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Iodine in PDB 1a31: Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex

Enzymatic activity of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex

All present enzymatic activity of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex:
5.99.1.2;

Protein crystallography data

The structure of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex, PDB code: 1a31 was solved by M.R.Redinbo, L.Stewart, P.Kuhn, J.J.Champoux, W.G.J.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 72.000, 66.600, 71.800, 90.00, 98.30, 90.00
R / Rfree (%) 24.7 / 31

Iodine Binding Sites:

The binding sites of Iodine atom in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex (pdb code 1a31). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 10 binding sites of Iodine where determined in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex, PDB code: 1a31:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 10 in 1a31

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Iodine binding site 1 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I9

b:61.2
occ:0.29
 I5 C:5IU9 0.0 61.2 0.3
C5 C:5IU9 1.9 37.0 1.0
C6 C:5IU9 2.9 40.9 1.0
C4 C:5IU9 2.9 40.1 1.0
O4 C:5IU9 3.1 38.1 1.0
C2' C:DC8 3.2 42.6 1.0
OP2 C:5IU9 3.4 35.2 1.0
O C:HOH1050 3.7 50.1 1.0
O C:HOH1327 3.7 57.1 1.0
O C:HOH1254 3.8 51.7 1.0
O C:HOH1097 3.9 58.7 1.0
C3' C:DC8 4.0 42.9 1.0
N1 C:DC8 4.1 38.9 1.0
C6 C:DC8 4.1 33.0 1.0
N3 C:5IU9 4.1 35.6 1.0
N1 C:5IU9 4.2 38.0 1.0
O C:HOH1070 4.2 64.2 1.0
C1' C:DC8 4.3 41.3 1.0
C5 C:DC8 4.5 31.3 1.0
C2 C:DC8 4.5 38.9 1.0
SD A:MET428 4.5 47.7 1.0
P C:5IU9 4.5 46.9 1.0
O5' C:5IU9 4.7 40.5 1.0
C2 C:5IU9 4.7 38.2 1.0
C4 C:DC8 4.7 35.1 1.0
O3' C:DC8 4.7 45.0 1.0
N3 C:DC8 4.8 34.5 1.0
CE A:LYS436 4.9 54.8 1.0
NZ A:LYS436 4.9 56.1 1.0
I5 C:5IU10 4.9 49.7 0.2
O4' C:DC8 5.0 43.0 1.0

Iodine binding site 2 out of 10 in 1a31

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Iodine binding site 2 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I10

b:49.7
occ:0.18
 I5 C:5IU10 0.0 49.7 0.2
C5 C:5IU10 1.9 37.5 1.0
C6 C:5IU10 2.9 37.4 1.0
C4 C:5IU10 2.9 37.2 1.0
O C:HOH1050 3.0 50.1 1.0
O4 C:5IU10 3.1 44.0 1.0
O C:HOH1070 3.5 64.2 1.0
C6 C:5IU9 4.0 40.9 1.0
O C:HOH1190 4.1 82.4 1.0
C2' C:5IU9 4.1 34.1 1.0
O4 C:DT11 4.1 56.9 1.0
N3 C:5IU10 4.2 35.0 1.0
C5 C:5IU9 4.2 37.0 1.0
N1 C:5IU9 4.2 38.0 1.0
N1 C:5IU10 4.2 37.2 1.0
C7 C:DT11 4.4 49.1 1.0
C2 C:5IU9 4.5 38.2 1.0
C4 C:5IU9 4.6 40.1 1.0
C4 C:DT11 4.6 50.6 1.0
N3 C:5IU9 4.7 35.6 1.0
C1' C:5IU9 4.7 33.2 1.0
C2 C:5IU10 4.8 35.6 1.0
C5 C:DT11 4.8 48.4 1.0
I5 C:5IU9 4.9 61.2 0.3

Iodine binding site 3 out of 10 in 1a31

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Iodine binding site 3 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I18

b:70.8
occ:0.33
 I5 C:5IU18 0.0 70.8 0.3
C5 C:5IU18 2.0 59.2 1.0
C6 C:5IU18 2.9 62.0 1.0
C4 C:5IU18 3.0 59.3 1.0
O4 C:5IU18 3.2 65.0 1.0
C8 C:DA17 4.1 47.4 1.0
C2' C:DA17 4.2 58.8 1.0
N3 C:5IU18 4.2 57.6 1.0
N1 C:5IU18 4.2 63.2 1.0
N7 C:DA17 4.4 46.8 1.0
O D:HOH1305 4.4 78.3 1.0
N9 C:DA17 4.5 52.8 1.0
C2 C:5IU18 4.8 60.6 1.0
C1' C:DA17 4.9 56.1 1.0
O4 C:5IU19 5.0 55.7 1.0

Iodine binding site 4 out of 10 in 1a31

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Iodine binding site 4 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I19

b:72.5
occ:0.48
 I5 C:5IU19 0.0 72.5 0.5
C5 C:5IU19 2.0 57.2 1.0
C6 C:5IU19 2.9 57.2 1.0
C4 C:5IU19 3.0 56.0 1.0
O4 C:5IU19 3.2 55.7 1.0
C2' C:5IU18 3.6 66.7 1.0
C6 C:5IU18 3.8 62.0 1.0
O4 C:5IU20 3.8 62.1 1.0
N1 C:5IU18 3.9 63.2 1.0
C1' C:5IU18 4.2 64.7 1.0
N1 C:5IU19 4.2 59.0 1.0
C5 C:5IU18 4.2 59.2 1.0
N3 C:5IU19 4.2 48.9 1.0
OP2 C:5IU19 4.4 64.6 1.0
O D:HOH1305 4.4 78.3 1.0
C2 C:5IU18 4.4 60.6 1.0
C4 C:5IU20 4.5 66.0 1.0
I5 C:5IU20 4.6 80.5 0.5
C4 C:5IU18 4.7 59.3 1.0
N3 C:5IU18 4.8 57.6 1.0
C2 C:5IU19 4.8 56.0 1.0
C5 C:5IU20 4.9 66.5 1.0
C3' C:5IU18 4.9 65.2 1.0

Iodine binding site 5 out of 10 in 1a31

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Iodine binding site 5 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I20

b:80.5
occ:0.54
 I5 C:5IU20 0.0 80.5 0.5
C5 C:5IU20 2.0 66.5 1.0
C6 C:5IU20 2.9 62.0 1.0
C4 C:5IU20 2.9 66.0 1.0
O4 C:5IU20 3.1 62.1 1.0
C6 C:5IU19 3.8 57.2 1.0
C2' C:5IU19 3.9 63.1 1.0
N3 C:5IU20 4.2 60.1 1.0
C5 C:5IU19 4.2 57.2 1.0
N1 C:5IU20 4.2 58.0 1.0
N1 C:5IU19 4.4 59.0 1.0
I5 C:5IU19 4.6 72.5 0.5
O4 C:5IU21 4.6 61.9 1.0
C1' C:5IU19 4.7 61.0 1.0
C2 C:5IU20 4.8 60.6 1.0
OP2 C:5IU20 4.9 62.0 1.0
I5 C:5IU21 4.9 85.2 0.4

Iodine binding site 6 out of 10 in 1a31

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Iodine binding site 6 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I21

b:85.2
occ:0.44
 I5 C:5IU21 0.0 85.2 0.4
C5 C:5IU21 2.0 69.5 1.0
C6 C:5IU21 2.9 65.4 1.0
C4 C:5IU21 2.9 64.8 1.0
O4 C:5IU21 3.2 61.9 1.0
C6 C:5IU20 3.7 62.0 1.0
C2' C:5IU20 3.7 60.6 1.0
N1 C:5IU20 3.9 58.0 1.0
C5 C:5IU20 4.1 66.5 1.0
N3 C:5IU21 4.2 62.4 1.0
N1 C:5IU21 4.2 60.0 1.0
C1' C:5IU20 4.3 58.5 1.0
C2 C:5IU20 4.6 60.6 1.0
OP2 C:5IU21 4.6 65.2 1.0
C4 C:5IU20 4.8 66.0 1.0
C2 C:5IU21 4.8 62.5 1.0
I5 C:5IU20 4.9 80.5 0.5
N3 C:5IU20 4.9 60.1 1.0

Iodine binding site 7 out of 10 in 1a31

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Iodine binding site 7 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I107

b:76.6
occ:0.29
 I5 D:5IU107 0.0 76.6 0.3
C5 D:5IU107 1.9 53.2 1.0
C6 D:5IU107 2.9 55.1 1.0
C4 D:5IU107 2.9 51.9 1.0
O4 D:5IU107 3.1 47.4 1.0
C6 D:DT106 3.9 49.2 1.0
C5 D:DT106 4.0 48.4 1.0
C2' D:DT106 4.1 57.9 1.0
N3 D:5IU107 4.2 49.6 1.0
N1 D:5IU107 4.2 56.0 1.0
N1 D:DT106 4.2 51.2 1.0
I5 D:5IU108 4.3 73.0 0.4
C7 D:DT106 4.4 49.1 1.0
O D:HOH1395 4.5 91.1 1.0
C4 D:DT106 4.6 47.7 1.0
O4 D:5IU108 4.6 55.9 1.0
C2 D:DT106 4.7 51.7 1.0
C2 D:5IU107 4.8 51.7 1.0
C1' D:DT106 4.8 55.2 1.0
N3 D:DT106 4.8 46.7 1.0

Iodine binding site 8 out of 10 in 1a31

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Iodine binding site 8 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I108

b:73.0
occ:0.38
 I5 D:5IU108 0.0 73.0 0.4
C5 D:5IU108 1.9 54.8 1.0
C6 D:5IU108 2.9 52.3 1.0
C4 D:5IU108 2.9 54.0 1.0
O4 D:5IU108 3.2 55.9 1.0
C6 D:5IU107 3.4 55.1 1.0
C2' D:5IU107 3.6 62.4 1.0
C5 D:5IU107 3.7 53.2 1.0
N1 D:5IU107 3.7 56.0 1.0
C1' D:5IU107 4.1 60.3 1.0
N1 D:5IU108 4.2 47.7 1.0
N3 D:5IU108 4.2 44.5 1.0
O D:HOH1395 4.2 91.1 1.0
O D:HOH1037 4.3 66.1 1.0
C2 D:5IU107 4.3 51.7 1.0
I5 D:5IU107 4.3 76.6 0.3
C4 D:5IU107 4.4 51.9 1.0
O D:HOH1277 4.4 54.5 1.0
N3 D:5IU107 4.6 49.6 1.0
OP2 D:5IU108 4.6 62.5 1.0
C2 D:5IU108 4.7 47.1 1.0
I5 D:5IU109 4.9 70.9 0.5

Iodine binding site 9 out of 10 in 1a31

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Iodine binding site 9 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I109

b:70.9
occ:0.45
 I5 D:5IU109 0.0 70.9 0.5
C5 D:5IU109 1.9 48.0 1.0
C4 D:5IU109 2.8 52.0 1.0
C6 D:5IU109 2.9 51.2 1.0
O D:HOH1277 3.0 54.5 1.0
O4 D:5IU109 3.0 49.8 1.0
C6 D:5IU108 3.9 52.3 1.0
O D:HOH1136 3.9 45.6 1.0
N1 D:5IU108 3.9 47.7 1.0
C5 D:5IU108 4.0 54.8 1.0
C2 D:5IU108 4.1 47.1 1.0
O4 D:5IU110 4.1 42.8 1.0
C2' D:5IU108 4.1 47.8 1.0
N3 D:5IU109 4.1 50.5 1.0
O D:HOH1037 4.1 66.1 1.0
N3 D:5IU108 4.1 44.5 1.0
N1 D:5IU109 4.1 54.5 1.0
C4 D:5IU108 4.2 54.0 1.0
C1' D:5IU108 4.6 47.9 1.0
O2 D:5IU108 4.6 50.1 1.0
I5 D:5IU110 4.6 67.7 0.3
C2 D:5IU109 4.7 55.5 1.0
C4 D:5IU110 4.7 42.3 1.0
O4 D:5IU108 4.8 55.9 1.0
I5 D:5IU108 4.9 73.0 0.4

Iodine binding site 10 out of 10 in 1a31

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Iodine binding site 10 out of 10 in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I110

b:67.7
occ:0.33
 I5 D:5IU110 0.0 67.7 0.3
C5 D:5IU110 1.9 44.4 1.0
C6 D:5IU110 2.9 48.7 1.0
C4 D:5IU110 2.9 42.3 1.0
O4 D:5IU110 3.1 42.8 1.0
O D:HOH1136 3.4 45.6 1.0
C2' D:5IU109 3.5 54.7 1.0
C6 D:5IU109 3.6 51.2 1.0
O D:HOH1194 3.7 59.8 1.0
O D:HOH1189 4.0 92.8 1.0
N1 D:5IU109 4.0 54.5 1.0
C5 D:5IU109 4.1 48.0 1.0
N4 D:DC111 4.1 40.3 1.0
OP2 D:5IU110 4.1 58.9 1.0
N3 D:5IU110 4.2 39.2 1.0
N1 D:5IU110 4.2 48.9 1.0
C1' D:5IU109 4.3 53.5 1.0
O D:HOH1342 4.3 67.4 1.0
I5 D:5IU109 4.6 70.9 0.5
C5 D:DC111 4.7 37.5 1.0
C4 D:DC111 4.7 37.4 1.0
C2 D:5IU110 4.7 45.8 1.0
C2 D:5IU109 4.9 55.5 1.0
C4 D:5IU109 4.9 52.0 1.0
C3' D:5IU109 4.9 56.6 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: Sun Aug 11 09:22:39 2024

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