Fluorine in PDB 6ea2: X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion, PDB code: 6ea2 was solved by N.Drinkwater, S.Mcgowan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.69 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.140, 108.930, 118.160, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 18.6

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion also contains other interesting chemical elements:

Magnesium	(Mg)	4 atoms
Zinc	(Zn)	1 atom

The binding sites of Fluorine atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion (pdb code 6ea2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion, PDB code: 6ea2:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:13.0 occ:1.00 FAD A:J1G1102 0.0 13.0 1.0 CAU A:J1G1102 1.4 12.4 1.0 CAZ A:J1G1102 2.4 12.7 1.0 CAK A:J1G1102 2.4 11.7 1.0 FAF A:J1G1102 2.7 15.9 1.0 CG A:GLN317 3.4 9.8 1.0 CG2 A:THR305 3.5 12.8 1.0 ND2 A:ASN458 3.5 12.5 1.0 O A:HOH2223 3.6 13.0 1.0 CAV A:J1G1102 3.6 12.6 1.0 SD A:MET1034 3.7 16.1 1.0 CAX A:J1G1102 3.7 12.4 1.0 O A:GLU319 3.9 10.6 1.0 O A:HOH1710 4.0 14.2 1.0 CD A:GLN317 4.2 10.2 1.0 CAL A:J1G1102 4.2 13.6 1.0 NE2 A:GLN317 4.2 10.5 1.0 O A:LEU304 4.2 11.0 1.0 CB A:ASN458 4.2 9.4 1.0 CG A:ASN458 4.4 9.8 1.0 CE A:MET1034 4.4 16.1 1.0 O A:HOH1728 4.5 12.4 1.0 CB A:GLN317 4.6 10.8 1.0 FAE A:J1G1102 4.7 14.2 1.0 CB A:THR305 4.7 12.4 1.0 CAW A:J1G1102 4.8 11.7 1.0 CA A:THR305 5.0 11.9 1.0

Fluorine binding site 2 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:14.2 occ:1.00 FAE A:J1G1102 0.0 14.2 1.0 CAV A:J1G1102 1.3 12.6 1.0 CAZ A:J1G1102 2.3 12.7 1.0 CAL A:J1G1102 2.3 13.6 1.0 FAF A:J1G1102 2.7 15.9 1.0 O A:HOH1850 3.2 13.9 1.0 N A:ALA320 3.4 10.9 1.0 CAU A:J1G1102 3.6 12.4 1.0 CA A:GLU572 3.6 19.5 1.0 CAX A:J1G1102 3.6 12.4 1.0 CG A:GLU572 3.7 19.9 1.0 CE2 A:TYR575 3.7 12.2 1.0 O A:GLU319 3.8 10.6 1.0 O A:MET571 3.8 19.2 1.0 N A:GLU572 3.9 20.1 1.0 C A:GLU319 4.0 10.2 1.0 CD2 A:TYR575 4.0 13.1 1.0 C A:MET571 4.0 17.1 1.0 CAK A:J1G1102 4.1 11.7 1.0 CB A:GLU572 4.1 21.0 1.0 CB A:ALA320 4.1 11.5 1.0 CZ A:TYR575 4.3 10.7 1.0 CA A:ALA320 4.4 10.7 1.0 CE A:MET1034 4.5 16.1 1.0 C A:GLU572 4.6 26.2 1.0 FAD A:J1G1102 4.7 13.0 1.0 OH A:TYR575 4.7 11.8 1.0 CB A:MET571 4.8 18.5 0.4 O A:HOH1479 4.8 17.5 1.0 CAW A:J1G1102 4.8 11.7 1.0 CB A:MET571 4.8 18.8 0.6 O A:GLU572 4.8 31.8 1.0 SD A:MET1034 4.8 16.1 1.0 CD A:GLU572 4.8 22.5 1.0 CG A:TYR575 4.9 11.3 1.0

Fluorine binding site 3 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6H) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:15.9 occ:1.00 FAF A:J1G1102 0.0 15.9 1.0 CAZ A:J1G1102 1.4 12.7 1.0 CAU A:J1G1102 2.4 12.4 1.0 CAV A:J1G1102 2.4 12.6 1.0 FAD A:J1G1102 2.7 13.0 1.0 FAE A:J1G1102 2.7 14.2 1.0 O A:HOH1479 3.2 17.5 1.0 CG A:GLU572 3.3 19.9 1.0 O A:HOH1710 3.4 14.2 1.0 OE2 A:GLU572 3.4 19.7 1.0 O A:GLU319 3.5 10.6 1.0 O A:HOH1850 3.6 13.9 1.0 CD A:GLU572 3.6 22.5 1.0 CG2 A:THR305 3.6 12.8 1.0 CAK A:J1G1102 3.7 11.7 1.0 CAL A:J1G1102 3.7 13.6 1.0 SD A:MET1034 3.8 16.1 1.0 CAX A:J1G1102 4.2 12.4 1.0 CB A:GLU572 4.2 21.0 1.0 C A:GLU319 4.3 10.2 1.0 N A:ALA320 4.3 10.9 1.0 CE A:MET1034 4.4 16.1 1.0 OE1 A:GLU572 4.5 22.1 1.0 CB A:THR305 4.7 12.4 1.0 CA A:GLU572 4.7 19.5 1.0

N.B.Vinh, N.Drinkwater, T.R.Malcolm, M.Kassiou, L.Lucantoni, P.M.Grin, G.S.Butler, S.Duffy, C.M.Overall, V.M.Avery, P.J.Scammells, S.Mcgowan. Hydroxamic Acid Inhibitors Provide Cross-Species Inhibition of Plasmodium M1 and M17 Aminopeptidases. J. Med. Chem. V. 62 622 2019.
ISSN: ISSN 1520-4804
PubMed: 30537832
DOI: 10.1021/ACS.JMEDCHEM.8B01310