Phosphorus in PDB 109d: Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2

Protein crystallography data

The structure of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2, PDB code: 109d was solved by A.Czarny, D.W.Boykin, A.A.Wood, C.M.Nunn, S.Neidle, M.Zhao, W.D.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 24.590, 40.440, 65.760, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 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 Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 (pdb code 109d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2, PDB code: 109d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 109d

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Phosphorus binding site 1 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 1 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:32.6
occ:1.00
P A:DG2 0.0 32.6 1.0
OP2 A:DG2 1.5 33.1 1.0
OP1 A:DG2 1.5 35.3 1.0
O3' A:DC1 1.6 32.8 1.0
O5' A:DG2 1.6 31.2 1.0
C5' A:DG2 2.5 28.3 1.0
C3' A:DC1 2.7 31.1 1.0
C2' A:DC1 3.5 27.0 1.0
O A:HOH37 3.6 35.8 1.0
O A:HOH44 3.7 47.4 1.0
C4' A:DC1 3.9 31.9 1.0
C4' A:DG2 3.9 24.8 1.0
C1' A:DC1 4.3 23.4 1.0
O A:HOH76 4.3 42.5 1.0
C3' A:DG2 4.3 22.1 1.0
O4' A:DG2 4.6 22.0 1.0
C2' A:DG2 4.6 17.3 1.0
O4' A:DC1 4.6 29.1 1.0
O A:HOH105 4.9 58.1 1.0
O5' A:DC1 4.9 44.2 1.0
O A:HOH65 4.9 31.9 1.0
C5' A:DC1 5.0 35.0 1.0

Phosphorus binding site 2 out of 22 in 109d

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Phosphorus binding site 2 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 2 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:27.1
occ:1.00
P A:DC3 0.0 27.1 1.0
OP2 A:DC3 1.5 29.2 1.0
OP1 A:DC3 1.5 26.3 1.0
O5' A:DC3 1.6 26.5 1.0
O3' A:DG2 1.6 26.6 1.0
C5' A:DC3 2.4 26.2 1.0
C3' A:DG2 2.8 22.1 1.0
C2' A:DG2 3.4 17.3 1.0
O A:HOH109 3.6 58.0 1.0
C4' A:DC3 3.8 24.0 1.0
C4' A:DG2 4.0 24.8 1.0
O A:HOH107 4.0 59.6 1.0
O A:HOH54 4.1 30.4 1.0
O A:HOH83 4.3 41.9 1.0
C1' A:DG2 4.3 18.5 1.0
C3' A:DC3 4.3 24.9 1.0
O4' A:DC3 4.4 23.0 1.0
O4' A:DG2 4.7 22.0 1.0
C2' A:DC3 4.7 25.8 1.0
O A:HOH93 4.9 51.0 1.0
C6 A:DC3 4.9 15.9 1.0

Phosphorus binding site 3 out of 22 in 109d

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Phosphorus binding site 3 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 3 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:29.9
occ:1.00
P A:DG4 0.0 29.9 1.0
OP2 A:DG4 1.5 27.1 1.0
OP1 A:DG4 1.5 36.8 1.0
O5' A:DG4 1.6 31.4 1.0
O3' A:DC3 1.6 28.8 1.0
C3' A:DC3 2.6 24.9 1.0
C5' A:DG4 2.7 27.6 1.0
C2' A:DC3 3.3 25.8 1.0
C4' A:DC3 3.9 24.0 1.0
C4' A:DG4 3.9 27.7 1.0
O A:HOH79 3.9 45.2 1.0
O4' A:DG4 4.2 26.4 1.0
O A:HOH49 4.3 47.0 1.0
C2' A:DG4 4.3 26.9 1.0
C1' A:DC3 4.3 20.3 1.0
C3' A:DG4 4.4 28.8 1.0
C8 A:DG4 4.4 17.7 1.0
O4' A:DC3 4.7 23.0 1.0
C1' A:DG4 4.8 24.8 1.0
C5' A:DC3 4.8 26.2 1.0
N9 A:DG4 4.9 20.8 1.0

Phosphorus binding site 4 out of 22 in 109d

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Phosphorus binding site 4 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 4 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:35.9
occ:1.00
P A:DA5 0.0 35.9 1.0
OP1 A:DA5 1.5 38.2 1.0
OP2 A:DA5 1.5 32.4 1.0
O5' A:DA5 1.6 29.6 1.0
O3' A:DG4 1.6 34.0 1.0
C5' A:DA5 2.6 26.0 1.0
C3' A:DG4 2.6 28.8 1.0
C2' A:DG4 3.3 26.9 1.0
C4' A:DA5 3.9 24.7 1.0
C4' A:DG4 3.9 27.7 1.0
O A:HOH29 4.1 47.6 1.0
C1' A:DG4 4.1 24.8 1.0
O4' A:DA5 4.3 23.1 1.0
C3' A:DA5 4.4 21.5 1.0
C2' A:DA5 4.5 20.1 1.0
O4' A:DG4 4.5 26.4 1.0
C8 A:DA5 4.5 18.0 1.0
C1' A:DA5 4.9 19.4 1.0
C5' A:DG4 5.0 27.6 1.0

Phosphorus binding site 5 out of 22 in 109d

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Phosphorus binding site 5 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 5 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 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
OP1 A:DA6 1.5 21.1 1.0
OP2 A:DA6 1.5 24.4 1.0
O3' A:DA5 1.6 23.6 1.0
O5' A:DA6 1.6 23.6 1.0
C5' A:DA6 2.6 18.8 1.0
C3' A:DA5 2.7 21.5 1.0
C2' A:DA5 3.3 20.1 1.0
O A:HOH115 3.6 25.8 1.0
O A:HOH116 3.8 36.4 1.0
C4' A:DA5 3.9 24.7 1.0
O A:HOH38 4.0 30.1 1.0
C4' A:DA6 4.0 19.0 1.0
C1' A:DA5 4.1 19.4 1.0
C3' A:DA6 4.4 18.5 1.0
O4' A:DA5 4.6 23.1 1.0
O4' A:DA6 4.6 17.9 1.0
O A:HOH111 4.6 32.8 1.0
MG A:MG26 4.7 22.1 1.0
C2' A:DA6 4.8 18.9 1.0

Phosphorus binding site 6 out of 22 in 109d

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Phosphorus binding site 6 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 6 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:22.3
occ:1.00
P A:DT7 0.0 22.3 1.0
OP1 A:DT7 1.5 20.2 1.0
OP2 A:DT7 1.5 17.8 1.0
O5' A:DT7 1.6 21.9 1.0
O3' A:DA6 1.6 18.5 1.0
C5' A:DT7 2.5 20.4 1.0
C3' A:DA6 2.7 18.5 1.0
C2' A:DA6 3.4 18.9 1.0
O A:HOH78 3.7 21.7 1.0
O A:HOH111 3.8 32.8 1.0
C4' A:DT7 3.9 19.2 1.0
C4' A:DA6 4.0 19.0 1.0
C1' A:DA6 4.3 15.7 1.0
O4' A:DT7 4.4 18.3 1.0
C3' A:DT7 4.4 20.1 1.0
O4' A:DA6 4.7 17.9 1.0
C2' A:DT7 4.9 19.4 1.0

Phosphorus binding site 7 out of 22 in 109d

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Phosphorus binding site 7 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 7 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:22.9
occ:1.00
P A:DT8 0.0 22.9 1.0
OP2 A:DT8 1.5 26.4 1.0
OP1 A:DT8 1.5 24.0 1.0
O3' A:DT7 1.6 21.9 1.0
O5' A:DT8 1.6 29.0 1.0
C5' A:DT8 2.6 24.5 1.0
C3' A:DT7 2.6 20.1 1.0
C2' A:DT7 3.4 19.4 1.0
O A:HOH58 3.7 63.6 1.0
C4' A:DT7 3.9 19.2 1.0
C4' A:DT8 4.0 18.7 1.0
O A:HOH50 4.2 66.1 1.0
C1' A:DT7 4.4 17.0 1.0
C3' A:DT8 4.5 20.9 1.0
O4' A:DT8 4.5 16.8 1.0
C5' A:DT7 4.7 20.4 1.0
O4' A:DT7 4.7 18.3 1.0
C2' A:DT8 4.9 20.4 1.0

Phosphorus binding site 8 out of 22 in 109d

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Phosphorus binding site 8 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 8 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:29.3
occ:1.00
P A:DC9 0.0 29.3 1.0
OP2 A:DC9 1.5 32.7 1.0
OP1 A:DC9 1.5 33.5 1.0
O3' A:DT8 1.6 30.8 1.0
O5' A:DC9 1.6 28.6 1.0
C5' A:DC9 2.6 25.6 1.0
C3' A:DT8 2.7 20.9 1.0
C2' A:DT8 3.3 20.4 1.0
C4' A:DT8 3.9 18.7 1.0
O A:HOH89 3.9 48.3 1.0
C4' A:DC9 4.0 30.4 1.0
C1' A:DT8 4.2 17.4 1.0
O A:HOH106 4.3 51.0 1.0
C3' A:DC9 4.3 31.7 1.0
O A:HOH108 4.6 53.9 1.0
O4' A:DC9 4.6 31.9 1.0
C2' A:DC9 4.6 30.6 1.0
O4' A:DT8 4.7 16.8 1.0
C6 A:DC9 4.9 28.1 1.0
C5' A:DT8 4.9 24.5 1.0
C6 A:IBB25 5.0 33.2 1.0

Phosphorus binding site 9 out of 22 in 109d

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Phosphorus binding site 9 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 9 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:39.3
occ:1.00
P A:DG10 0.0 39.3 1.0
OP2 A:DG10 1.5 37.1 1.0
OP1 A:DG10 1.5 42.9 1.0
O3' A:DC9 1.6 37.5 1.0
O5' A:DG10 1.6 38.0 1.0
C5' A:DG10 2.5 33.8 1.0
C3' A:DC9 2.6 31.7 1.0
C2' A:DC9 3.4 30.6 1.0
O A:HOH33 3.7 66.3 1.0
C4' A:DC9 3.8 30.4 1.0
O A:HOH108 3.8 53.9 1.0
O A:HOH92 3.8 55.3 1.0
C4' A:DG10 3.9 34.9 1.0
O A:HOH88 3.9 52.6 1.0
O A:HOH42 4.0 44.2 1.0
C1' A:DC9 4.3 28.6 1.0
O A:HOH94 4.4 49.4 1.0
O4' A:DG10 4.4 34.2 1.0
C3' A:DG10 4.5 35.0 1.0
O4' A:DC9 4.6 31.9 1.0
C2' A:DG10 4.6 34.4 1.0
C5' A:DC9 4.6 25.6 1.0

Phosphorus binding site 10 out of 22 in 109d

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Phosphorus binding site 10 out of 22 in the Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2


Mono view


Stereo pair view

A full contact list of Phosphorus with other atoms in the P binding site number 10 of Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:37.1
occ:1.00
P A:DC11 0.0 37.1 1.0
OP2 A:DC11 1.5 38.9 1.0
OP1 A:DC11 1.5 41.8 1.0
O5' A:DC11 1.6 35.8 1.0
O3' A:DG10 1.6 38.4 1.0
C5' A:DC11 2.5 32.2 1.0
C3' A:DG10 2.7 35.0 1.0
C4' A:DG10 3.7 34.9 1.0
C2' A:DG10 3.7 34.4 1.0
C4' A:DC11 3.8 33.4 1.0
C6 A:DC11 4.0 21.7 1.0
O4' A:DC11 4.0 32.2 1.0
C2' A:DC11 4.4 33.0 1.0
C1' A:DG10 4.4 31.6 1.0
C3' A:DC11 4.4 34.1 1.0
O4' A:DG10 4.5 34.2 1.0
C1' A:DC11 4.6 28.7 1.0
C5' A:DG10 4.7 33.8 1.0
N1 A:DC11 4.7 25.4 1.0
C5 A:DC11 4.7 24.0 1.0

Reference:

A.A.Wood, C.M.Nunn, A.Czarny, D.W.Boykin, S.Neidle. Variability in Dna Minor Groove Width Recognised By Ligand Binding: the Crystal Structure of A Bis-Benzimidazole Compound Bound to the Dna Duplex D(Cgcgaattcgcg)2. Nucleic Acids Res. V. 23 3678 1995.
ISSN: ISSN 0305-1048
PubMed: 7478996
DOI: 10.1093/NAR/23.18.3678
Page generated: Fri Sep 25 11:06:11 2020

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