Phosphorus in PDB 198d: A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution

Protein crystallography data

The structure of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution, PDB code: 198d was solved by A.Dautant, B.Langlois D'estaintot, B.Gallois, T.Brown, W.N.Hunter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 1.97
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 52.996, 52.996, 33.065, 90.00, 90.00, 120.00
R / Rfree (%) n/a / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Phosphorus atom in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution (pdb code 198d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 20 binding sites of Phosphorus where determined in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution, PDB code: 198d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 20 in 198d

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Phosphorus binding site 1 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:28.1
occ:1.00
P A:DG2 0.0 28.1 1.0
OP2 A:DG2 1.5 24.7 1.0
OP1 A:DG2 1.5 26.8 1.0
O5' A:DG2 1.6 25.4 1.0
O3' A:DC1 1.7 25.2 1.0
C5' A:DG2 2.7 24.4 1.0
C3' A:DC1 2.7 19.6 1.0
C4' A:DC1 3.7 20.6 1.0
C2' A:DC1 3.8 17.1 1.0
C4' A:DG2 3.9 22.7 1.0
O5' A:DC1 4.1 22.3 1.0
O4' A:DG2 4.3 20.8 1.0
C5' A:DC1 4.3 21.8 1.0
C3' A:DG2 4.3 23.4 1.0
C2' A:DG2 4.5 20.8 1.0
O4' A:DC1 4.9 18.8 1.0
O A:HOH92 5.0 37.4 1.0
C1' A:DC1 5.0 12.7 1.0
C1' A:DG2 5.0 17.3 1.0

Phosphorus binding site 2 out of 20 in 198d

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Phosphorus binding site 2 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:28.0
occ:1.00
P A:DA3 0.0 28.0 1.0
OP2 A:DA3 1.5 26.9 1.0
OP1 A:DA3 1.5 27.7 1.0
O3' A:DG2 1.6 26.1 1.0
O5' A:DA3 1.6 26.1 1.0
C3' A:DG2 2.6 23.4 1.0
C5' A:DA3 2.7 23.2 1.0
C4' A:DG2 3.5 22.7 1.0
C2' A:DG2 3.8 20.8 1.0
C4' A:DA3 4.0 19.4 1.0
C8 A:DA3 4.1 9.8 1.0
O4' A:DA3 4.4 17.2 1.0
O A:HOH148 4.5 30.0 1.0
C1' A:DG2 4.5 17.3 1.0
C5' A:DG2 4.5 24.4 1.0
C3' A:DA3 4.6 20.8 1.0
O4' A:DG2 4.6 20.8 1.0
N1 A:SPM29 4.7 36.5 1.0
N7 A:DA3 4.9 10.2 1.0
C2' A:DA3 4.9 18.3 1.0
N9 A:DA3 4.9 11.4 1.0
C2 A:SPM29 4.9 36.1 1.0

Phosphorus binding site 3 out of 20 in 198d

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Phosphorus binding site 3 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:23.7
occ:1.00
P A:DT4 0.0 23.7 1.0
OP2 A:DT4 1.5 22.6 1.0
OP1 A:DT4 1.5 25.7 1.0
O3' A:DA3 1.6 23.6 1.0
O5' A:DT4 1.6 21.4 1.0
C5' A:DT4 2.6 18.7 1.0
C3' A:DA3 2.7 20.8 1.0
C2' A:DA3 3.3 18.3 1.0
C4' A:DT4 3.9 17.5 1.0
C6 A:SPM29 3.9 35.7 1.0
C4' A:DA3 3.9 19.4 1.0
O A:HOH106 4.1 43.5 1.0
O A:HOH97 4.1 20.7 1.0
O A:HOH46 4.1 31.2 1.0
C1' A:DA3 4.3 13.5 1.0
C3' A:DT4 4.4 18.4 1.0
O4' A:DT4 4.4 16.5 1.0
O A:HOH80 4.4 15.9 1.0
C7 A:SPM29 4.4 35.9 1.0
O4' A:DA3 4.6 17.2 1.0
O A:HOH96 4.6 24.9 1.0
O A:HOH143 4.8 30.2 1.0

Phosphorus binding site 4 out of 20 in 198d

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Phosphorus binding site 4 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:21.2
occ:1.00
P A:DC5 0.0 21.2 1.0
OP2 A:DC5 1.5 21.7 1.0
OP1 A:DC5 1.5 23.6 1.0
O5' A:DC5 1.6 20.1 1.0
O3' A:DT4 1.6 21.4 1.0
C5' A:DC5 2.6 18.3 1.0
C3' A:DT4 2.7 18.4 1.0
C2' A:DT4 3.6 17.2 1.0
C4' A:DC5 3.8 17.3 1.0
C11 A:SPM29 3.9 35.0 1.0
C4' A:DT4 3.9 17.5 1.0
O A:HOH40 4.0 24.5 1.0
O A:HOH119 4.0 40.3 1.0
N10 A:SPM29 4.1 37.0 1.0
O4' A:DC5 4.2 16.7 1.0
C3' A:DC5 4.3 16.4 1.0
C2' A:DC5 4.5 14.3 1.0
C1' A:DT4 4.5 13.2 1.0
C9 A:SPM29 4.6 35.9 1.0
O A:HOH74 4.7 22.4 1.0
O A:HOH46 4.8 31.2 1.0
C5' A:DT4 4.8 18.7 1.0
C12 A:SPM29 4.8 34.8 1.0
O4' A:DT4 4.8 16.5 1.0
C1' A:DC5 4.9 11.7 1.0
O A:HOH34 4.9 31.5 1.0

Phosphorus binding site 5 out of 20 in 198d

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Phosphorus binding site 5 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:18.1
occ:1.00
P A:DG6 0.0 18.1 1.0
OP2 A:DG6 1.5 18.1 1.0
OP1 A:DG6 1.5 19.2 1.0
O5' A:DG6 1.6 16.1 1.0
O3' A:DC5 1.6 18.8 1.0
C5' A:DG6 2.6 15.2 1.0
C3' A:DC5 2.6 16.4 1.0
C4' A:DC5 3.7 17.3 1.0
C2' A:DC5 3.8 14.3 1.0
C4' A:DG6 3.9 14.8 1.0
N14 A:SPM29 4.1 34.9 1.0
C3' A:DG6 4.2 13.0 1.0
C8 A:DG6 4.3 6.3 1.0
O4' A:DG6 4.4 16.2 1.0
C2' A:DG6 4.5 13.4 1.0
C5' A:DC5 4.5 18.3 1.0
C13 A:SPM29 4.6 35.2 1.0
C1' A:DC5 4.7 11.7 1.0
O A:HOH40 4.8 24.5 1.0
O5' A:DC5 4.8 20.1 1.0
O4' A:DC5 4.8 16.7 1.0
C1' A:DG6 4.9 10.5 1.0
N9 A:DG6 4.9 6.9 1.0

Phosphorus binding site 6 out of 20 in 198d

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Phosphorus binding site 6 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P8

b:26.6
occ:1.00
P B:DG8 0.0 26.6 1.0
OP2 B:DG8 1.5 26.9 1.0
OP1 B:DG8 1.5 25.8 1.0
O5' B:DG8 1.6 24.7 1.0
O3' B:DC7 1.6 24.0 1.0
C5' B:DG8 2.7 21.0 1.0
C3' B:DC7 2.7 20.4 1.0
C4' B:DC7 3.7 19.9 1.0
C2' B:DC7 3.7 17.8 1.0
C4' B:DG8 4.0 17.8 1.0
O4' B:DG8 4.2 16.3 1.0
O B:HOH140 4.5 41.1 1.0
O4' B:DC7 4.6 17.5 1.0
C3' B:DG8 4.6 18.1 1.0
C1' B:DC7 4.7 14.0 1.0
C5' B:DC7 4.8 19.9 1.0
O B:HOH123 4.9 43.6 1.0

Phosphorus binding site 7 out of 20 in 198d

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Phosphorus binding site 7 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P9

b:21.7
occ:1.00
P B:DA9 0.0 21.7 1.0
OP1 B:DA9 1.5 23.1 1.0
OP2 B:DA9 1.5 23.0 1.0
O3' B:DG8 1.6 20.1 1.0
O5' B:DA9 1.6 23.2 1.0
C5' B:DA9 2.6 21.7 1.0
C3' B:DG8 2.6 18.1 1.0
C2' B:DG8 3.6 15.1 1.0
C4' B:DA9 3.8 20.1 1.0
C4' B:DG8 3.8 17.8 1.0
O4' B:DA9 3.9 18.6 1.0
C8 B:DA9 4.2 7.2 1.0
O B:HOH167 4.5 47.3 1.0
C3' B:DA9 4.5 20.5 1.0
C1' B:DG8 4.6 10.7 1.0
C5' B:DG8 4.7 21.0 1.0
C1' B:DA9 4.8 15.0 1.0
N9 B:DA9 4.8 11.1 1.0
O4' B:DG8 4.8 16.3 1.0
C2' B:DA9 4.9 18.0 1.0

Phosphorus binding site 8 out of 20 in 198d

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Phosphorus binding site 8 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P10

b:25.9
occ:1.00
P B:DT10 0.0 25.9 1.0
OP2 B:DT10 1.5 25.0 1.0
OP1 B:DT10 1.5 24.3 1.0
O5' B:DT10 1.6 24.1 1.0
O3' B:DA9 1.6 22.2 1.0
C5' B:DT10 2.7 23.7 1.0
C3' B:DA9 2.7 20.5 1.0
C2' B:DA9 3.5 18.0 1.0
C4' B:DA9 3.9 20.1 1.0
C4' B:DT10 4.0 23.2 1.0
O B:HOH41 4.2 3.5 1.0
O4' B:DT10 4.3 21.3 1.0
O B:HOH91 4.6 21.5 1.0
C1' B:DA9 4.6 15.0 1.0
C3' B:DT10 4.7 24.5 1.0
O4' B:DA9 4.9 18.6 1.0
C5' B:DA9 4.9 21.7 1.0

Phosphorus binding site 9 out of 20 in 198d

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Phosphorus binding site 9 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P11

b:27.9
occ:1.00
P B:DC11 0.0 27.9 1.0
OP2 B:DC11 1.5 27.2 1.0
OP1 B:DC11 1.5 27.5 1.0
O3' B:DT10 1.6 26.7 1.0
O5' B:DC11 1.6 27.1 1.0
C5' B:DC11 2.6 24.9 1.0
C3' B:DT10 2.7 24.5 1.0
C2' B:DT10 3.6 23.1 1.0
C4' B:DT10 3.9 23.2 1.0
C4' B:DC11 3.9 23.6 1.0
O B:HOH89 4.1 32.4 1.0
O4' B:DC11 4.2 23.8 1.0
C5' B:DT10 4.3 23.7 1.0
C3' B:DC11 4.7 23.5 1.0
O B:HOH90 4.7 31.9 1.0
O5' B:DT10 4.9 24.1 1.0
C1' B:DT10 4.9 20.0 1.0
C2' B:DC11 4.9 21.1 1.0
O4' B:DT10 5.0 21.3 1.0

Phosphorus binding site 10 out of 20 in 198d

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Phosphorus binding site 10 out of 20 in the A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of A Trigonal Form of the Idarubicin-D(Cgatcg) Complex: Crystal and Molecular Structure at 2.0 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:P12

b:23.8
occ:1.00
P B:DG12 0.0 23.8 1.0
OP2 B:DG12 1.5 24.8 1.0
OP1 B:DG12 1.5 24.7 1.0
O3' B:DC11 1.6 23.6 1.0
O5' B:DG12 1.6 21.2 1.0
C5' B:DG12 2.6 18.4 1.0
C3' B:DC11 2.7 23.5 1.0
C4' B:DC11 3.7 23.6 1.0
C2' B:DC11 3.8 21.1 1.0
C4' B:DG12 3.9 15.8 1.0
O B:HOH94 4.1 43.2 1.0
C8 B:DG12 4.2 7.6 1.0
C3' B:DG12 4.2 15.2 1.0
O B:HOH61 4.3 41.1 1.0
C2' B:DG12 4.4 13.4 1.0
C5' B:DC11 4.5 24.9 1.0
C1' B:DC11 4.6 19.2 1.0
O4' B:DC11 4.7 23.8 1.0
O B:HOH43 4.8 20.0 1.0
N9 B:DG12 4.9 8.0 1.0
O4' B:DG12 4.9 12.8 1.0
C1' B:DG12 5.0 10.9 1.0

Reference:

A.Dautant, B.Langlois D'estaintot, B.Gallois, T.Brown, W.N.Hunter. A Trigonal Form of the Idarubicin:D(Cgatcg) Complex; Crystal and Molecular Structure at 2.0 A Resolution. Nucleic Acids Res. V. 23 1710 1995.
ISSN: ISSN 0305-1048
PubMed: 7784175
DOI: 10.1093/NAR/23.10.1710
Page generated: Fri Sep 25 11:53:54 2020

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