Fluorine in PDB 6ey7: Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound

The structure of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound, PDB code: 6ey7 was solved by S.Bongarzone, M.Nadal, Z.Kaczmarska, C.Machon, M.Alvarez, F.Albericio, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.87 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	81.650, 87.650, 186.580, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.8

The structure of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound also contains other interesting chemical elements:

Manganese	(Mn)	10 atoms
Chlorine	(Cl)	1 atom

The binding sites of Fluorine atom in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound (pdb code 6ey7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound, PDB code: 6ey7:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:0.4 occ:1.00 F A:C3W704 0.0 0.4 1.0 C5 A:C3W704 1.4 0.5 1.0 C4 A:C3W704 2.4 0.5 1.0 C6 A:C3W704 2.4 0.1 1.0 O A:GLY580 3.5 0.6 1.0 C3 A:C3W704 3.6 0.7 1.0 C7 A:C3W704 3.6 0.9 1.0 CA A:GLY580 3.6 0.9 1.0 C A:GLY580 3.8 0.3 1.0 O A:MET579 3.9 0.7 1.0 N A:GLY580 4.0 0.7 1.0 C A:MET579 4.1 0.7 1.0 C2 A:C3W704 4.1 0.0 1.0 CG A:MET579 4.5 0.2 1.0 CB A:MET579 4.8 99.3 1.0 N A:ARG581 4.9 0.5 1.0

Fluorine binding site 2 out of 4 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:F703 b:0.5 occ:1.00 F B:C3W703 0.0 0.5 1.0 C5 B:C3W703 1.4 0.3 1.0 C6 B:C3W703 2.4 0.2 1.0 C4 B:C3W703 2.4 0.2 1.0 C7 B:C3W703 3.6 0.8 1.0 C3 B:C3W703 3.6 0.6 1.0 O B:GLY580 3.7 0.2 1.0 O B:MET579 3.8 0.3 1.0 CA B:GLY580 3.9 0.7 1.0 C B:MET579 4.0 0.9 1.0 N B:GLY580 4.0 99.7 1.0 C B:GLY580 4.1 0.3 1.0 C2 B:C3W703 4.1 0.6 1.0 CG B:MET579 4.2 0.5 1.0 CB B:MET579 4.5 97.0 1.0 CE B:MET579 4.8 1.0 1.0 CA B:MET579 4.9 95.4 1.0 CD B:LYS583 5.0 0.3 1.0

Fluorine binding site 3 out of 4 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ C:F704 b:0.8 occ:1.00 F C:C3W704 0.0 0.8 1.0 C5 C:C3W704 1.4 0.5 1.0 C6 C:C3W704 2.3 0.3 1.0 C4 C:C3W704 2.4 0.4 1.0 O C:MET579 3.6 0.5 1.0 C7 C:C3W704 3.6 0.1 1.0 C3 C:C3W704 3.6 0.5 1.0 CA C:GLY580 3.9 0.1 1.0 C C:MET579 3.9 0.4 1.0 O C:GLY580 3.9 0.3 1.0 N C:GLY580 4.0 0.7 1.0 C2 C:C3W704 4.1 0.9 1.0 C C:GLY580 4.2 0.1 1.0 CG C:MET579 4.4 0.1 1.0 CB C:MET579 4.5 0.3 1.0 ND2 C:ASN536 4.6 1.0 1.0 CA C:MET579 4.8 0.6 1.0 SD C:MET579 4.9 0.8 1.0

Fluorine binding site 4 out of 4 in the Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Human Cytomegalovirus Terminase Nuclease Domain, Mn Soaked, Inhibitor Bound within 5.0Å range: probe atom residue distance (Å) B Occ D:F703 b:0.5 occ:1.00 F D:C3W703 0.0 0.5 1.0 C5 D:C3W703 1.4 0.8 1.0 C4 D:C3W703 2.4 0.9 1.0 C6 D:C3W703 2.4 0.1 1.0 O D:GLY580 3.4 0.9 1.0 C3 D:C3W703 3.6 0.0 1.0 C7 D:C3W703 3.6 0.4 1.0 CA D:GLY580 3.7 0.9 1.0 C D:GLY580 3.7 0.4 1.0 O D:MET579 4.1 0.3 1.0 N D:GLY580 4.1 99.1 1.0 C2 D:C3W703 4.1 0.8 1.0 C D:MET579 4.3 0.6 1.0 CG D:MET579 4.7 0.8 1.0 N D:ARG581 4.8 0.6 1.0

S.Bongarzone, M.Nadal, Z.Kaczmarska, C.Machon, M.Alvarez, F.Albericio, M.Coll. Structure-Driven Discovery of Alpha , Gamma-Diketoacid Inhibitors Against UL89 Herpesvirus Terminase. Acs Omega V. 3 8497 2018.
ISSN: ESSN 2470-1343
PubMed: 31458978
DOI: 10.1021/ACSOMEGA.8B01472