Phosphorus in PDB 166d: Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2

Protein crystallography data

The structure of Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2, PDB code: 166d was solved by C.M.Nunn, T.C.Jenkins, 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 (°) 24.690, 40.330, 66.470, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 19.8

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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 (pdb code 166d). This binding sites where shown within 5.0 Angstroms radius around Phosphorus atom.
In total 22 binding sites of Phosphorus where determined in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2, PDB code: 166d:
Jump to Phosphorus binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Phosphorus binding site 1 out of 22 in 166d

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Phosphorus binding site 1 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P2

b:33.4
occ:1.00
P A:DG2 0.0 33.4 1.0
OP2 A:DG2 1.5 33.8 1.0
OP1 A:DG2 1.5 35.5 1.0
O5' A:DG2 1.6 31.5 1.0
O3' A:DC1 1.6 31.0 1.0
C5' A:DG2 2.5 28.9 1.0
C3' A:DC1 2.6 27.9 1.0
C2' A:DC1 3.5 24.8 1.0
C4' A:DG2 3.8 26.4 1.0
C4' A:DC1 3.8 28.2 1.0
C3' A:DG2 3.9 25.9 1.0
C2' A:DG2 4.2 23.4 1.0
C1' A:DC1 4.3 22.7 1.0
C5' A:DC1 4.5 30.0 1.0
O4' A:DG2 4.6 26.1 1.0
O4' A:DC1 4.7 25.6 1.0
O A:HOH61 4.8 33.5 1.0
C8 A:DG2 4.9 16.9 1.0
C1' A:DG2 5.0 21.8 1.0

Phosphorus binding site 2 out of 22 in 166d

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Phosphorus binding site 2 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P3

b:30.3
occ:1.00
P A:DC3 0.0 30.3 1.0
OP2 A:DC3 1.5 28.7 1.0
OP1 A:DC3 1.5 30.1 1.0
O5' A:DC3 1.6 27.7 1.0
O3' A:DG2 1.6 27.6 1.0
C5' A:DC3 2.4 25.8 1.0
C3' A:DG2 2.7 25.9 1.0
C2' A:DG2 3.5 23.4 1.0
C4' A:DC3 3.7 23.9 1.0
C4' A:DG2 3.9 26.4 1.0
C1' A:DG2 4.2 21.8 1.0
O4' A:DC3 4.5 21.0 1.0
O A:HOH61 4.6 33.5 1.0
O4' A:DG2 4.6 26.1 1.0
C3' A:DC3 4.6 25.2 1.0

Phosphorus binding site 3 out of 22 in 166d

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Phosphorus binding site 3 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P4

b:29.5
occ:1.00
P A:DG4 0.0 29.5 1.0
OP1 A:DG4 1.5 30.9 1.0
OP2 A:DG4 1.5 29.7 1.0
O5' A:DG4 1.5 29.0 1.0
O3' A:DC3 1.6 28.4 1.0
C5' A:DG4 2.4 27.3 1.0
C3' A:DC3 2.5 25.2 1.0
C2' A:DC3 3.2 23.1 1.0
C4' A:DG4 3.8 26.2 1.0
C4' A:DC3 3.9 23.9 1.0
O A:HOH44 4.2 59.3 1.0
O A:HOH78 4.2 33.9 1.0
C8 A:DG4 4.2 19.9 1.0
O4' A:DG4 4.3 23.6 1.0
C3' A:DG4 4.3 26.9 1.0
C2' A:DG4 4.3 24.9 1.0
C1' A:DC3 4.5 18.5 1.0
O A:HOH86 4.6 48.7 1.0
C5' A:DC3 4.7 25.8 1.0
O4' A:DC3 4.7 21.0 1.0
C1' A:DG4 4.7 22.2 1.0
O A:HOH74 4.7 66.2 1.0
N9 A:DG4 4.8 19.9 1.0
O5' A:DC3 4.9 27.7 1.0

Phosphorus binding site 4 out of 22 in 166d

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Phosphorus binding site 4 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P5

b:32.4
occ:1.00
P A:DA5 0.0 32.4 1.0
OP1 A:DA5 1.5 32.4 1.0
OP2 A:DA5 1.5 31.2 1.0
O3' A:DG4 1.6 30.5 1.0
O5' A:DA5 1.6 30.1 1.0
C5' A:DA5 2.6 26.3 1.0
C3' A:DG4 2.6 26.9 1.0
C2' A:DG4 3.3 24.9 1.0
C4' A:DG4 3.8 26.2 1.0
C4' A:DA5 3.9 24.9 1.0
C1' A:DG4 4.1 22.2 1.0
C3' A:DA5 4.3 25.1 1.0
O4' A:DA5 4.4 23.2 1.0
C2' A:DA5 4.4 23.2 1.0
O4' A:DG4 4.5 23.6 1.0
C8 A:DA5 4.6 19.1 1.0
O A:HOH78 4.6 33.9 1.0
C5' A:DG4 5.0 27.3 1.0
C1' A:DA5 5.0 21.1 1.0

Phosphorus binding site 5 out of 22 in 166d

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Phosphorus binding site 5 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P6

b:28.8
occ:1.00
P A:DA6 0.0 28.8 1.0
OP1 A:DA6 1.5 28.6 1.0
OP2 A:DA6 1.5 29.6 1.0
O3' A:DA5 1.6 26.8 1.0
O5' A:DA6 1.6 28.0 1.0
C3' A:DA5 2.7 25.1 1.0
C5' A:DA6 2.7 23.7 1.0
C2' A:DA5 3.4 23.2 1.0
C4' A:DA5 3.8 24.9 1.0
O A:HOH59 3.9 48.2 1.0
C4' A:DA6 4.0 20.6 1.0
C1' A:DA5 4.1 21.1 1.0
O4' A:DA6 4.4 20.4 1.0
O4' A:DA5 4.4 23.2 1.0
C3' A:DA6 4.5 19.9 1.0
O B:HOH69 4.5 58.2 1.0
C2' A:DA6 4.7 18.5 1.0
C5' A:DA5 4.9 26.3 1.0
C8 A:DA6 5.0 13.1 1.0

Phosphorus binding site 6 out of 22 in 166d

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Phosphorus binding site 6 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P7

b:24.6
occ:1.00
P A:DT7 0.0 24.6 1.0
OP2 A:DT7 1.5 25.5 1.0
OP1 A:DT7 1.5 24.3 1.0
O5' A:DT7 1.5 24.0 1.0
O3' A:DA6 1.6 22.7 1.0
C5' A:DT7 2.4 21.3 1.0
C3' A:DA6 2.5 19.9 1.0
O A:HOH43 3.0 62.5 1.0
C2' A:DA6 3.2 18.5 1.0
C4' A:DA6 3.7 20.6 1.0
C4' A:DT7 3.8 21.5 1.0
C1' A:DA6 4.0 17.2 1.0
C3' A:DT7 4.3 22.1 1.0
O4' A:DT7 4.3 20.4 1.0
O4' A:DA6 4.4 20.4 1.0
O A:HOH68 4.6 52.4 1.0
O A:HOH40 4.7 40.3 1.0
C5' A:DA6 4.7 23.7 1.0
C2' A:DT7 4.7 19.6 1.0

Phosphorus binding site 7 out of 22 in 166d

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Phosphorus binding site 7 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P8

b:29.3
occ:1.00
P A:DT8 0.0 29.3 1.0
OP2 A:DT8 1.5 29.7 1.0
OP1 A:DT8 1.5 29.6 1.0
O3' A:DT7 1.6 26.1 1.0
O5' A:DT8 1.6 28.5 1.0
C5' A:DT8 2.5 27.8 1.0
C3' A:DT7 2.6 22.1 1.0
C2' A:DT7 3.4 19.6 1.0
C4' A:DT7 3.8 21.5 1.0
C4' A:DT8 3.9 26.5 1.0
C1' A:DT7 4.3 17.6 1.0
O4' A:DT8 4.4 26.3 1.0
C3' A:DT8 4.5 26.6 1.0
C5' A:DT7 4.7 21.3 1.0
O4' A:DT7 4.7 20.4 1.0
C2' A:DT8 4.7 25.1 1.0
O A:HOH46 4.9 39.8 1.0

Phosphorus binding site 8 out of 22 in 166d

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Phosphorus binding site 8 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P9

b:31.8
occ:1.00
P A:DC9 0.0 31.8 1.0
OP1 A:DC9 1.5 32.0 1.0
OP2 A:DC9 1.5 32.4 1.0
O5' A:DC9 1.5 30.3 1.0
O3' A:DT8 1.6 30.2 1.0
C5' A:DC9 2.6 31.3 1.0
C3' A:DT8 2.7 26.6 1.0
C2' A:DT8 3.5 25.1 1.0
C4' A:DT8 3.8 26.5 1.0
C4' A:DC9 3.8 31.7 1.0
C3' A:DC9 4.0 32.8 1.0
C2' A:DC9 4.1 32.2 1.0
C1' A:DT8 4.2 23.6 1.0
O4' A:DC9 4.4 30.9 1.0
O4' A:DT8 4.6 26.3 1.0
O A:HOH87 4.7 35.8 1.0
O A:HOH50 4.8 77.5 1.0
C6 A:DC9 4.8 28.6 1.0
C5' A:DT8 4.8 27.8 1.0
C1' A:DC9 4.9 30.3 1.0

Phosphorus binding site 9 out of 22 in 166d

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Phosphorus binding site 9 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P10

b:37.1
occ:1.00
P A:DG10 0.0 37.1 1.0
OP1 A:DG10 1.5 37.7 1.0
OP2 A:DG10 1.5 37.6 1.0
O5' A:DG10 1.6 37.5 1.0
O3' A:DC9 1.6 35.8 1.0
C3' A:DC9 2.7 32.8 1.0
C5' A:DG10 2.7 35.7 1.0
O A:HOH87 3.4 35.8 1.0
C2' A:DC9 3.6 32.2 1.0
C4' A:DC9 3.9 31.7 1.0
C4' A:DG10 4.0 35.0 1.0
C2' A:DG10 4.3 33.7 1.0
C3' A:DG10 4.4 34.9 1.0
C1' A:DC9 4.4 30.3 1.0
O4' A:DG10 4.5 33.5 1.0
O A:HOH62 4.6 40.7 1.0
O4' A:DC9 4.7 30.9 1.0
C5' A:DC9 4.9 31.3 1.0
O5' A:DC9 4.9 30.3 1.0
C1' A:DG10 5.0 33.0 1.0
C8 A:DG10 5.0 29.6 1.0

Phosphorus binding site 10 out of 22 in 166d

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Phosphorus binding site 10 out of 22 in the Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with 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 Drug-Dna Minor Groove Recognition: Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:P11

b:39.2
occ:1.00
P A:DC11 0.0 39.2 1.0
OP2 A:DC11 1.5 37.9 1.0
OP1 A:DC11 1.5 38.5 1.0
O3' A:DG10 1.6 36.7 1.0
O5' A:DC11 1.6 38.5 1.0
C5' A:DC11 2.5 38.7 1.0
C3' A:DG10 2.6 34.9 1.0
C2' A:DG10 3.6 33.7 1.0
O A:HOH88 3.6 39.6 1.0
C4' A:DG10 3.7 35.0 1.0
O A:HOH90 3.9 51.8 1.0
C4' A:DC11 3.9 38.6 1.0
C6 A:DC11 4.0 31.3 1.0
C1' A:DG10 4.2 33.0 1.0
O4' A:DC11 4.3 37.9 1.0
O4' A:DG10 4.5 33.5 1.0
C2' A:DC11 4.5 37.0 1.0
C3' A:DC11 4.5 38.5 1.0
C5 A:DC11 4.6 31.2 1.0
C5' A:DG10 4.7 35.7 1.0
C1' A:DC11 4.8 35.2 1.0
N1 A:DC11 4.8 32.6 1.0

Reference:

C.M.Nunn, T.C.Jenkins, S.Neidle. Crystal Structure of Gamma-Oxapentamidine Complexed with D(Cgcgaattcgcg)2. the Effects of Drug Structural Change on Dna Minor-Groove Recognition. Eur.J.Biochem. V. 226 953 1994.
ISSN: ISSN 0014-2956
PubMed: 7813486
DOI: 10.1111/J.1432-1033.1994.00953.X
Page generated: Fri Sep 25 11:36:57 2020

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