Phosphorus in PDB 173d: Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna

Protein crystallography data

The structure of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna, PDB code: 173d was solved by S.Kamitori, F.Takusagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 3.00
Space group F 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 69.900, 61.410, 54.250, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Phosphorus atom in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna (pdb code 173d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 14 binding sites of Phosphorus where determined in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna, PDB code: 173d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 14 in 173d

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Phosphorus binding site 1 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:9.8
occ:1.00
 P A:DA2 0.0 9.8 1.0
OP2 A:DA2 1.5 9.8 1.0
OP1 A:DA2 1.5 9.8 1.0
O3' A:DG1 1.6 9.5 1.0
O5' A:DA2 1.6 9.8 1.0
C5' A:DA2 2.7 8.1 1.0
C3' A:DG1 2.8 10.9 1.0
O A:HOH2021 3.4 6.0 1.0
C4' A:DG1 3.5 10.9 1.0
C2' A:DG1 3.7 10.9 1.0
C5' A:DG1 3.8 10.9 1.0
C4' A:DA2 3.9 8.1 1.0
O A:HOH2023 4.3 6.0 1.0
O4' A:DA2 4.3 8.1 1.0
C2' A:DA2 4.3 8.1 1.0
C3' A:DA2 4.3 8.1 1.0
C8 A:DA2 4.4 13.7 1.0
O5' A:DG1 4.6 9.5 1.0
C1' A:DA2 4.7 13.7 1.0
O4' A:DG1 4.8 10.9 1.0
O A:HOH2025 4.8 16.4 1.0
C1' A:DG1 4.9 15.7 1.0
N9 A:DA2 4.9 13.7 1.0

Phosphorus binding site 2 out of 14 in 173d

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Phosphorus binding site 2 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:13.6
occ:1.00
 P A:DA3 0.0 13.6 1.0
OP1 A:DA3 1.5 13.6 1.0
OP2 A:DA3 1.5 13.6 1.0
O5' A:DA3 1.6 13.6 1.0
O3' A:DA2 1.6 9.8 1.0
C5' A:DA3 2.6 14.1 1.0
C3' A:DA2 2.7 8.1 1.0
C2' A:DA2 3.3 8.1 1.0
C4' A:DA3 4.0 14.1 1.0
C4' A:DA2 4.0 8.1 1.0
O3' A:DA3 4.2 13.6 1.0
C1' A:DA2 4.2 13.7 1.0
O A:HOH2028 4.2 21.7 1.0
O A:HOH2029 4.4 7.8 1.0
C3' A:DA3 4.4 14.1 1.0
O4' A:DA3 4.5 14.1 1.0
O A:HOH2026 4.6 6.0 1.0
O4' A:DA2 4.7 8.1 1.0
O A:HOH2021 4.7 6.0 1.0
OP2 A:DG4 4.8 18.3 1.0
P A:DG4 4.9 18.3 1.0

Phosphorus binding site 3 out of 14 in 173d

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Phosphorus binding site 3 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:18.3
occ:1.00
 P A:DG4 0.0 18.3 1.0
OP2 A:DG4 1.5 18.3 1.0
OP1 A:DG4 1.5 18.3 1.0
O5' A:DG4 1.6 18.3 1.0
O3' A:DA3 1.6 13.6 1.0
C3' A:DA3 2.6 14.1 1.0
C5' A:DG4 2.7 13.5 1.0
C2' A:DA3 3.5 14.1 1.0
O3' A:DG4 3.7 18.3 1.0
C3' A:DG4 3.8 13.5 1.0
C4' A:DA3 3.8 14.1 1.0
O5' A:DA3 3.9 13.6 1.0
C4' A:DG4 4.0 13.5 1.0
C8 A:DG4 4.0 6.0 1.0
C5' A:DA3 4.1 14.1 1.0
OP2 A:DC5 4.2 7.6 1.0
O A:HOH2028 4.3 21.7 1.0
O A:HOH2031 4.4 7.0 1.0
P A:DC5 4.4 7.6 1.0
O A:HOH2029 4.4 7.8 1.0
O4' A:DA3 4.5 14.1 1.0
O4' A:DG4 4.7 13.5 1.0
OP1 A:DA3 4.7 13.6 1.0
C1' A:DA3 4.7 6.0 1.0
N9 A:DG4 4.7 6.0 1.0
N7 A:DG4 4.7 6.0 1.0
OP1 A:DC5 4.9 7.6 1.0
P A:DA3 4.9 13.6 1.0
O A:HOH2034 4.9 6.0 1.0
C1' A:DG4 4.9 6.0 1.0
O A:HOH2033 5.0 18.9 1.0

Phosphorus binding site 4 out of 14 in 173d

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Phosphorus binding site 4 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:7.6
occ:1.00
 P A:DC5 0.0 7.6 1.0
OP2 A:DC5 1.5 7.6 1.0
OP1 A:DC5 1.5 7.6 1.0
O3' A:DG4 1.6 18.3 1.0
O5' A:DC5 1.7 7.6 1.0
C5' A:DC5 2.8 34.3 1.0
C3' A:DG4 2.9 13.5 1.0
C2' A:DG4 3.3 13.5 1.0
O3 C:PXZ6 3.6 6.0 0.5
N2 C:PXZ6 3.9 6.0 0.5
O5' A:DG4 3.9 18.3 1.0
O A:HOH2031 3.9 7.0 1.0
O A:HOH2033 4.0 18.9 1.0
O A:HOH2034 4.0 6.0 1.0
C4' A:DC5 4.2 34.3 1.0
C4' A:DG4 4.3 13.5 1.0
OP1 A:DG4 4.3 18.3 1.0
OP2 A:DG4 4.3 18.3 1.0
O4' A:DC5 4.3 34.3 1.0
P A:DG4 4.4 18.3 1.0
C6 A:DC5 4.4 6.0 1.0
C1' A:DG4 4.4 6.0 1.0
C3 C:PXZ6 4.4 6.0 1.0
C8 A:DG4 4.5 6.0 1.0
C5' A:DG4 4.5 13.5 1.0
C2 C:PXZ6 4.6 6.0 1.0
N9 A:DG4 4.8 6.0 1.0
C2' A:DC5 4.9 34.3 1.0
C1' A:DC5 4.9 6.0 1.0
N1 A:DC5 4.9 6.0 1.0

Phosphorus binding site 5 out of 14 in 173d

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Phosphorus binding site 5 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:9.8
occ:1.00
 P A:DT6 0.0 9.8 1.0
OP2 A:DT6 1.5 9.8 1.0
OP1 A:DT6 1.5 9.8 1.0
O5' A:DT6 1.6 9.8 1.0
O3' A:DC5 1.6 7.6 1.0
C5' A:DT6 2.6 7.0 1.0
C3' A:DC5 2.7 34.3 1.0
C6 A:DT6 3.7 6.0 1.0
O A:HOH2037 3.7 6.0 1.0
C7 A:DT6 3.7 6.0 1.0
O A:HOH2035 3.7 6.0 1.0
C4' A:DC5 3.8 34.3 1.0
C2' A:DC5 4.0 34.3 1.0
C5 A:DT6 4.0 6.0 1.0
C4' A:DT6 4.0 7.0 1.0
O A:HOH2014 4.3 7.1 1.0
O4' A:DC5 4.4 34.3 1.0
O A:HOH2010 4.4 13.2 1.0
O A:HOH2036 4.5 6.0 1.0
C1' A:DC5 4.5 6.0 1.0
N1 A:DT6 4.5 6.0 1.0
C3' A:DT6 4.6 7.0 1.0
C2' A:DT6 4.7 7.0 1.0
O4' A:DT6 4.7 7.0 1.0
C1' A:DT6 4.9 6.0 1.0
O A:HOH2009 4.9 6.3 1.0

Phosphorus binding site 6 out of 14 in 173d

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Phosphorus binding site 6 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:16.1
occ:1.00
 P A:DT7 0.0 16.1 1.0
OP2 A:DT7 1.5 16.1 1.0
OP1 A:DT7 1.5 16.1 1.0
O5' A:DT7 1.6 16.1 1.0
O3' A:DT6 1.6 9.8 1.0
C5' A:DT7 2.6 10.4 1.0
C3' A:DT6 2.7 7.0 1.0
C2' A:DT6 3.1 7.0 1.0
O A:HOH2040 3.5 14.0 1.0
C1' A:DT6 3.9 6.0 1.0
C4' A:DT6 3.9 7.0 1.0
C4' A:DT7 4.0 10.4 1.0
O4' A:DT6 4.0 7.0 1.0
C3' A:DT7 4.1 10.4 1.0
O A:HOH2044 4.2 6.0 1.0
C2' A:DT7 4.6 10.4 1.0
O4' A:DT7 4.8 10.4 1.0
O A:HOH2043 4.8 6.0 1.0

Phosphorus binding site 7 out of 14 in 173d

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Phosphorus binding site 7 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:11.0
occ:1.00
 P A:DC8 0.0 11.0 1.0
OP1 A:DC8 1.5 11.0 1.0
OP2 A:DC8 1.5 11.0 1.0
O5' A:DC8 1.6 11.0 1.0
O3' A:DT7 1.6 16.1 1.0
C3' A:DT7 2.6 10.4 1.0
C5' A:DC8 2.6 9.1 1.0
O4' A:DC8 3.2 9.1 1.0
C2' A:DT7 3.6 10.4 1.0
C4' A:DC8 3.7 9.1 1.0
O A:HOH2044 3.7 6.0 1.0
O A:HOH2043 3.8 6.0 1.0
C4' A:DT7 3.8 10.4 1.0
C6 A:DC8 3.8 6.0 1.0
C1' A:DC8 4.0 6.0 1.0
C2' A:DC8 4.2 9.1 1.0
C1' A:DT7 4.3 6.0 1.0
N1 A:DC8 4.4 6.0 1.0
C3' A:DC8 4.5 9.1 1.0
C5' A:DT7 4.6 10.4 1.0
O5' A:DT7 4.6 16.1 1.0
O4' A:DT7 4.7 10.4 1.0
C5 A:DC8 4.9 6.0 1.0

Phosphorus binding site 8 out of 14 in 173d

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Phosphorus binding site 8 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:24.8
occ:1.00
 P B:DA10 0.0 24.8 1.0
OP2 B:DA10 1.5 24.8 1.0
OP1 B:DA10 1.5 24.8 1.0
O5' B:DA10 1.6 24.8 1.0
O3' B:DG9 1.7 16.0 1.0
C5' B:DA10 2.7 6.0 1.0
C3' B:DG9 2.8 23.1 1.0
O4' B:DA10 3.2 6.0 1.0
C4' B:DA10 3.7 6.0 1.0
C4' B:DG9 3.8 23.1 1.0
C8 B:DA10 3.8 18.6 1.0
O5' B:DG9 3.9 16.0 1.0
O B:HOH2016 3.9 6.0 1.0
C3' B:DA10 4.0 6.0 1.0
C2' B:DG9 4.1 23.1 1.0
C1' B:DA10 4.3 18.6 1.0
N9 B:DA10 4.4 18.6 1.0
C5' B:DG9 4.4 23.1 1.0
C2' B:DA10 4.6 6.0 1.0
O B:HOH2001 4.6 6.0 1.0
N7 B:DA10 4.9 18.6 1.0
O3' B:DA10 4.9 24.8 1.0
C1' B:DG9 4.9 9.8 1.0
O4' B:DG9 5.0 23.1 1.0

Phosphorus binding site 9 out of 14 in 173d

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Phosphorus binding site 9 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:20.5
occ:1.00
 P B:DA11 0.0 20.5 1.0
OP1 B:DA11 1.5 20.5 1.0
OP2 B:DA11 1.5 20.5 1.0
O5' B:DA11 1.6 20.5 1.0
O3' B:DA10 1.6 24.8 1.0
C5' B:DA11 2.7 14.0 1.0
C3' B:DA10 2.7 6.0 1.0
C2' B:DA10 3.3 6.0 1.0
O B:HOH2020 3.9 6.0 1.0
O3' B:DA11 3.9 20.5 1.0
C4' B:DA11 3.9 14.0 1.0
C4' B:DA10 4.1 6.0 1.0
C3' B:DA11 4.1 14.0 1.0
O5' B:DA10 4.4 24.8 1.0
O4' B:DA11 4.4 14.0 1.0
O B:HOH2021 4.5 6.0 1.0
C5' B:DA10 4.6 6.0 1.0
O B:HOH2008 4.7 6.0 1.0
C1' B:DA10 4.7 18.6 1.0
O4' B:DA10 4.9 6.0 1.0
O B:HOH2019 4.9 14.4 1.0

Phosphorus binding site 10 out of 14 in 173d

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Phosphorus binding site 10 out of 14 in the Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2- Actinomycin D Complexes and Its Host Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:8.8
occ:1.00
 P B:DG12 0.0 8.8 1.0
OP2 B:DG12 1.5 8.8 1.0
OP1 B:DG12 1.5 8.8 1.0
O5' B:DG12 1.6 8.8 1.0
O3' B:DA11 1.7 20.5 1.0
C5' B:DG12 2.6 6.0 1.0
C3' B:DA11 2.9 14.0 1.0
C8 B:DG12 3.4 23.9 1.0
C2' B:DA11 3.6 14.0 1.0
N7 B:DG12 3.8 23.9 1.0
C4' B:DG12 3.8 6.0 1.0
O4' B:DG12 4.0 6.0 1.0
O5' B:DA11 4.2 20.5 1.0
C8 B:DA11 4.3 10.5 1.0
C4' B:DA11 4.3 14.0 1.0
C3' B:DG12 4.4 6.0 1.0
N9 B:DG12 4.5 23.9 1.0
N9 B:DA11 4.6 10.5 1.0
OP2 B:DA11 4.7 20.5 1.0
O B:HOH2018 4.7 6.0 1.0
C1' B:DA11 4.7 10.5 1.0
C1' B:DG12 4.8 23.9 1.0
C5' B:DA11 4.8 14.0 1.0
O4' B:DA11 4.9 14.0 1.0

Reference:

S.Kamitori, F.Takusagawa. Multiple Binding Modes of Anticancer Drug Actinomycin D: X-Ray, Molecular Modeling, and Spectroscopic Studies of D(Gaagcttc)2-Actinomycin D Complexes and Its Host Dna J.Am.Chem.Soc. V. 116 4154 1994.
ISSN: ISSN 0002-7863
DOI: 10.1021/JA00089A002
Page generated: Fri Sep 25 11:42:12 2020

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