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Iodine in PDB 1k4s: Human Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex

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

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

Protein crystallography data

The structure of Human Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex, PDB code: 1k4s was solved by B.L.Staker, K.Hjerrild, M.D.Feese, C.A.Behnke, A.B.Burgin Jr., L.J.Stewart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.20
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 73.235, 73.235, 186.632, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Iodine atom in the Human Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex (pdb code 1k4s). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 15 binding sites of Iodine where determined in the Human Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex, PDB code: 1k4s:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 15 in 1k4s

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Iodine binding site 1 out of 15 in the Human 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 Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I9

b:41.2
occ:1.00
 I5 B:5IU9 0.0 41.2 1.0
C5 B:5IU9 2.0 31.6 1.0
OP2 B:5IU9 2.6 40.7 1.0
C2' B:DC8 2.8 32.4 1.0
C6 B:5IU9 2.9 30.8 1.0
C4 B:5IU9 2.9 30.9 1.0
O4 B:5IU9 3.2 28.4 1.0
NZ A:LYS436 3.2 33.0 1.0
N1 B:DC8 3.3 29.0 1.0
C1' B:DC8 3.4 30.7 1.0
C6 B:DC8 3.5 28.7 1.0
SD A:MET428 3.6 29.0 1.0
C2 B:DC8 3.9 27.5 1.0
P B:5IU9 3.9 42.2 1.0
C3' B:DC8 4.0 34.6 1.0
C5 B:DC8 4.1 28.0 1.0
N1 B:5IU9 4.2 30.9 1.0
N3 B:5IU9 4.2 30.5 1.0
O3' B:DC8 4.2 38.9 1.0
CE A:MET428 4.2 27.9 1.0
CE A:LYS436 4.4 33.9 1.0
O2 B:DC8 4.4 27.5 1.0
N3 B:DC8 4.5 26.3 1.0
C4 B:DC8 4.5 27.1 1.0
O4' B:DC8 4.7 30.8 1.0
O5' B:5IU9 4.7 40.1 1.0
C2 B:5IU9 4.8 30.7 1.0
I5 B:5IU10 4.8 47.9 1.0
O4 B:5IU10 4.9 35.3 1.0

Iodine binding site 2 out of 15 in 1k4s

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Iodine binding site 2 out of 15 in the Human 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 Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I10

b:47.9
occ:1.00
 I5 B:5IU10 0.0 47.9 1.0
C5 B:5IU10 2.0 37.3 1.0
C6 B:5IU10 2.9 36.0 1.0
C4 B:5IU10 2.9 36.7 1.0
O4 B:5IU10 3.2 35.3 1.0
C6 B:5IU9 3.5 30.8 1.0
C2' B:5IU9 3.5 33.9 1.0
N1 B:5IU9 3.8 30.9 1.0
C5 B:5IU9 3.9 31.6 1.0
OP2 B:5IU9 4.0 40.7 1.0
N3 B:5IU10 4.2 35.0 1.0
N1 B:5IU10 4.2 33.9 1.0
C1' B:5IU9 4.2 33.0 1.0
C5M C:SPT11 4.4 44.5 1.0
O5' B:5IU9 4.4 40.1 1.0
C2 B:5IU9 4.5 30.7 1.0
C4 B:5IU9 4.6 30.9 1.0
N3 B:5IU9 4.7 30.5 1.0
C2 B:5IU10 4.8 34.2 1.0
ND2 A:ASN722 4.8 53.4 1.0
C3' B:5IU9 4.8 34.4 1.0
I5 B:5IU9 4.8 41.2 1.0
P B:5IU9 4.9 42.2 1.0

Iodine binding site 3 out of 15 in 1k4s

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Iodine binding site 3 out of 15 in the Human 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 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:69.3
occ:1.00
 I5 C:5IU18 0.0 69.3 1.0
C5 C:5IU18 2.0 66.5 1.0
C6 C:5IU18 2.9 66.5 1.0
C4 C:5IU18 3.0 66.0 1.0
O4 C:5IU18 3.3 67.3 1.0
C2' C:DA17 3.9 45.2 1.0
C8 C:DA17 3.9 35.4 1.0
N9 C:DA17 4.0 36.7 1.0
N1 C:5IU18 4.2 66.2 1.0
N7 C:DA17 4.2 34.4 1.0
N3 C:5IU18 4.2 66.7 1.0
C4 C:DA17 4.3 34.6 1.0
C1' C:DA17 4.4 41.7 1.0
I5 C:5IU19 4.4 73.3 1.0
C5 C:DA17 4.5 34.6 1.0
C5' C:5IU18 4.7 63.3 1.0
C2 C:5IU18 4.8 66.5 1.0

Iodine binding site 4 out of 15 in 1k4s

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Iodine binding site 4 out of 15 in the Human 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 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:73.3
occ:1.00
 I5 C:5IU19 0.0 73.3 1.0
C5 C:5IU19 2.0 69.9 1.0
C6 C:5IU19 2.9 69.2 1.0
C4 C:5IU19 3.0 69.5 1.0
O4 C:5IU19 3.2 70.5 1.0
C2' C:5IU18 3.3 66.4 1.0
C6 C:5IU18 3.6 66.5 1.0
N1 C:5IU18 3.8 66.2 1.0
C5 C:5IU18 4.0 66.5 1.0
C1' C:5IU18 4.2 65.8 1.0
N1 C:5IU19 4.2 69.0 1.0
N3 C:5IU19 4.2 70.1 1.0
I5 C:5IU18 4.4 69.3 1.0
C3' C:5IU18 4.4 66.7 1.0
C2 C:5IU18 4.5 66.5 1.0
C4 C:5IU18 4.7 66.0 1.0
C2 C:5IU19 4.8 69.2 1.0
N3 C:5IU18 4.8 66.7 1.0
O4 C:5IU20 4.9 64.3 1.0

Iodine binding site 5 out of 15 in 1k4s

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Iodine binding site 5 out of 15 in the Human 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 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:67.3
occ:1.00
 I5 C:5IU20 0.0 67.3 1.0
C5 C:5IU20 2.0 63.5 1.0
C6 C:5IU20 2.8 63.5 1.0
C4 C:5IU20 2.9 63.3 1.0
O4 C:5IU20 3.2 64.3 1.0
C6 C:5IU19 3.7 69.2 1.0
C2' C:5IU19 3.7 70.2 1.0
N1 C:5IU19 3.8 69.0 1.0
C5 C:5IU19 4.0 69.9 1.0
N1 C:5IU20 4.1 64.3 1.0
N3 C:5IU20 4.2 64.4 1.0
C1' C:5IU19 4.3 69.1 1.0
C2 C:5IU19 4.3 69.2 1.0
O4 C:5IU21 4.4 79.5 1.0
I5 C:5IU21 4.4 78.3 1.0
C4 C:5IU19 4.5 69.5 1.0
N3 C:5IU19 4.5 70.1 1.0
C5' C:5IU20 4.7 67.6 1.0
C2 C:5IU20 4.7 64.3 1.0
O2 C:5IU19 4.9 70.0 1.0

Iodine binding site 6 out of 15 in 1k4s

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Iodine binding site 6 out of 15 in the Human 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 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:78.3
occ:1.00
 I5 C:5IU21 0.0 78.3 1.0
C5 C:5IU21 2.0 77.2 1.0
C6 C:5IU21 2.9 76.4 1.0
C4 C:5IU21 3.0 76.9 1.0
O4 C:5IU21 3.2 79.5 1.0
C2' C:5IU20 3.4 66.7 1.0
C6 C:5IU20 3.7 63.5 1.0
N1 C:5IU20 3.9 64.3 1.0
C5 C:5IU20 4.0 63.5 1.0
N1 C:5IU21 4.2 76.0 1.0
N3 C:5IU21 4.2 76.5 1.0
O4 C:DT22 4.2 70.9 1.0
C1' C:5IU20 4.3 65.3 1.0
I5 C:5IU20 4.4 67.3 1.0
C2 C:5IU20 4.5 64.3 1.0
C3' C:5IU20 4.5 67.3 1.0
C4 C:5IU20 4.5 63.3 1.0
N3 C:5IU20 4.7 64.4 1.0
OP2 C:5IU21 4.7 71.7 1.0
C2 C:5IU21 4.8 75.5 1.0
C4 C:DT22 5.0 69.9 1.0

Iodine binding site 7 out of 15 in 1k4s

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Iodine binding site 7 out of 15 in the Human 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 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:69.1
occ:1.00
 I5 D:5IU107 0.0 69.1 1.0
C5 D:5IU107 2.0 63.8 1.0
NH2 A:ARG708 2.7 84.6 1.0
C6 D:5IU107 2.9 63.1 1.0
C4 D:5IU107 3.0 63.2 1.0
O4 D:5IU107 3.2 65.0 1.0
CZ A:ARG708 3.3 84.5 1.0
NH1 A:ARG708 3.4 84.6 1.0
C2' D:DT106 3.6 55.7 1.0
C6 D:DT106 4.1 49.0 1.0
N1 D:DT106 4.2 52.0 1.0
N1 D:5IU107 4.2 62.1 1.0
N3 D:5IU107 4.2 63.3 1.0
NE A:ARG708 4.5 83.9 1.0
C1' D:DT106 4.5 54.3 1.0
C5 D:DT106 4.5 47.9 1.0
C2 D:DT106 4.6 51.0 1.0
I5 D:5IU108 4.7 63.2 1.0
C3' D:DT106 4.8 56.7 1.0
C2 D:5IU107 4.8 62.3 1.0
N3 D:DT106 4.9 49.7 1.0
C4 D:DT106 4.9 48.5 1.0
O4 D:5IU108 4.9 60.2 1.0
OP2 D:5IU107 5.0 61.3 1.0

Iodine binding site 8 out of 15 in 1k4s

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Iodine binding site 8 out of 15 in the Human 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 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:63.2
occ:1.00
 I5 D:5IU108 0.0 63.2 1.0
C5 D:5IU108 2.0 60.2 1.0
C6 D:5IU108 2.9 60.1 1.0
C4 D:5IU108 3.0 60.0 1.0
O4 D:5IU108 3.2 60.2 1.0
C2' D:5IU107 3.5 63.4 1.0
CD1 A:LEU716 3.6 64.0 1.0
C6 D:5IU107 3.6 63.1 1.0
N1 D:5IU107 3.8 62.1 1.0
C5 D:5IU107 4.0 63.8 1.0
C1' D:5IU107 4.2 62.5 1.0
N1 D:5IU108 4.2 60.3 1.0
N3 D:5IU108 4.2 61.1 1.0
C2 D:5IU107 4.3 62.3 1.0
C4 D:5IU107 4.6 63.2 1.0
N3 D:5IU107 4.7 63.3 1.0
OP2 D:5IU108 4.7 66.5 1.0
I5 D:5IU107 4.7 69.1 1.0
C2 D:5IU108 4.8 60.9 1.0
CG A:LEU716 4.8 64.6 1.0
NH2 A:ARG708 4.9 84.6 1.0
C3' D:5IU107 4.9 63.8 1.0
CB A:LEU716 4.9 64.5 1.0
I5 D:5IU109 4.9 58.3 1.0
O2 D:5IU107 5.0 62.6 1.0

Iodine binding site 9 out of 15 in 1k4s

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Iodine binding site 9 out of 15 in the Human 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 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:58.3
occ:1.00
 I5 D:5IU109 0.0 58.3 1.0
C5 D:5IU109 2.0 58.0 1.0
C6 D:5IU109 2.9 58.2 1.0
C4 D:5IU109 3.0 58.4 1.0
O4 D:5IU109 3.2 59.2 1.0
C6 D:5IU108 3.8 60.1 1.0
N1 D:5IU108 3.9 60.3 1.0
C2' D:5IU108 4.0 62.3 1.0
C5 D:5IU108 4.1 60.2 1.0
C2 D:5IU108 4.2 60.9 1.0
N1 D:5IU109 4.2 59.4 1.0
N3 D:5IU109 4.2 59.9 1.0
N3 D:5IU108 4.4 61.1 1.0
C4 D:5IU108 4.4 60.0 1.0
CD1 A:LEU716 4.5 64.0 1.0
C1' D:5IU108 4.5 61.0 1.0
I5 D:5IU110 4.5 57.4 1.0
O2 D:5IU108 4.8 62.0 1.0
C2 D:5IU109 4.8 59.8 1.0
I5 D:5IU108 4.9 63.2 1.0
O4 D:5IU110 4.9 50.8 1.0
OP2 D:5IU109 5.0 66.1 1.0

Iodine binding site 10 out of 15 in 1k4s

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Iodine binding site 10 out of 15 in the Human 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 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:57.4
occ:1.00
 I5 D:5IU110 0.0 57.4 1.0
C5 D:5IU110 2.0 50.3 1.0
C6 D:5IU110 2.9 49.9 1.0
C4 D:5IU110 3.0 49.8 1.0
O4 D:5IU110 3.2 50.8 1.0
C6 D:5IU109 3.5 58.2 1.0
N1 D:5IU109 3.7 59.4 1.0
C5 D:5IU109 3.7 58.0 1.0
C2' D:5IU109 3.8 61.7 1.0
C2 D:5IU109 4.1 59.8 1.0
C4 D:5IU109 4.1 58.4 1.0
N1 D:5IU110 4.2 49.9 1.0
N3 D:5IU109 4.2 59.9 1.0
N3 D:5IU110 4.2 49.4 1.0
C1' D:5IU109 4.3 60.4 1.0
N4 D:DC111 4.3 24.0 1.0
I5 D:5IU109 4.5 58.3 1.0
O2 D:5IU109 4.7 60.8 1.0
C2 D:5IU110 4.8 49.3 1.0
O4 D:5IU109 4.8 59.2 1.0
C5 D:DC111 5.0 24.1 1.0

Reference:

B.L.Staker, K.Hjerrild, M.D.Feese, C.A.Behnke, A.B.Burgin Jr., L.J.Stewart. The Mechanism of Topoisomerase I Poisoning By A Camptothecin Analog Proc.Natl.Acad.Sci.Usa V. 99 15387 2002.
ISSN: ISSN 0027-8424
PubMed: 12426403
DOI: 10.1073/PNAS.242259599
Page generated: Sun Aug 11 12:22:47 2024

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