Phosphorus in PDB 1a36: Topoisomerase I/Dna Complex

Enzymatic activity of Topoisomerase I/Dna Complex

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

Protein crystallography data

The structure of Topoisomerase I/Dna Complex, PDB code: 1a36 was solved by L.Stewart, M.R.Redinbo, X.Qiu, 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) 8.00 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.500, 118.400, 71.500, 90.00, 101.20, 90.00
R / Rfree (%) 22.4 / 31.2

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 42;

Binding sites:

The binding sites of Phosphorus atom in the Topoisomerase I/Dna Complex (pdb code 1a36). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 42 binding sites of Phosphorus where determined in the Topoisomerase I/Dna Complex, PDB code: 1a36:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 42 in 1a36

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Phosphorus binding site 1 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P2

b:96.7
occ:1.00
P B:DA2 0.0 96.7 1.0
OP2 B:DA2 1.5 98.2 1.0
OP1 B:DA2 1.5 99.0 1.0
O5' B:DA2 1.6 90.8 1.0
O3' B:DA1 1.6 93.3 1.0
C5' B:DA2 2.6 86.1 1.0
C3' B:DA1 2.6 95.2 1.0
C2' B:DA1 2.9 92.8 1.0
C1' B:DA1 3.3 86.1 1.0
C4' B:DA1 3.6 96.5 1.0
C4' B:DA2 3.7 83.6 1.0
C3' B:DA2 3.7 82.5 1.0
O4' B:DA1 3.8 93.3 1.0
C2' B:DA2 4.0 75.9 1.0
C8 B:DA2 4.4 48.5 1.0
O4' B:DA2 4.5 80.4 1.0
N9 B:DA1 4.7 73.0 1.0
C1' B:DA2 4.7 69.6 1.0
N9 B:DA2 5.0 55.6 1.0

Phosphorus binding site 2 out of 42 in 1a36

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Phosphorus binding site 2 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P3

b:86.2
occ:1.00
P B:DA3 0.0 86.2 1.0
OP1 B:DA3 1.5 90.2 1.0
OP2 B:DA3 1.5 85.5 1.0
O3' B:DA2 1.6 83.7 1.0
O5' B:DA3 1.6 85.2 1.0
C3' B:DA2 2.6 82.5 1.0
C5' B:DA3 2.7 77.0 1.0
C2' B:DA2 3.2 75.9 1.0
C4' B:DA2 3.9 83.6 1.0
C4' B:DA3 4.0 69.5 1.0
C1' B:DA2 4.2 69.6 1.0
C3' B:DA3 4.5 67.3 1.0
O4' B:DA3 4.5 64.7 1.0
O4' B:DA2 4.5 80.4 1.0
C2' B:DA3 4.7 63.7 1.0

Phosphorus binding site 3 out of 42 in 1a36

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Phosphorus binding site 3 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P4

b:72.1
occ:1.00
P B:DA4 0.0 72.1 1.0
OP1 B:DA4 1.5 74.6 1.0
OP2 B:DA4 1.5 70.8 1.0
O3' B:DA3 1.6 70.6 1.0
O5' B:DA4 1.6 77.0 1.0
C3' B:DA3 2.6 67.3 1.0
C5' B:DA4 2.7 73.1 1.0
C4' B:DA3 3.6 69.5 1.0
C2' B:DA3 3.7 63.7 1.0
C4' B:DA4 3.8 70.5 1.0
O4' B:DA4 4.1 68.8 1.0
C3' B:DA4 4.2 70.3 1.0
C1' B:DA3 4.3 56.6 1.0
C2' B:DA4 4.4 66.7 1.0
O4' B:DA3 4.5 64.7 1.0
C8 B:DA4 4.6 43.9 1.0
C5' B:DA3 4.7 77.0 1.0
C1' B:DA4 4.8 62.1 1.0

Phosphorus binding site 4 out of 42 in 1a36

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Phosphorus binding site 4 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P5

b:67.9
occ:1.00
P B:DA5 0.0 67.9 1.0
OP1 B:DA5 1.5 69.0 1.0
OP2 B:DA5 1.5 70.0 1.0
O5' B:DA5 1.6 62.4 1.0
O3' B:DA4 1.6 67.7 1.0
C5' B:DA5 2.6 59.2 1.0
C3' B:DA4 2.6 70.3 1.0
C2' B:DA4 3.0 66.7 1.0
C4' B:DA5 3.9 56.5 1.0
C1' B:DA4 3.9 62.1 1.0
C4' B:DA4 3.9 70.5 1.0
C3' B:DA5 4.1 55.3 1.0
O4' B:DA5 4.5 59.8 1.0
O4' B:DA4 4.5 68.8 1.0
C2' B:DA5 4.5 54.5 1.0
C8 B:DA5 4.8 47.9 1.0

Phosphorus binding site 5 out of 42 in 1a36

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Phosphorus binding site 5 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P6

b:61.5
occ:1.00
P B:DG6 0.0 61.5 1.0
OP2 B:DG6 1.5 57.9 1.0
OP1 B:DG6 1.5 60.2 1.0
O5' B:DG6 1.6 51.3 1.0
O3' B:DA5 1.6 60.6 1.0
C5' B:DG6 2.6 40.7 1.0
C3' B:DA5 2.6 55.3 1.0
C2' B:DA5 3.2 54.5 1.0
C4' B:DG6 3.9 28.1 1.0
C4' B:DA5 3.9 56.5 1.0
C1' B:DA5 4.2 54.1 1.0
O4' B:DG6 4.3 22.6 1.0
CD1 A:ILE424 4.4 24.6 1.0
C3' B:DG6 4.5 28.4 1.0
O4' B:DA5 4.6 59.8 1.0
C2' B:DG6 5.0 26.6 1.0
C5' B:DA5 5.0 59.2 1.0

Phosphorus binding site 6 out of 42 in 1a36

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Phosphorus binding site 6 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P7

b:29.0
occ:1.00
P B:DA7 0.0 29.0 1.0
OP2 B:DA7 1.5 29.7 1.0
OP1 B:DA7 1.5 37.1 1.0
O5' B:DA7 1.6 28.7 1.0
O3' B:DG6 1.6 30.6 1.0
C5' B:DA7 2.6 27.8 1.0
C3' B:DG6 2.6 28.4 1.0
C2' B:DG6 3.2 26.6 1.0
OH A:TYR426 3.7 28.2 1.0
NE1 A:TRP412 3.7 16.9 1.0
C4' B:DA7 3.9 31.8 1.0
C4' B:DG6 3.9 28.1 1.0
CE2 A:TYR426 4.0 27.6 1.0
C1' B:DG6 4.2 23.1 1.0
C3' B:DA7 4.3 32.8 1.0
CZ A:TYR426 4.3 15.5 1.0
CE2 A:TRP412 4.4 13.0 1.0
CZ2 A:TRP412 4.4 7.3 1.0
O4' B:DA7 4.6 31.8 1.0
CG1 A:VAL410 4.6 28.5 1.0
NH1 A:ARG405 4.7 40.5 1.0
O4' B:DG6 4.7 22.6 1.0
CD1 A:TRP412 4.8 18.1 1.0
C2' B:DA7 4.8 34.6 1.0
C5' B:DG6 5.0 40.7 1.0

Phosphorus binding site 7 out of 42 in 1a36

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Phosphorus binding site 7 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:39.0
occ:1.00
P B:DC8 0.0 39.0 1.0
OP2 B:DC8 1.5 38.6 1.0
OP1 B:DC8 1.5 39.9 1.0
O5' B:DC8 1.6 38.5 1.0
O3' B:DA7 1.6 30.8 1.0
C3' B:DA7 2.6 32.8 1.0
C5' B:DC8 2.6 41.4 1.0
OG1 A:THR411 3.2 44.4 1.0
C2' B:DA7 3.2 34.6 1.0
N A:THR411 3.5 27.9 1.0
CE A:MET428 3.9 45.4 1.0
C4' B:DA7 3.9 31.8 1.0
C4' B:DC8 3.9 34.9 1.0
CB A:THR411 4.1 39.2 1.0
CG2 A:THR411 4.1 43.3 1.0
C1' B:DA7 4.1 35.0 1.0
NZ A:LYS216 4.1 64.0 1.0
CA A:VAL410 4.1 26.1 1.0
CB A:VAL410 4.2 25.8 1.0
C A:VAL410 4.3 24.9 1.0
CA A:THR411 4.3 30.2 1.0
CD1 A:TRP412 4.4 18.1 1.0
O4' B:DC8 4.4 32.5 1.0
CG1 A:VAL410 4.4 28.5 1.0
O4' B:DA7 4.6 31.8 1.0
C3' B:DC8 4.6 37.1 1.0
N A:TRP412 4.8 22.6 1.0
O A:HOH1030 5.0 47.0 1.0
C2' B:DC8 5.0 35.0 1.0
C5' B:DA7 5.0 27.8 1.0
C A:THR411 5.0 26.8 1.0

Phosphorus binding site 8 out of 42 in 1a36

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Phosphorus binding site 8 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:40.3
occ:1.00
P B:DT9 0.0 40.3 1.0
OP1 B:DT9 1.5 42.1 1.0
OP2 B:DT9 1.5 41.0 1.0
O3' B:DC8 1.6 40.3 1.0
O5' B:DT9 1.6 41.0 1.0
C3' B:DC8 2.6 37.1 1.0
C5' B:DT9 2.6 28.6 1.0
NZ A:LYS439 3.2 42.2 1.0
C2' B:DC8 3.2 35.0 1.0
CE A:LYS439 3.9 51.0 1.0
CD A:LYS439 3.9 43.6 1.0
C4' B:DC8 3.9 34.9 1.0
C4' B:DT9 3.9 22.0 1.0
C1' B:DC8 4.0 32.9 1.0
NZ A:LYS436 4.3 40.5 1.0
O4' B:DT9 4.4 17.8 1.0
CE A:LYS436 4.4 29.7 1.0
CD A:LYS436 4.5 26.4 1.0
C3' B:DT9 4.5 20.4 1.0
C6 B:DT9 4.6 27.3 1.0
O4' B:DC8 4.6 32.5 1.0
C2' B:DT9 4.8 21.6 1.0
O A:HOH1030 5.0 47.0 1.0

Phosphorus binding site 9 out of 42 in 1a36

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Phosphorus binding site 9 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:16.9
occ:1.00
P B:DT10 0.0 16.9 1.0
OP1 B:DT10 1.5 14.1 1.0
OP2 B:DT10 1.5 25.0 1.0
O5' B:DT10 1.6 20.1 1.0
O3' B:DT9 1.6 16.4 1.0
C5' B:DT10 2.6 18.4 1.0
C3' B:DT9 2.6 20.4 1.0
NZ A:LYS587 3.1 41.5 1.0
C2' B:DT9 3.3 21.6 1.0
NZ A:LYS443 3.5 24.9 1.0
C4' B:DT10 3.8 23.1 1.0
C4' B:DT9 3.9 22.0 1.0
CD A:LYS443 4.1 20.0 1.0
O4' B:DT10 4.1 20.5 1.0
CB A:ASN722 4.2 40.1 1.0
CE A:LYS587 4.2 34.0 1.0
CE A:LYS443 4.2 20.0 1.0
C1' B:DT9 4.3 20.2 1.0
ND2 A:ASN722 4.3 41.6 1.0
O A:ASN722 4.4 29.2 1.0
C3' B:DT10 4.6 26.0 1.0
O4' B:DT9 4.7 17.8 1.0
CG A:ASN722 4.8 37.4 1.0
C2' B:DT10 4.9 20.1 1.0
CA A:ASN722 5.0 39.1 1.0

Phosphorus binding site 10 out of 42 in 1a36

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Phosphorus binding site 10 out of 42 in the Topoisomerase I/Dna Complex


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:51.1
occ:1.00
P B:DA11 0.0 51.1 1.0
OP1 B:DA11 1.5 49.4 1.0
OP2 B:DA11 1.5 49.0 1.0
O5' B:DA11 1.6 48.0 1.0
O3' B:DT10 1.6 36.8 1.0
C5' B:DA11 2.6 46.1 1.0
C3' B:DT10 2.6 26.0 1.0
CE2 A:PHE723 3.4 57.3 1.0
C2' B:DT10 3.4 20.1 1.0
CZ A:PHE723 3.5 54.2 1.0
NE2 A:HIS632 3.6 54.9 1.0
NH2 A:ARG488 3.8 52.8 1.0
C4' B:DA11 3.8 41.8 1.0
C4' B:DT10 3.8 23.1 1.0
C3' B:DA11 3.9 40.7 1.0
C1' B:DT10 4.1 20.0 1.0
CE1 A:HIS632 4.2 51.3 1.0
NH1 A:ARG590 4.3 32.6 1.0
C2' B:DA11 4.6 37.7 1.0
CD2 A:PHE723 4.6 51.6 1.0
O4' B:DT10 4.6 20.5 1.0
CD2 A:HIS632 4.7 57.4 1.0
O4' B:DA11 4.8 39.7 1.0
CZ A:ARG488 4.8 48.8 1.0
CE1 A:PHE723 4.9 56.5 1.0
C5' B:DT10 4.9 18.4 1.0
NZ A:LYS532 4.9 34.7 1.0
NE A:ARG488 4.9 33.1 1.0

Reference:

L.Stewart, M.R.Redinbo, X.Qiu, W.G.Hol, J.J.Champoux. A Model For the Mechanism of Human Topoisomerase I. Science V. 279 1534 1998.
ISSN: ISSN 0036-8075
PubMed: 9488652
DOI: 10.1126/SCIENCE.279.5356.1534
Page generated: Fri Sep 25 12:06:45 2020

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