Fluorine in PDB 8db7: Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor

The structure of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor, PDB code: 8db7 was solved by S.N.Muellers, K.N.Allen, B.J.Stockman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.99 / 2.33
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.651, 74.537, 85.641, 83.02, 80.9, 89.9
R / Rfree (%)	19.6 / 25.6

The structure of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Fluorine atom in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor (pdb code 8db7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor, PDB code: 8db7:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:F402 b:49.0 occ:1.00 F01 B:R2O402 0.0 49.0 1.0 C02 B:R2O402 1.4 49.0 1.0 C03 B:R2O402 2.3 45.8 1.0 C13 B:R2O402 2.4 42.6 1.0 CA B:ILE161 2.9 31.7 1.0 N B:ILE161 3.1 33.8 1.0 C B:ASN160 3.2 30.9 1.0 CD1 B:ILE161 3.3 30.8 1.0 O B:ASN160 3.3 32.9 1.0 CB B:ILE161 3.4 33.7 1.0 C04 B:R2O402 3.6 45.3 1.0 C12 B:R2O402 3.6 40.8 1.0 CD1 B:ILE79 3.7 47.5 1.0 CG1 B:ILE161 3.9 32.7 1.0 CB B:ASN160 4.0 35.7 1.0 OD1 B:ASN160 4.1 28.6 1.0 C05 B:R2O402 4.1 40.6 1.0 CG B:ASN160 4.1 36.0 1.0 CA B:ASN160 4.3 35.3 1.0 C B:ILE161 4.3 33.3 1.0 CG2 B:ILE161 4.8 28.8 1.0 O B:ILE161 4.8 28.8 1.0 ND2 B:ASN160 4.8 29.9 1.0 CB B:PHE167 5.0 29.8 1.0

Fluorine binding site 2 out of 3 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ C:F402 b:45.9 occ:1.00 F01 C:R2O402 0.0 45.9 1.0 C02 C:R2O402 1.4 40.4 1.0 C03 C:R2O402 2.4 37.5 1.0 C13 C:R2O402 2.4 36.9 1.0 CG A:PRO77 3.4 35.8 1.0 CD A:PRO77 3.6 33.2 1.0 C04 C:R2O402 3.6 33.6 1.0 C12 C:R2O402 3.7 38.2 1.0 CD1 C:ILE79 3.7 39.0 1.0 ND1 A:HIS78 4.0 37.4 1.0 C05 C:R2O402 4.1 34.4 1.0 N A:HIS78 4.4 36.7 1.0 CG A:HIS78 4.4 36.0 1.0 N A:PRO77 4.5 39.4 1.0 CB A:HIS78 4.5 32.7 1.0 CE1 A:HIS78 4.6 35.3 1.0 O C:TYR164 4.7 37.5 1.0 CB A:PRO77 4.7 35.7 1.0 O A:GLU75 4.7 29.6 1.0 O C:GLY165 4.8 39.1 1.0 CA C:GLY165 4.9 34.2 1.0

Fluorine binding site 3 out of 3 in the Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Adenosine/Guanosine Nucleoside Hydrolase Bound to A Fragment Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ D:F402 b:53.6 occ:1.00 F01 D:R2O402 0.0 53.6 1.0 C02 D:R2O402 1.4 53.4 1.0 C03 D:R2O402 2.4 50.9 1.0 C13 D:R2O402 2.4 50.1 1.0 N D:ILE161 3.0 47.8 1.0 CA D:ILE161 3.1 44.6 1.0 C D:ASN160 3.4 45.8 1.0 CB D:ILE161 3.4 47.6 1.0 CD1 D:ILE161 3.6 41.7 1.0 C04 D:R2O402 3.6 52.1 1.0 C12 D:R2O402 3.6 50.1 1.0 O D:ASN160 3.7 46.3 1.0 CB D:ASN160 3.8 42.4 1.0 OD1 D:ASN160 4.0 42.3 1.0 CG D:ASN160 4.0 48.5 1.0 CG1 D:ILE161 4.1 41.1 1.0 C05 D:R2O402 4.1 50.8 1.0 CA D:ASN160 4.2 42.8 1.0 CD1 D:ILE79 4.3 62.4 1.0 CG1 D:ILE79 4.5 64.8 1.0 C D:ILE161 4.5 41.8 1.0 CG2 D:ILE161 4.7 38.5 1.0 ND2 D:ASN160 4.8 43.4 1.0 CD1 D:PHE167 4.9 39.0 1.0 CE2 D:PHE230 5.0 62.4 1.0

S.N.Muellers, M.M.Nyitray, N.Reynarowych, E.Saljanin, A.L.Benzie, A.R.Schoenfeld, B.J.Stockman, K.N.Allen. Structure-Guided Insight Into the Specificity and Mechanism of A Parasitic Nucleoside Hydrolase. Biochemistry V. 61 1853 2022.
ISSN: ISSN 0006-2960
PubMed: 35994320
DOI: 10.1021/ACS.BIOCHEM.2C00361