Fluorine in PDB 5d7y: Crystal Structure of Hepatitis B Virus T=4 Capsid in Complex with the Allosteric Modulator HAP18

The structure of Crystal Structure of Hepatitis B Virus T=4 Capsid in Complex with the Allosteric Modulator HAP18, PDB code: 5d7y was solved by B.Venkatakrishnan, S.P.Katen, A.Zlotnick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.68 / 3.89
Space group	C 1 2 1 9
Cell size a, b, c (Å), α, β, γ (°)	529.375, 367.411, 542.002, 90.00, 104.79, 90.00
R / Rfree (%)	26.3 / 27.3

The structure of Crystal Structure of Hepatitis B Virus T=4 Capsid in Complex with the Allosteric Modulator HAP18 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Hepatitis B Virus T=4 Capsid in Complex with the Allosteric Modulator HAP18 (pdb code 5d7y). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of Hepatitis B Virus T=4 Capsid in Complex with the Allosteric Modulator HAP18, PDB code: 5d7y:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Hepatitis B Virus T=4 Capsid in Complex with the Allosteric Modulator HAP18


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Hepatitis B Virus T=4 Capsid in Complex with the Allosteric Modulator HAP18 within 5.0Å range: probe atom residue distance (Å) B Occ B:F201 b:0.1 occ:1.00 F34 B:58H201 0.0 0.1 1.0 C33 B:58H201 1.3 0.1 1.0 C32 B:58H201 2.3 0.1 1.0 C35 B:58H201 2.3 0.1 1.0 OG1 B:THR33 2.8 0.5 1.0 CD2 B:LEU30 3.1 0.8 1.0 CB B:THR33 3.2 0.5 1.0 CA B:LEU30 3.3 0.1 1.0 CD1 B:LEU30 3.3 0.8 1.0 O B:ASP29 3.4 0.2 1.0 C30 B:58H201 3.6 0.1 1.0 C36 B:58H201 3.6 0.1 1.0 CG B:LEU30 3.7 0.8 1.0 CG2 B:THR33 3.8 0.5 1.0 C B:ASP29 3.9 0.2 1.0 N B:LEU30 3.9 0.1 1.0 O B:LEU30 4.0 0.1 1.0 CB B:LEU30 4.0 0.8 1.0 C B:LEU30 4.1 0.1 1.0 C29 B:58H201 4.1 0.1 1.0 CA B:THR33 4.6 0.9 1.0 CG B:PRO25 4.7 0.7 1.0 CG2 C:VAL124 4.7 0.2 1.0 CD1 B:ILE105 4.7 0.8 1.0 N B:THR33 5.0 0.9 1.0 CG2 B:ILE105 5.0 0.8 1.0 CL3 B:58H201 5.0 0.1 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Hepatitis B Virus T=4 Capsid in Complex with the Allosteric Modulator HAP18


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Hepatitis B Virus T=4 Capsid in Complex with the Allosteric Modulator HAP18 within 5.0Å range: probe atom residue distance (Å) B Occ C:F201 b:0.1 occ:1.00 F34 C:58H201 0.0 0.1 1.0 C33 C:58H201 1.3 0.1 1.0 C32 C:58H201 2.3 0.1 1.0 C35 C:58H201 2.3 0.1 1.0 OG1 C:THR33 2.7 0.3 1.0 CG2 C:THR33 3.3 0.3 1.0 CB C:THR33 3.5 0.3 1.0 C36 C:58H201 3.6 0.1 1.0 C30 C:58H201 3.6 0.1 1.0 CD1 C:LEU30 3.7 0.9 1.0 C29 C:58H201 4.1 0.1 1.0 CG2 C:ILE105 4.4 0.3 1.0 CA C:LEU30 4.6 0.5 1.0 CD2 C:LEU30 4.7 0.9 1.0 CG C:LEU30 4.7 0.9 1.0 O C:ASP29 4.8 0.9 1.0 CA C:THR33 4.9 0.3 1.0 CL3 C:58H201 5.0 0.1 1.0

B.Venkatakrishnan, S.P.Katen, S.Francis, S.Chirapu, M.G.Finn, A.Zlotnick. Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket. J.Virol. V. 90 3994 2016.
ISSN: ESSN 1098-5514
PubMed: 26842475
DOI: 10.1128/JVI.03058-15