Phosphorus in PDB 110d: Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl

Protein crystallography data

The structure of Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl, PDB code: 110d was solved by G.A.Leonard, T.W.Hambley, K.Mcauley-Hecht, T.Brown, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 7.00 / 1.90
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 28.070, 28.070, 53.350, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

The binding sites of Phosphorus atom in the Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl (pdb code 110d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 5 binding sites of Phosphorus where determined in the Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl, PDB code: 110d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5;

Phosphorus binding site 1 out of 5 in 110d

Go back to Phosphorus Binding Sites List in 110d
Phosphorus binding site 1 out of 5 in the Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:75.8
occ:1.00
P A:DG2 0.0 75.8 1.0
OP1 A:DG2 1.5 65.4 1.0
OP2 A:DG2 1.5 69.5 1.0
O3' A:DC1 1.5 63.3 1.0
O5' A:DG2 1.6 58.2 1.0
C5' A:DG2 2.7 33.0 1.0
C3' A:DC1 2.8 51.4 1.0
O A:HOH33 3.3 64.0 1.0
O A:HOH10 3.5 73.9 1.0
C2' A:DC1 3.8 44.6 1.0
O A:HOH44 3.8 56.3 1.0
C4' A:DC1 3.8 31.9 1.0
C4' A:DG2 4.0 22.4 1.0
O4' A:DG2 4.3 21.9 1.0
C5' A:DC1 4.4 45.6 1.0
C3' A:DG2 4.5 32.6 1.0
O A:HOH54 4.6 79.8 1.0
C2' A:DG2 4.6 21.4 1.0
C1' A:DC1 4.9 21.4 1.0
O4' A:DC1 5.0 34.7 1.0

Phosphorus binding site 2 out of 5 in 110d

Go back to Phosphorus Binding Sites List in 110d
Phosphorus binding site 2 out of 5 in the Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:54.3
occ:1.00
P A:DG3 0.0 54.3 1.0
OP2 A:DG3 1.5 69.4 1.0
OP1 A:DG3 1.5 16.7 1.0
O5' A:DG3 1.6 23.1 1.0
O3' A:DG2 1.6 48.6 1.0
C5' A:DG3 2.5 15.2 1.0
C3' A:DG2 2.6 32.6 1.0
C4' A:DG3 3.4 27.6 1.0
C2' A:DG3 3.6 23.8 1.0
C2' A:DG2 3.6 21.4 1.0
O4' A:DG3 3.6 20.4 1.0
C8 A:DG3 3.7 8.7 1.0
C3' A:DG3 3.8 15.8 1.0
C4' A:DG2 3.8 22.4 1.0
C1' A:DG3 4.0 15.4 1.0
N9 A:DG3 4.2 10.4 1.0
C1' A:DG2 4.3 24.8 1.0
O4' A:DG2 4.7 21.9 1.0
N7 A:DG3 4.9 6.4 1.0
C5' A:DG2 4.9 33.0 1.0

Phosphorus binding site 3 out of 5 in 110d

Go back to Phosphorus Binding Sites List in 110d
Phosphorus binding site 3 out of 5 in the Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:27.5
occ:1.00
P A:DC4 0.0 27.5 1.0
OP2 A:DC4 1.5 33.5 1.0
OP1 A:DC4 1.6 11.9 1.0
O3' A:DG3 1.6 29.0 1.0
O5' A:DC4 1.6 19.0 1.0
C5' A:DC4 2.6 9.3 1.0
C3' A:DG3 2.7 15.8 1.0
O A:HOH28 3.3 37.1 1.0
C2' A:DG3 3.5 23.8 1.0
C4' A:DC4 3.8 22.4 1.0
C4' A:DG3 3.9 27.6 1.0
O4' A:DC4 4.0 19.6 1.0
O A:HOH13 4.0 66.6 1.0
C1' A:DG3 4.3 15.4 1.0
C3' A:DC4 4.4 41.6 1.0
O A:HOH47 4.6 38.4 1.0
O A:HOH9 4.6 39.8 1.0
O4' A:DG3 4.7 20.4 1.0

Phosphorus binding site 4 out of 5 in 110d

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Phosphorus binding site 4 out of 5 in the Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:47.8
occ:1.00
P A:DC5 0.0 47.8 1.0
OP1 A:DC5 1.5 59.7 1.0
OP2 A:DC5 1.5 62.7 1.0
O5' A:DC5 1.6 48.6 1.0
O3' A:DC4 1.6 62.1 1.0
C5' A:DC5 2.6 35.3 1.0
C3' A:DC4 2.7 41.6 1.0
C2' A:DC4 3.5 30.0 1.0
O4' A:DC5 3.6 35.1 1.0
O A:HOH41 3.6 56.4 1.0
C4' A:DC5 3.8 16.9 1.0
C4' A:DC4 3.8 22.4 1.0
O A:HOH37 4.3 43.6 1.0
C5' A:DC4 4.4 9.3 1.0
C3' A:DC5 4.5 29.5 1.0
C2' A:DC5 4.6 14.9 1.0
O A:HOH38 4.6 72.1 1.0
C1' A:DC4 4.7 9.4 1.0
C1' A:DC5 4.8 5.4 1.0
O4' A:DC4 4.9 19.6 1.0
O5' A:DC4 4.9 19.0 1.0

Phosphorus binding site 5 out of 5 in 110d

Go back to Phosphorus Binding Sites List in 110d
Phosphorus binding site 5 out of 5 in the Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Anthracycline-Dna Interactions at Unfavourable Base Base- Pair Triplet-Binding Sites: Structures of D(Cggccg) /Daunomycin and D(Tggcca)/Adriamycin Compl within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:23.7
occ:1.00
P A:DG6 0.0 23.7 1.0
OP2 A:DG6 1.4 10.8 1.0
OP1 A:DG6 1.5 42.4 1.0
O5' A:DG6 1.6 22.5 1.0
O3' A:DC5 1.7 23.4 1.0
C5' A:DG6 2.6 42.6 1.0
C3' A:DC5 2.7 29.5 1.0
C4' A:DC5 3.6 16.9 1.0
C4' A:DG6 3.7 45.7 1.0
C3' A:DG6 3.8 46.8 1.0
O A:HOH17 3.9 35.9 1.0
C2' A:DC5 4.0 14.9 1.0
O4' A:DG6 4.0 29.2 1.0
C8 A:DG6 4.3 2.0 1.0
O A:HOH12 4.4 33.5 1.0
C5' A:DC5 4.4 35.3 1.0
O3' A:DG6 4.4 54.0 1.0
O A:HOH31 4.6 77.4 1.0
C1' A:DC5 4.7 5.4 1.0
O4' A:DC5 4.8 35.1 1.0
C1' A:DG6 4.9 22.4 1.0
N9 A:DG6 4.9 9.6 1.0
C2' A:DG6 5.0 35.7 1.0

Reference:

G.A.Leonard, T.W.Hambley, K.Mcauley-Hecht, T.Brown, W.N.Hunter. Anthracycline-Dna Interactions at Unfavourable Base-Pair Triplet-Binding Sites: Structures of D(Cggccg)/Daunomycin and D(Tggcca)/Adriamycin Complexes. Acta Crystallogr.,Sect.D V. 49 458 1993.
ISSN: ISSN 0907-4449
PubMed: 15299505
DOI: 10.1107/S090744499300527X
Page generated: Fri Sep 25 11:07:18 2020

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