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

Go back to Phosphorus Binding Sites List in 1a36
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

Go back to Phosphorus Binding Sites List in 1a36
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

Go back to Phosphorus Binding Sites List in 1a36
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

Go back to Phosphorus Binding Sites List in 1a36
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

Go back to Phosphorus Binding Sites List in 1a36
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

Go back to Phosphorus Binding Sites List in 1a36
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

Go back to Phosphorus Binding Sites List in 1a36
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

Go back to Phosphorus Binding Sites List in 1a36
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

Go back to Phosphorus Binding Sites List in 1a36
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

Go back to Phosphorus Binding Sites List in 1a36
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy