Phosphorus in PDB 102d: Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine

Protein crystallography data

The structure of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine, PDB code: 102d was solved by C.M.Nunn, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.780, 41.160, 65.510, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / n/a

Phosphorus Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Phosphorus atom in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine (pdb code 102d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine, PDB code: 102d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 102d

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Phosphorus binding site 1 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine 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
OP1 A:DG2 1.5 26.6 1.0
OP2 A:DG2 1.5 29.4 1.0
O5' A:DG2 1.6 25.9 1.0
O3' A:DC1 1.7 27.5 1.0
C5' A:DG2 2.6 22.3 1.0
C3' A:DC1 2.8 25.7 1.0
C2' A:DC1 3.4 25.0 1.0
C4' A:DG2 3.8 20.2 1.0
O A:HOH34 4.0 33.9 1.0
C4' A:DC1 4.1 26.2 1.0
C3' A:DG2 4.1 19.9 1.0
C1' A:DC1 4.2 23.4 1.0
C2' A:DG2 4.4 18.6 1.0
O4' A:DG2 4.5 18.9 1.0
O4' A:DC1 4.7 25.4 1.0
C8 A:DG2 4.9 15.3 1.0

Phosphorus binding site 2 out of 22 in 102d

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Phosphorus binding site 2 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:21.8
occ:1.00
P A:DC3 0.0 21.8 1.0
OP2 A:DC3 1.5 21.6 1.0
OP1 A:DC3 1.5 21.6 1.0
O5' A:DC3 1.6 20.6 1.0
O3' A:DG2 1.6 21.0 1.0
C5' A:DC3 2.5 20.7 1.0
C3' A:DG2 2.7 19.9 1.0
C2' A:DG2 3.3 18.6 1.0
C4' A:DC3 3.9 20.7 1.0
C4' A:DG2 4.1 20.2 1.0
C1' A:DG2 4.2 17.9 1.0
O4' A:DC3 4.4 18.9 1.0
C3' A:DC3 4.4 21.8 1.0
O A:HOH41 4.6 57.6 1.0
O4' A:DG2 4.7 18.9 1.0
C6 A:DC3 4.7 17.5 1.0
C2' A:DC3 4.8 20.9 1.0

Phosphorus binding site 3 out of 22 in 102d

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Phosphorus binding site 3 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:26.7
occ:1.00
P A:DA4 0.0 26.7 1.0
OP1 A:DA4 1.5 26.9 1.0
OP2 A:DA4 1.5 26.5 1.0
O5' A:DA4 1.6 25.7 1.0
O3' A:DC3 1.7 24.8 1.0
C5' A:DA4 2.5 23.2 1.0
C3' A:DC3 2.7 21.8 1.0
C2' A:DC3 3.3 20.9 1.0
C4' A:DA4 3.7 22.4 1.0
C4' A:DC3 3.9 20.7 1.0
C3' A:DA4 4.0 21.9 1.0
C2' A:DA4 4.2 20.0 1.0
O4' A:DA4 4.4 21.4 1.0
C1' A:DC3 4.4 18.1 1.0
C8 A:DA4 4.5 14.3 1.0
O4' A:DC3 4.7 18.9 1.0
C1' A:DA4 4.8 18.5 1.0
C5' A:DC3 4.9 20.7 1.0

Phosphorus binding site 4 out of 22 in 102d

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Phosphorus binding site 4 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:26.1
occ:1.00
P A:DA5 0.0 26.1 1.0
OP1 A:DA5 1.5 26.4 1.0
OP2 A:DA5 1.5 26.4 1.0
O3' A:DA4 1.6 23.9 1.0
O5' A:DA5 1.6 25.6 1.0
C3' A:DA4 2.6 21.9 1.0
C5' A:DA5 2.7 23.7 1.0
C2' A:DA4 3.3 20.0 1.0
C4' A:DA4 3.7 22.4 1.0
O A:HOH81 4.0 55.2 1.0
C4' A:DA5 4.0 21.0 1.0
C1' A:DA4 4.1 18.5 1.0
O A:HOH74 4.1 56.5 1.0
O4' A:DA4 4.3 21.4 1.0
C2' A:DA5 4.4 18.1 1.0
C3' A:DA5 4.4 20.6 1.0
O4' A:DA5 4.5 19.3 1.0
C8 A:DA5 4.6 11.6 1.0
C1' A:DA5 4.9 16.3 1.0
C5' A:DA4 4.9 23.2 1.0

Phosphorus binding site 5 out of 22 in 102d

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Phosphorus binding site 5 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:24.6
occ:1.00
P A:DA6 0.0 24.6 1.0
OP2 A:DA6 1.5 24.7 1.0
OP1 A:DA6 1.5 25.4 1.0
O5' A:DA6 1.6 24.5 1.0
O3' A:DA5 1.6 22.9 1.0
C5' A:DA6 2.6 21.8 1.0
C3' A:DA5 2.6 20.6 1.0
C2' A:DA5 3.3 18.1 1.0
O A:HOH82 3.8 54.3 1.0
C4' A:DA5 3.8 21.0 1.0
O A:HOH64 3.9 29.3 1.0
C4' A:DA6 4.0 19.6 1.0
C1' A:DA5 4.0 16.3 1.0
C3' A:DA6 4.4 19.8 1.0
O4' A:DA5 4.4 19.3 1.0
O A:HOH53 4.5 20.6 1.0
O4' A:DA6 4.5 18.8 1.0
C2' A:DA6 4.6 17.6 1.0
C8 A:DA6 5.0 13.1 1.0
C5' A:DA5 5.0 23.7 1.0

Phosphorus binding site 6 out of 22 in 102d

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Phosphorus binding site 6 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:21.1
occ:1.00
P A:DT7 0.0 21.1 1.0
OP2 A:DT7 1.5 20.0 1.0
OP1 A:DT7 1.5 21.6 1.0
O3' A:DA6 1.6 20.0 1.0
O5' A:DT7 1.6 21.1 1.0
C5' A:DT7 2.6 18.8 1.0
C3' A:DA6 2.6 19.8 1.0
C2' A:DA6 3.3 17.6 1.0
C4' A:DA6 3.9 19.6 1.0
O A:HOH53 3.9 20.6 1.0
C4' A:DT7 4.0 18.5 1.0
C1' A:DA6 4.1 16.2 1.0
C3' A:DT7 4.4 19.3 1.0
O4' A:DA6 4.5 18.8 1.0
O4' A:DT7 4.5 18.5 1.0
C2' A:DT7 4.6 18.7 1.0

Phosphorus binding site 7 out of 22 in 102d

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Phosphorus binding site 7 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:21.4
occ:1.00
P A:DT8 0.0 21.4 1.0
OP2 A:DT8 1.4 21.5 1.0
OP1 A:DT8 1.5 23.0 1.0
O3' A:DT7 1.6 20.2 1.0
O5' A:DT8 1.6 22.7 1.0
C5' A:DT8 2.5 21.4 1.0
C3' A:DT7 2.6 19.3 1.0
C4' A:DT7 3.5 18.5 1.0
C2' A:DT7 3.7 18.7 1.0
C4' A:DT8 3.9 22.4 1.0
O A:HOH71 4.2 67.5 1.0
C1' A:DT7 4.3 17.2 1.0
C5' A:DT7 4.4 18.8 1.0
C3' A:DT8 4.4 22.5 1.0
O4' A:DT7 4.4 18.5 1.0
O4' A:DT8 4.5 22.7 1.0
C2' A:DT8 4.7 21.9 1.0

Phosphorus binding site 8 out of 22 in 102d

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Phosphorus binding site 8 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:26.0
occ:1.00
P A:DT9 0.0 26.0 1.0
OP2 A:DT9 1.5 27.7 1.0
OP1 A:DT9 1.5 27.3 1.0
O5' A:DT9 1.6 27.2 1.0
O3' A:DT8 1.6 25.6 1.0
C5' A:DT9 2.5 27.2 1.0
C3' A:DT8 2.8 22.5 1.0
C2' A:DT8 3.6 21.9 1.0
C4' A:DT9 3.8 28.6 1.0
C4' A:DT8 3.8 22.4 1.0
C3' A:DT9 4.0 29.3 1.0
C1' A:DT8 4.2 21.0 1.0
O4' A:DT8 4.4 22.7 1.0
C2' A:DT9 4.4 28.5 1.0
O4' A:DT9 4.5 28.7 1.0
C6 A:DT9 4.9 26.1 1.0

Phosphorus binding site 9 out of 22 in 102d

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Phosphorus binding site 9 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:34.0
occ:1.00
P A:DG10 0.0 34.0 1.0
OP1 A:DG10 1.5 33.6 1.0
OP2 A:DG10 1.5 33.2 1.0
O3' A:DT9 1.6 32.1 1.0
O5' A:DG10 1.6 33.2 1.0
C3' A:DT9 2.6 29.3 1.0
C5' A:DG10 2.7 31.2 1.0
C2' A:DT9 3.3 28.5 1.0
C4' A:DT9 3.8 28.6 1.0
C4' A:DG10 4.0 30.7 1.0
O A:HOH54 4.2 51.7 1.0
O A:HOH65 4.2 56.0 1.0
C1' A:DT9 4.2 27.1 1.0
O A:HOH35 4.2 31.1 1.0
C2' A:DG10 4.3 29.1 1.0
C3' A:DG10 4.3 31.3 1.0
O4' A:DT9 4.5 28.7 1.0
O4' A:DG10 4.5 29.6 1.0
C5' A:DT9 4.8 27.2 1.0
C8 A:DG10 5.0 23.2 1.0
C1' A:DG10 5.0 26.7 1.0

Phosphorus binding site 10 out of 22 in 102d

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Phosphorus binding site 10 out of 22 in the Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Sequence-Dependent Drug Binding to the Minor Groove of Dna: the Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg) 2 Complexed with Propamidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:36.7
occ:1.00
P A:DC11 0.0 36.7 1.0
OP2 A:DC11 1.5 36.7 1.0
OP1 A:DC11 1.5 35.8 1.0
O5' A:DC11 1.6 35.8 1.0
O3' A:DG10 1.6 34.4 1.0
C5' A:DC11 2.5 34.2 1.0
C3' A:DG10 2.8 31.3 1.0
C4' A:DG10 3.8 30.7 1.0
C2' A:DG10 3.8 29.1 1.0
O A:HOH69 3.8 57.7 1.0
C4' A:DC11 3.8 32.9 1.0
C6 A:DC11 4.2 25.4 1.0
C1' A:DG10 4.3 26.7 1.0
C3' A:DC11 4.3 32.5 1.0
O4' A:DC11 4.3 31.6 1.0
C2' A:DC11 4.4 30.6 1.0
O4' A:DG10 4.5 29.6 1.0
O A:HOH91 4.6 65.9 1.0
C1' A:DC11 4.9 28.8 1.0
O A:HOH86 4.9 66.2 1.0
C5' A:DG10 4.9 31.2 1.0
N1 A:DC11 5.0 25.5 1.0
C5 A:DC11 5.0 24.3 1.0

Reference:

C.M.Nunn, S.Neidle. Sequence-Dependent Drug Binding to the Minor Groove of Dna: Crystal Structure of the Dna Dodecamer D(Cgcaaatttgcg)2 Complexed with Propamidine. J.Med.Chem. V. 38 2317 1995.
ISSN: ISSN 0022-2623
PubMed: 7608897
DOI: 10.1021/JM00013A008
Page generated: Fri Sep 25 11:01:49 2020

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