1a35

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Bromine binding site 6 out of 8 in the Human Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br110

b:57.1
occ:0.29
 BR D:BRU110 0.0 57.1 0.3
C5 D:BRU110 2.1 34.5 1.0
C6 D:BRU110 3.0 40.2 1.0
C4 D:BRU110 3.1 29.1 1.0
O D:HOH1116 3.2 48.7 1.0
O4 D:BRU110 3.3 25.7 1.0
O D:HOH1140 3.3 69.5 1.0
C2' D:BRU109 3.4 42.7 1.0
OP2 D:BRU110 3.9 64.6 1.0
C6 D:BRU109 4.0 27.1 1.0
N1 D:BRU109 4.1 35.3 1.0
C1' D:BRU109 4.2 39.9 1.0
N3 D:BRU110 4.3 21.5 1.0
N1 D:BRU110 4.3 43.3 1.0
C5 D:BRU109 4.6 21.5 1.0
N4 D:DC111 4.6 16.5 1.0
C2 D:BRU109 4.7 33.2 1.0
C3' D:BRU109 4.8 47.3 1.0
C2 D:BRU110 4.9 37.3 1.0

Bromine binding site 7 out of 8 in 1a35

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Bromine binding site 7 out of 8 in the Human Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br112

b:69.2
occ:0.44
 BR D:BRU112 0.0 69.2 0.4
C5 D:BRU112 2.1 23.5 1.0
O D:HOH1115 2.7 48.5 1.0
C6 D:BRU112 3.0 28.5 1.0
C4 D:BRU112 3.0 23.4 1.0
O D:HOH1025 3.2 32.3 1.0
O4 D:BRU112 3.2 24.6 1.0
O D:HOH1107 3.5 65.9 1.0
O D:HOH1164 4.0 46.3 1.0
CB A:ASN352 4.0 32.2 1.0
CG A:ASN352 4.2 32.8 1.0
ND2 A:ASN352 4.3 32.1 1.0
N3 D:BRU112 4.3 19.2 1.0
C5 D:DC111 4.3 13.6 1.0
C6 D:DC111 4.3 20.0 1.0
N1 D:BRU112 4.3 27.2 1.0
C2' D:DC111 4.7 26.6 1.0
OD1 A:ASN352 4.8 36.3 1.0
C2 D:BRU112 4.9 25.0 1.0

Bromine binding site 8 out of 8 in 1a35

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Bromine binding site 8 out of 8 in the Human Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br121

b:65.6
occ:0.43
 BR D:BRU121 0.0 65.6 0.4
C5 D:BRU121 2.1 34.4 1.0
O D:HOH1062 2.9 61.4 1.0
C6 D:BRU121 3.0 23.1 1.0
O D:HOH1208 3.1 40.9 1.0
C4 D:BRU121 3.1 33.2 1.0
C2' D:DT120 3.3 38.8 1.0
O4 D:BRU121 3.3 33.6 1.0
C6 D:DT120 3.6 22.1 1.0
N1 D:DT120 3.8 24.0 1.0
O D:HOH1194 3.9 64.6 1.0
C1' D:DT120 4.1 29.1 1.0
O D:HOH1124 4.1 40.5 1.0
C5 D:DT120 4.1 14.6 1.0
N1 D:BRU121 4.3 20.0 1.0
N3 D:BRU121 4.3 16.3 1.0
C2 D:DT120 4.5 23.7 1.0
C3' D:DT120 4.6 43.8 1.0
C7 D:DT120 4.6 14.4 1.0
C4 D:DT120 4.8 14.0 1.0
C2 D:BRU121 4.9 20.8 1.0
N3 D:DT120 4.9 8.6 1.0
OP2 D:BRU121 5.0 56.2 1.0

Reference:

M.R.Redinbo, L.Stewart, P.Kuhn, J.J.Champoux, W.G.Hol. Crystal Structures of Human Topoisomerase I in Covalent and Noncovalent Complexes with Dna. Science V. 279 1504 1998.
ISSN: ISSN 0036-8075
PubMed: 9488644
DOI: 10.1126/SCIENCE.279.5356.1504
Page generated: Sat Dec 12 01:59:31 2020

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