Phosphorus in PDB 1a35: Human Topoisomerase I/Dna Complex

Enzymatic activity of Human Topoisomerase I/Dna Complex

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

Protein crystallography data

The structure of Human Topoisomerase I/Dna Complex, PDB code: 1a35 was solved by M.R.Redinbo, L.Stewart, P.Kuhn, J.J.Champoux, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.800, 66.300, 71.800, 90.00, 98.40, 90.00
R / Rfree (%) 20.9 / 30.8

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 Human Topoisomerase I/Dna Complex (pdb code 1a35). 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 Topoisomerase I/Dna Complex, PDB code: 1a35:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 42 in 1a35

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Phosphorus binding site 1 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P2

b:78.4
occ:1.00
P C:DA2 0.0 78.4 1.0
OP2 C:DA2 1.5 78.4 1.0
OP1 C:DA2 1.5 78.2 1.0
O5' C:DA2 1.6 75.2 1.0
O3' C:DA1 1.6 74.2 1.0
C3' C:DA1 2.6 71.3 1.0
C5' C:DA2 2.6 70.5 1.0
C2' C:DA1 3.2 67.9 1.0
C4' C:DA1 3.9 72.0 1.0
C4' C:DA2 3.9 65.2 1.0
C1' C:DA1 4.2 61.3 1.0
C3' C:DA2 4.4 63.1 1.0
O4' C:DA1 4.5 68.7 1.0
O4' C:DA2 4.6 61.3 1.0
C2' C:DA2 4.7 55.9 1.0

Phosphorus binding site 2 out of 42 in 1a35

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Phosphorus binding site 2 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P3

b:70.2
occ:1.00
P C:DA3 0.0 70.2 1.0
OP2 C:DA3 1.5 77.3 1.0
OP1 C:DA3 1.5 72.3 1.0
O5' C:DA3 1.6 65.7 1.0
O3' C:DA2 1.6 68.0 1.0
C5' C:DA3 2.6 61.3 1.0
C3' C:DA2 2.6 63.1 1.0
C2' C:DA2 3.2 55.9 1.0
C4' C:DA3 3.9 55.5 1.0
C4' C:DA2 3.9 65.2 1.0
C1' C:DA2 4.0 51.4 1.0
C8 C:DA3 4.0 32.2 1.0
O4' C:DA3 4.2 53.1 1.0
C3' C:DA3 4.4 53.6 1.0
C2' C:DA3 4.5 46.9 1.0
O4' C:DA2 4.5 61.3 1.0
C1' C:DA3 4.8 44.8 1.0
N9 C:DA3 4.8 35.5 1.0
N7 C:DA3 4.9 29.4 1.0

Phosphorus binding site 3 out of 42 in 1a35

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Phosphorus binding site 3 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P4

b:60.2
occ:1.00
P C:DA4 0.0 60.2 1.0
OP1 C:DA4 1.5 61.0 1.0
OP2 C:DA4 1.5 62.0 1.0
O5' C:DA4 1.6 54.9 1.0
O3' C:DA3 1.6 56.4 1.0
C5' C:DA4 2.6 47.6 1.0
C3' C:DA3 2.6 53.6 1.0
C2' C:DA3 3.2 46.9 1.0
C4' C:DA4 3.9 45.8 1.0
C4' C:DA3 3.9 55.5 1.0
O C:HOH1167 4.1 57.3 1.0
C1' C:DA3 4.2 44.8 1.0
C3' C:DA4 4.2 43.1 1.0
O4' C:DA4 4.5 39.8 1.0
O4' C:DA3 4.6 53.1 1.0
C2' C:DA4 4.6 36.2 1.0
C8 C:DA4 4.8 23.9 1.0

Phosphorus binding site 4 out of 42 in 1a35

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Phosphorus binding site 4 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P5

b:47.5
occ:1.00
P C:DA5 0.0 47.5 1.0
OP2 C:DA5 1.5 52.0 1.0
OP1 C:DA5 1.5 49.3 1.0
O5' C:DA5 1.6 46.0 1.0
O3' C:DA4 1.6 45.6 1.0
C5' C:DA5 2.6 38.2 1.0
C3' C:DA4 2.6 43.1 1.0
C2' C:DA4 3.2 36.2 1.0
C4' C:DA5 3.9 36.1 1.0
C4' C:DA4 3.9 45.8 1.0
C1' C:DA4 4.2 32.8 1.0
C3' C:DA5 4.3 36.0 1.0
O4' C:DA5 4.4 37.2 1.0
O4' C:DA4 4.6 39.8 1.0
C2' C:DA5 4.7 37.2 1.0
C5' C:DA4 5.0 47.6 1.0

Phosphorus binding site 5 out of 42 in 1a35

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Phosphorus binding site 5 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P6

b:44.6
occ:1.00
P C:DG6 0.0 44.6 1.0
OP2 C:DG6 1.5 51.1 1.0
OP1 C:DG6 1.5 45.9 1.0
O5' C:DG6 1.6 47.9 1.0
O3' C:DA5 1.6 41.4 1.0
C5' C:DG6 2.6 41.0 1.0
C3' C:DA5 2.6 36.0 1.0
C2' C:DA5 3.2 37.2 1.0
C4' C:DG6 3.9 32.6 1.0
C4' C:DA5 3.9 36.1 1.0
CD1 A:ILE424 4.0 27.7 1.0
C1' C:DA5 4.1 31.1 1.0
C3' C:DG6 4.3 33.2 1.0
O4' C:DG6 4.5 28.3 1.0
O4' C:DA5 4.6 37.2 1.0
O A:HOH1018 4.7 47.5 1.0
O C:HOH1268 4.7 51.4 1.0
C2' C:DG6 4.8 32.0 1.0
CG1 A:ILE424 5.0 26.2 1.0
C5' C:DA5 5.0 38.2 1.0

Phosphorus binding site 6 out of 42 in 1a35

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Phosphorus binding site 6 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P7

b:25.6
occ:1.00
P C:DA7 0.0 25.6 1.0
OP1 C:DA7 1.5 28.5 1.0
OP2 C:DA7 1.5 23.5 1.0
O5' C:DA7 1.6 28.8 1.0
O3' C:DG6 1.6 30.3 1.0
C5' C:DA7 2.6 26.4 1.0
C3' C:DG6 2.6 33.2 1.0
C2' C:DG6 3.3 32.0 1.0
OH A:TYR426 3.4 21.2 1.0
NE1 A:TRP412 3.6 21.1 1.0
O C:HOH1171 3.8 55.8 1.0
C4' C:DA7 3.9 27.0 1.0
C4' C:DG6 3.9 32.6 1.0
CE2 A:TYR426 4.2 21.9 1.0
CZ A:TYR426 4.2 22.1 1.0
C1' C:DG6 4.3 23.9 1.0
C3' C:DA7 4.4 27.5 1.0
CE2 A:TRP412 4.4 20.6 1.0
O A:HOH1058 4.4 47.0 1.0
O4' C:DA7 4.4 28.8 1.0
CZ2 A:TRP412 4.5 16.9 1.0
CD1 A:TRP412 4.6 17.4 1.0
C2' C:DA7 4.7 25.5 1.0
O4' C:DG6 4.8 28.3 1.0
CG1 A:VAL410 4.8 17.2 1.0
C5' C:DG6 5.0 41.0 1.0

Phosphorus binding site 7 out of 42 in 1a35

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Phosphorus binding site 7 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P8

b:31.8
occ:1.00
P C:DC8 0.0 31.8 1.0
OP1 C:DC8 1.5 29.9 1.0
OP2 C:DC8 1.5 36.7 1.0
O5' C:DC8 1.6 36.2 1.0
O3' C:DA7 1.6 27.4 1.0
C5' C:DC8 2.6 39.3 1.0
C3' C:DA7 2.6 27.5 1.0
OG1 A:THR411 3.0 41.0 1.0
C2' C:DA7 3.4 25.5 1.0
N A:THR411 3.6 29.1 1.0
C4' C:DC8 3.9 37.9 1.0
C4' C:DA7 3.9 27.0 1.0
CG2 A:THR411 3.9 24.9 1.0
CB A:THR411 3.9 31.5 1.0
O4' C:DC8 4.1 36.0 1.0
CE A:MET428 4.2 48.3 1.0
C1' C:DA7 4.3 26.3 1.0
CA A:THR411 4.4 27.4 1.0
CA A:VAL410 4.4 28.2 1.0
C A:VAL410 4.5 28.4 1.0
CB A:VAL410 4.6 31.1 1.0
O4' C:DA7 4.7 28.8 1.0
C3' C:DC8 4.7 38.7 1.0
CD1 A:TRP412 4.7 17.4 1.0
C5' C:DA7 4.9 26.4 1.0
N A:TRP412 4.9 23.6 1.0

Phosphorus binding site 8 out of 42 in 1a35

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Phosphorus binding site 8 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P9

b:51.7
occ:1.00
P C:DT9 0.0 51.7 1.0
OP1 C:DT9 1.5 46.5 1.0
OP2 C:DT9 1.5 45.6 1.0
O5' C:DT9 1.6 48.9 1.0
O3' C:DC8 1.6 45.0 1.0
C3' C:DC8 2.6 38.7 1.0
C5' C:DT9 2.6 42.1 1.0
C2' C:DC8 3.3 41.0 1.0
NZ A:LYS439 3.3 70.8 1.0
C6 C:DT9 3.8 24.5 1.0
C4' C:DT9 3.9 37.0 1.0
C4' C:DC8 3.9 37.9 1.0
O4' C:DT9 4.0 34.0 1.0
C7 C:DT9 4.1 17.2 1.0
C1' C:DC8 4.1 33.6 1.0
CE A:LYS436 4.2 53.1 1.0
NZ A:LYS436 4.3 48.2 1.0
CE A:LYS439 4.3 69.4 1.0
CD A:LYS436 4.3 53.1 1.0
C5 C:DT9 4.4 17.3 1.0
C3' C:DT9 4.5 33.5 1.0
O A:HOH1179 4.5 38.6 1.0
C2' C:DT9 4.6 33.3 1.0
O4' C:DC8 4.7 36.0 1.0
C1' C:DT9 4.7 30.1 1.0
N1 C:DT9 4.8 26.4 1.0
C5' C:DC8 4.9 39.3 1.0

Phosphorus binding site 9 out of 42 in 1a35

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Phosphorus binding site 9 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P10

b:35.2
occ:1.00
P C:DT10 0.0 35.2 1.0
OP1 C:DT10 1.5 26.5 1.0
OP2 C:DT10 1.5 32.4 1.0
O5' C:DT10 1.6 33.6 1.0
O3' C:DT9 1.6 32.9 1.0
C5' C:DT10 2.6 31.8 1.0
C3' C:DT9 2.6 33.5 1.0
C2' C:DT9 3.3 33.3 1.0
NZ A:LYS443 3.5 28.9 1.0
O A:HOH1022 3.7 33.9 1.0
C4' C:DT10 3.9 34.2 1.0
C4' C:DT9 3.9 37.0 1.0
ND2 A:ASN722 4.0 43.6 1.0
CD A:LYS443 4.1 33.4 1.0
C1' C:DT9 4.2 30.1 1.0
CE A:LYS443 4.3 35.0 1.0
O A:ASN722 4.3 30.4 1.0
NZ A:LYS587 4.4 61.3 1.0
C3' C:DT10 4.4 39.3 1.0
O4' C:DT10 4.5 33.4 1.0
CB A:ASN722 4.6 36.6 1.0
O4' C:DT9 4.7 34.0 1.0
O A:HOH1089 4.7 22.7 1.0
CG A:ASN722 4.8 38.6 1.0
C2' C:DT10 4.8 36.2 1.0
O A:HOH1081 4.8 55.7 1.0
CE A:LYS587 4.8 52.5 1.0
O A:HOH1141 5.0 58.2 1.0

Phosphorus binding site 10 out of 42 in 1a35

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Phosphorus binding site 10 out of 42 in the Human 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 Human Topoisomerase I/Dna Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:P11

b:53.6
occ:1.00
P C:DA11 0.0 53.6 1.0
OP1 C:DA11 1.5 49.9 1.0
OP2 C:DA11 1.5 53.8 1.0
O3' C:DT10 1.6 48.7 1.0
O5' C:DA11 1.6 50.6 1.0
C3' C:DT10 2.6 39.3 1.0
C5' C:DA11 2.6 41.8 1.0
C2' C:DT10 3.5 36.2 1.0
CZ A:PHE723 3.8 45.0 1.0
CE1 A:PHE723 3.8 42.8 1.0
C4' C:DT10 3.8 34.2 1.0
NE2 A:HIS632 3.8 55.3 1.0
C4' C:DA11 3.9 39.1 1.0
O A:HOH1080 3.9 59.7 1.0
NH2 A:ARG488 4.2 44.4 1.0
C1' C:DT10 4.2 31.9 1.0
O4' C:DA11 4.2 36.4 1.0
NH1 A:ARG590 4.3 30.4 1.0
CD2 A:HIS632 4.5 55.8 1.0
O A:HOH1148 4.5 61.4 1.0
C3' C:DA11 4.5 36.3 1.0
O A:HOH1088 4.6 52.2 1.0
O4' C:DT10 4.6 33.4 1.0
NE A:ARG488 4.8 38.7 1.0
C5' C:DT10 4.9 31.8 1.0
NZ A:LYS532 4.9 43.5 1.0
CE1 A:HIS632 4.9 56.4 1.0
NH2 A:ARG590 4.9 30.2 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: Fri Sep 25 12:04:43 2020

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