Phosphorus in PDB 1a31: 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;

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

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 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 Phosphorus atom.
In total 42 binding sites of Phosphorus where determined in the Human Reconstituted Dna Topoisomerase I in Covalent Complex with A 22 Base Pair Dna Duplex, PDB code: 1a31:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 42 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 Phosphorus with other atoms in the P 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:P2 b:63.5 occ:1.00 P C:DA2 0.0 63.5 1.0 OP2 C:DA2 1.5 62.6 1.0 OP1 C:DA2 1.5 68.2 1.0 O5' C:DA2 1.6 60.6 1.0 O3' C:DA1 1.6 65.3 1.0 C3' C:DA1 2.6 65.5 1.0 C5' C:DA2 2.6 54.1 1.0 C2' C:DA1 3.3 65.6 1.0 O C:HOH1122 3.9 60.6 1.0 C4' C:DA1 3.9 65.8 1.0 C4' C:DA2 3.9 51.0 1.0 C1' C:DA1 4.2 63.0 1.0 C3' C:DA2 4.4 48.7 1.0 O4' C:DA1 4.6 64.9 1.0 O4' C:DA2 4.9 48.8 1.0 C5' C:DA1 5.0 66.8 1.0

Phosphorus binding site 2 out of 42 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 Phosphorus with other atoms in the P 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:P3 b:53.5 occ:1.00 P C:DA3 0.0 53.5 1.0 OP1 C:DA3 1.5 52.3 1.0 OP2 C:DA3 1.5 55.5 1.0 O5' C:DA3 1.6 52.4 1.0 O3' C:DA2 1.6 49.4 1.0 C5' C:DA3 2.6 51.4 1.0 C3' C:DA2 2.7 48.7 1.0 C2' C:DA2 3.2 45.5 1.0 O C:HOH1108 3.8 70.8 1.0 C4' C:DA3 3.9 48.4 1.0 C4' C:DA2 3.9 51.0 1.0 C1' C:DA2 4.0 46.8 1.0 O A:HOH1207 4.0 70.1 1.0 C8 C:DA3 4.2 41.9 1.0 O4' C:DA3 4.4 49.6 1.0 O4' C:DA2 4.4 48.8 1.0 C3' C:DA3 4.5 46.2 1.0 C2' C:DA3 4.7 44.4 1.0 C1' C:DA3 5.0 47.6 1.0 N9 C:DA3 5.0 44.6 1.0

Phosphorus binding site 3 out of 42 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 Phosphorus with other atoms in the P 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:P4 b:52.5 occ:1.00 P C:DA4 0.0 52.5 1.0 OP1 C:DA4 1.5 48.4 1.0 OP2 C:DA4 1.5 47.5 1.0 O5' C:DA4 1.6 45.3 1.0 O3' C:DA3 1.6 45.6 1.0 C5' C:DA4 2.6 42.2 1.0 C3' C:DA3 2.6 46.2 1.0 O C:HOH1163 3.2 55.7 1.0 C2' C:DA3 3.2 44.4 1.0 O C:HOH1201 3.7 68.8 1.0 C4' C:DA4 3.9 40.8 1.0 C4' C:DA3 3.9 48.4 1.0 C1' C:DA3 4.2 47.6 1.0 C3' C:DA4 4.3 43.1 1.0 O4' C:DA4 4.4 41.3 1.0 O4' C:DA3 4.6 49.6 1.0 C2' C:DA4 4.7 40.2 1.0

Phosphorus binding site 4 out of 42 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 Phosphorus with other atoms in the P 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:P5 b:52.2 occ:1.00 P C:DA5 0.0 52.2 1.0 OP2 C:DA5 1.5 51.6 1.0 OP1 C:DA5 1.5 49.9 1.0 O5' C:DA5 1.6 49.2 1.0 O3' C:DA4 1.6 49.6 1.0 C5' C:DA5 2.6 44.9 1.0 C3' C:DA4 2.6 43.1 1.0 C2' C:DA4 3.3 40.2 1.0 O C:HOH1148 3.7 82.9 1.0 C4' C:DA5 3.9 44.2 1.0 C4' C:DA4 3.9 40.8 1.0 C1' C:DA4 4.2 41.1 1.0 C3' C:DA5 4.3 45.0 1.0 O4' C:DA5 4.4 42.5 1.0 O4' C:DA4 4.6 41.3 1.0 C2' C:DA5 4.7 43.3 1.0 C5' C:DA4 5.0 42.2 1.0

Phosphorus binding site 5 out of 42 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 Phosphorus with other atoms in the P 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:P6 b:51.5 occ:1.00 P C:DG6 0.0 51.5 1.0 OP1 C:DG6 1.5 50.6 1.0 OP2 C:DG6 1.5 52.3 1.0 O5' C:DG6 1.6 45.9 1.0 O3' C:DA5 1.6 47.9 1.0 C5' C:DG6 2.6 39.4 1.0 C3' C:DA5 2.6 45.0 1.0 C2' C:DA5 3.2 43.3 1.0 O C:HOH1134 3.6 68.8 1.0 O C:HOH1105 3.8 75.3 1.0 C4' C:DG6 3.9 35.2 1.0 C4' C:DA5 3.9 44.2 1.0 CD1 A:ILE424 4.1 49.1 1.0 C1' C:DA5 4.1 40.2 1.0 C3' C:DG6 4.4 34.7 1.0 O4' C:DG6 4.5 34.0 1.0 O4' C:DA5 4.6 42.5 1.0

Phosphorus binding site 6 out of 42 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 Phosphorus with other atoms in the P 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:P7 b:31.2 occ:1.00 P C:DA7 0.0 31.2 1.0 OP1 C:DA7 1.5 34.0 1.0 OP2 C:DA7 1.5 28.6 1.0 O5' C:DA7 1.6 27.0 1.0 O3' C:DG6 1.6 30.6 1.0 C5' C:DA7 2.6 26.8 1.0 C3' C:DG6 2.6 34.7 1.0 C2' C:DG6 3.2 34.2 1.0 O C:HOH1106 3.4 49.5 1.0 O C:HOH1208 3.4 58.3 1.0 OH A:TYR426 3.5 31.3 1.0 NE1 A:TRP412 3.7 33.4 1.0 C4' C:DA7 3.9 31.6 1.0 C4' C:DG6 3.9 35.2 1.0 O A:HOH1068 4.2 46.9 1.0 C1' C:DG6 4.3 29.3 1.0 CE1 A:TYR426 4.3 29.8 1.0 CZ A:TYR426 4.3 30.5 1.0 C3' C:DA7 4.3 35.2 1.0 CE2 A:TRP412 4.4 32.3 1.0 O4' C:DA7 4.4 31.9 1.0 CZ2 A:TRP412 4.4 33.6 1.0 CG1 A:VAL410 4.6 31.4 1.0 C2' C:DA7 4.7 35.0 1.0 O4' C:DG6 4.7 34.0 1.0 CD1 A:TRP412 4.8 33.0 1.0 C5' C:DG6 4.9 39.4 1.0

Phosphorus binding site 7 out of 42 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 Phosphorus with other atoms in the P 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 C:P8 b:31.1 occ:1.00 P C:DC8 0.0 31.1 1.0 OP1 C:DC8 1.5 44.0 1.0 OP2 C:DC8 1.5 42.9 1.0 O5' C:DC8 1.6 45.3 1.0 O3' C:DA7 1.6 41.3 1.0 C3' C:DA7 2.6 35.2 1.0 C5' C:DC8 2.6 41.6 1.0 C2' C:DA7 3.3 35.0 1.0 OG1 A:THR411 3.5 32.0 1.0 C4' C:DC8 3.6 42.5 1.0 N A:THR411 3.8 33.8 1.0 O4' C:DC8 3.9 43.0 1.0 C4' C:DA7 3.9 31.6 1.0 CG2 A:THR411 4.0 31.4 1.0 C1' C:DA7 4.2 33.5 1.0 CB A:THR411 4.2 27.9 1.0 CE A:MET428 4.2 46.2 1.0 O A:HOH1222 4.4 63.2 1.0 CA A:VAL410 4.5 32.7 1.0 CA A:THR411 4.6 30.6 1.0 CB A:VAL410 4.6 29.6 1.0 C A:VAL410 4.6 33.3 1.0 O4' C:DA7 4.6 31.9 1.0 CD1 A:TRP412 4.7 33.0 1.0 C3' C:DC8 4.9 42.9 1.0 C5' C:DA7 4.9 26.8 1.0

Phosphorus binding site 8 out of 42 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 Phosphorus with other atoms in the P 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 C:P9 b:46.9 occ:1.00 P C:5IU9 0.0 46.9 1.0 OP2 C:5IU9 1.5 35.2 1.0 OP1 C:5IU9 1.5 45.5 1.0 O5' C:5IU9 1.6 40.5 1.0 O3' C:DC8 1.6 45.0 1.0 C3' C:DC8 2.6 42.9 1.0 C5' C:5IU9 2.6 37.5 1.0 C2' C:DC8 3.2 42.6 1.0 CD A:LYS439 3.9 70.5 1.0 C4' C:5IU9 3.9 35.4 1.0 C4' C:DC8 4.0 42.5 1.0 O C:HOH1050 4.0 50.1 1.0 NZ A:LYS439 4.0 73.5 1.0 CE A:LYS436 4.1 54.8 1.0 C6 C:5IU9 4.1 40.9 1.0 CD A:LYS436 4.1 51.5 1.0 O4' C:5IU9 4.2 33.1 1.0 O C:HOH1341 4.3 71.5 1.0 C3' C:5IU9 4.5 35.1 1.0 C2' C:5IU9 4.5 34.1 1.0 C1' C:DC8 4.5 41.3 1.0 CE A:LYS439 4.5 72.7 1.0 I5 C:5IU9 4.5 61.2 0.3 NZ A:LYS436 4.7 56.1 1.0 C5' C:DC8 4.7 41.6 1.0 C5 C:5IU9 4.8 37.0 1.0 C1' C:5IU9 4.9 33.2 1.0 O4' C:DC8 4.9 43.0 1.0

Phosphorus binding site 9 out of 42 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 Phosphorus with other atoms in the P 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 C:P10 b:37.6 occ:1.00 P C:5IU10 0.0 37.6 1.0 OP2 C:5IU10 1.5 37.4 1.0 OP1 C:5IU10 1.5 32.4 1.0 O3' C:5IU9 1.6 37.8 1.0 O5' C:5IU10 1.6 38.0 1.0 C3' C:5IU9 2.6 35.1 1.0 C5' C:5IU10 2.7 34.1 1.0 C2' C:5IU9 3.2 34.1 1.0 NZ A:LYS587 3.7 72.0 1.0 O A:HOH1118 3.8 53.3 1.0 NZ A:LYS443 3.9 37.0 1.0 C4' C:5IU9 3.9 35.4 1.0 C1' C:5IU9 4.0 33.2 1.0 C4' C:5IU10 4.0 35.2 1.0 CD A:LYS443 4.0 41.4 1.0 O4' C:5IU10 4.4 32.9 1.0 CE A:LYS443 4.4 43.8 1.0 C3' C:5IU10 4.5 38.9 1.0 O C:HOH1385 4.5 94.8 1.0 O4' C:5IU9 4.5 33.1 1.0 OD1 A:ASN722 4.6 46.9 1.0 O A:ASN722 4.7 40.4 1.0 O A:HOH1157 4.8 59.0 1.0 CB A:ASN722 4.9 44.1 1.0 CE A:LYS587 4.9 67.2 1.0

Phosphorus binding site 10 out of 42 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 Phosphorus with other atoms in the P 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 C:P12 b:56.6 occ:1.00 P C:DG12 0.0 56.6 1.0 OP2 C:DG12 1.5 57.8 1.0 OP1 C:DG12 1.5 60.5 1.0 O5' C:DG12 1.6 58.0 1.0 O3' C:DT11 1.6 59.3 1.0 C5' C:DG12 2.6 61.2 1.0 C3' C:DT11 2.7 59.8 1.0 C2' C:DT11 3.3 57.2 1.0 C4' C:DG12 3.9 60.7 1.0 C4' C:DT11 3.9 62.2 1.0 C8 C:DG12 4.0 42.6 1.0 O C:HOH1330 4.1 76.5 1.0 O4' C:DG12 4.3 62.4 1.0 C3' C:DG12 4.6 62.7 1.0 C2' C:DG12 4.6 60.5 1.0 C1' C:DT11 4.7 55.4 1.0 C5' C:DT11 4.7 59.6 1.0 N7 C:DG12 4.8 41.4 1.0 N9 C:DG12 4.8 48.4 1.0 C1' C:DG12 4.8 57.5 1.0 O4' C:DT11 5.0 61.0 1.0

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