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Fluorine in PDB 3nyp: A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex with A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains

Protein crystallography data

The structure of A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex with A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains, PDB code: 3nyp was solved by N.H.Campbell, S.Neidle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.99 / 1.18
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.800, 44.460, 28.140, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 18.8

Other elements in 3nyp:

The structure of A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex with A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains also contains other interesting chemical elements:

Potassium (K) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex with A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains (pdb code 3nyp). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex with A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains, PDB code: 3nyp:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 3nyp

Go back to Fluorine Binding Sites List in 3nyp
Fluorine binding site 1 out of 2 in the A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex with A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex with A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F17

b:23.6
occ:0.90
F23 A:RNR17 0.0 23.6 0.9
C22 A:RNR17 1.3 22.7 0.7
C21 A:RNR17 2.3 22.5 0.5
C24 A:RNR17 2.3 22.4 1.0
N20 A:RNR17 3.2 17.5 0.8
C25 A:RNR17 3.3 19.8 1.0
O B:HOH112 3.8 39.6 1.0
O3' B:DG12 4.4 12.9 1.0
O B:HOH31 4.5 16.5 1.0
C19 A:RNR17 4.6 10.3 1.0

Fluorine binding site 2 out of 2 in 3nyp

Go back to Fluorine Binding Sites List in 3nyp
Fluorine binding site 2 out of 2 in the A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex with A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of A Bimolecular Anti-Parallel-Stranded Oxytricha Nova Telomeric Quadruplex in Complex with A 3,6-Disubstituted Acridine Ligand Containing Bis-3-Fluoropyrrolidine End Side Chains within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F17

b:56.1
occ:1.00
F34 A:RNR17 0.0 56.1 1.0
C33 A:RNR17 1.3 43.0 1.0
C35 A:RNR17 2.3 42.0 1.0
C32 A:RNR17 2.3 28.4 1.0
C36 A:RNR17 3.1 33.1 1.0
N31 A:RNR17 3.2 25.8 1.0
O A:HOH110 3.7 39.8 1.0
OP1 A:DT7 4.2 18.5 1.0
O A:HOH147 4.5 35.2 0.5
C30 A:RNR17 4.6 16.8 1.0
O A:HOH92 5.0 33.8 1.0

Reference:

N.H.Campbell, D.L.Smith, A.P.Reszka, S.Neidle, D.O'hagan. Fluorine in Medicinal Chemistry: Beta-Fluorination of Peripheral Pyrrolidines Attached to Acridine Ligands Affects Their Interactions with G-Quadruplex Dna. Org.Biomol.Chem. V. 9 1328 2011.
ISSN: ISSN 1477-0520
PubMed: 21221451
DOI: 10.1039/C0OB00886A
Page generated: Sun Dec 13 11:52:00 2020

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