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Fluorine in PDB 1nd3: The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound

Protein crystallography data

The structure of The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound, PDB code: 1nd3 was solved by Y.Zhang, A.A.Simpson, C.M.Bator, S.Chakravarty, D.C.Pevear, G.A.Skochko, T.M.Tull, G.Diana, M.G.Rossmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.80
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 360.301, 343.331, 332.632, 90.00, 90.00, 90.00
R / Rfree (%) 24.7 / 24.3

Other elements in 1nd3:

The structure of The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound (pdb code 1nd3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound, PDB code: 1nd3:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 1nd3

Go back to Fluorine Binding Sites List in 1nd3
Fluorine binding site 1 out of 3 in the The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F7001

b:34.2
occ:0.35
F1 A:W117001 0.0 34.2 0.3
CM4 A:W117001 1.4 32.7 0.3
C3A A:W117001 2.2 31.8 0.3
F2 A:W117001 2.2 34.4 0.3
F3 A:W117001 2.3 35.7 0.3
N3A A:W117001 2.4 30.7 0.3
CD1 A:LEU217 3.4 23.0 1.0
O1A A:W117001 3.5 30.7 0.3
CB A:TYR142 3.6 16.0 1.0
O A:TYR142 3.7 19.4 1.0
C2A A:W117001 3.8 29.4 0.3
CZ A:PHE179 3.8 15.9 1.0
CE A:MET124 3.8 30.6 1.0
C A:TYR142 3.9 18.0 1.0
CE2 A:PHE179 4.0 16.5 1.0
N A:MET143 4.3 17.5 1.0
N1A A:W117001 4.3 30.2 0.3
CA A:TYR142 4.4 17.3 1.0
N A:TYR144 4.4 19.8 1.0
C A:MET143 4.5 18.8 1.0
CG2 A:VAL168 4.6 20.8 1.0
CA A:MET143 4.6 17.6 1.0
CB A:TYR144 4.8 20.9 1.0
CG A:TYR142 4.8 16.2 1.0
SD A:MET124 4.8 31.0 1.0
CG A:LEU217 4.9 23.4 1.0
CE1 A:PHE179 4.9 16.0 1.0
C4B A:W117001 4.9 25.7 0.3
CA A:TYR144 5.0 19.8 1.0
O A:MET143 5.0 19.3 1.0
C3B A:W117001 5.0 22.6 0.3
CB A:VAL168 5.0 19.1 1.0

Fluorine binding site 2 out of 3 in 1nd3

Go back to Fluorine Binding Sites List in 1nd3
Fluorine binding site 2 out of 3 in the The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F7001

b:34.4
occ:0.35
F2 A:W117001 0.0 34.4 0.3
CM4 A:W117001 1.3 32.7 0.3
F1 A:W117001 2.2 34.2 0.3
F3 A:W117001 2.2 35.7 0.3
C3A A:W117001 2.5 31.8 0.3
CG2 A:VAL168 2.6 20.8 1.0
O1A A:W117001 3.1 30.7 0.3
CE2 A:PHE179 3.3 16.5 1.0
CB A:VAL168 3.4 19.1 1.0
N3A A:W117001 3.5 30.7 0.3
O A:TYR142 3.6 19.4 1.0
CZ A:PHE179 3.6 15.9 1.0
N A:VAL168 3.7 19.0 1.0
CD2 A:PHE179 4.0 17.1 1.0
CA A:VAL168 4.1 19.0 1.0
C A:SER167 4.2 19.3 1.0
O A:ALA166 4.4 20.0 1.0
C A:TYR142 4.4 18.0 1.0
CB A:TYR142 4.5 16.0 1.0
CA A:SER167 4.5 18.8 1.0
CE1 A:PHE179 4.5 16.0 1.0
N1A A:W117001 4.5 30.2 0.3
C2A A:W117001 4.6 29.4 0.3
CG1 A:VAL168 4.7 18.0 1.0
C A:ALA166 4.8 20.0 1.0
CG A:PHE179 4.8 17.9 1.0
O A:SER167 4.8 19.8 1.0
N A:SER167 4.9 18.9 1.0
CD1 A:PHE179 5.0 17.6 1.0

Fluorine binding site 3 out of 3 in 1nd3

Go back to Fluorine Binding Sites List in 1nd3
Fluorine binding site 3 out of 3 in the The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of The Structure of HRV16, When Complexed with Pleconaril, An Antiviral Compound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F7001

b:35.7
occ:0.35
F3 A:W117001 0.0 35.7 0.3
CM4 A:W117001 1.3 32.7 0.3
F2 A:W117001 2.2 34.4 0.3
C3A A:W117001 2.3 31.8 0.3
F1 A:W117001 2.3 34.2 0.3
O A:ALA166 2.8 20.0 1.0
O A:TYR142 2.8 19.4 1.0
O1A A:W117001 2.9 30.7 0.3
N A:TYR144 2.9 19.8 1.0
CA A:MET143 3.3 17.6 1.0
C A:MET143 3.3 18.8 1.0
C A:TYR142 3.4 18.0 1.0
N3A A:W117001 3.4 30.7 0.3
N A:MET143 3.6 17.5 1.0
C A:ALA166 3.6 20.0 1.0
CB A:TYR144 3.7 20.9 1.0
CA A:SER167 3.8 18.8 1.0
CA A:TYR144 3.8 19.8 1.0
N A:SER167 4.1 18.9 1.0
N A:VAL168 4.1 19.0 1.0
N1A A:W117001 4.2 30.2 0.3
O A:MET143 4.2 19.3 1.0
C A:SER167 4.3 19.3 1.0
C2A A:W117001 4.3 29.4 0.3
CB A:TYR142 4.5 16.0 1.0
CG2 A:VAL168 4.5 20.8 1.0
CA A:TYR142 4.5 17.3 1.0
CD1 A:LEU217 4.6 23.0 1.0
CB A:MET143 4.7 15.9 1.0
CB A:ALA166 4.7 16.7 1.0
CA A:ALA166 4.8 19.6 1.0

Reference:

Y.Zhang, A.A.Simpson, R.M.Ledford, C.M.Bator, S.Chakravarty, G.A.Skochko, T.M.Demenczuk, A.Watanyar, D.C.Pevear, M.G.Rossmann. Structural and Virological Studies of the Stages of Virus Replication That Are Affected By Antirhinovirus Compounds J.Virol. V. 78 11061 2004.
ISSN: ISSN 0022-538X
PubMed: 15452226
DOI: 10.1128/JVI.78.20.11061-11069.2004
Page generated: Sun Dec 13 11:31:16 2020

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