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

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) and Catalytic Zinc Ion, PDB code: 6eab 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)	35.36 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.030, 109.101, 118.240, 90.00, 90.00, 90.00
R / Rfree (%)	14.8 / 19.1

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) 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 (6J) and Catalytic Zinc Ion (pdb code 6eab). 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 (6J) and Catalytic Zinc Ion, PDB code: 6eab:
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 (6J) 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 (6J) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:14.8 occ:1.00 FAD A:J2D1102 0.0 14.8 1.0 CAV A:J2D1102 1.4 14.6 1.0 CBA A:J2D1102 2.4 17.6 1.0 CAK A:J2D1102 2.5 8.9 1.0 FAF A:J2D1102 2.7 20.4 1.0 CG A:GLN317 3.4 13.3 1.0 ND2 A:ASN458 3.5 15.5 1.0 CG2 A:THR305 3.5 12.5 1.0 O A:HOH2062 3.6 13.8 1.0 SD A:MET1034 3.6 18.6 1.0 CAW A:J2D1102 3.7 15.9 1.0 CAY A:J2D1102 3.7 10.8 1.0 O A:GLU319 3.9 13.1 1.0 O A:HOH1462 4.0 18.7 1.0 CB A:ASN458 4.2 9.6 1.0 CD A:GLN317 4.2 16.4 1.0 O A:LEU304 4.2 13.9 1.0 NE2 A:GLN317 4.2 10.1 1.0 CAL A:J2D1102 4.2 11.2 1.0 CG A:ASN458 4.3 12.3 1.0 CE A:MET1034 4.3 21.5 1.0 O A:HOH1633 4.5 12.3 1.0 CB A:GLN317 4.6 10.2 1.0 CB A:THR305 4.7 18.7 1.0 FAE A:J2D1102 4.7 15.8 1.0 CAX A:J2D1102 4.8 12.6 1.0 CA A:THR305 5.0 13.8 1.0

Fluorine binding site 2 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) 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 (6J) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:20.4 occ:1.00 FAF A:J2D1102 0.0 20.4 1.0 CBA A:J2D1102 1.5 17.6 1.0 CAV A:J2D1102 2.4 14.6 1.0 CAW A:J2D1102 2.5 15.9 1.0 FAD A:J2D1102 2.7 14.8 1.0 FAE A:J2D1102 2.8 15.8 1.0 CG A:GLU572 3.2 26.4 1.0 O A:HOH1604 3.2 17.4 1.0 OE2 A:GLU572 3.3 27.2 1.0 O A:HOH1462 3.4 18.7 1.0 CG2 A:THR305 3.5 12.5 1.0 CD A:GLU572 3.5 30.4 1.0 O A:HOH1625 3.5 11.7 1.0 O A:GLU319 3.6 13.1 1.0 CAK A:J2D1102 3.7 8.9 1.0 SD A:MET1034 3.8 18.6 1.0 CAL A:J2D1102 3.8 11.2 1.0 CAY A:J2D1102 4.2 10.8 1.0 CB A:GLU572 4.3 23.3 1.0 N A:ALA320 4.4 9.8 1.0 C A:GLU319 4.4 12.2 1.0 OE1 A:GLU572 4.5 29.6 1.0 CB A:THR305 4.5 18.7 1.0 CE A:MET1034 4.5 21.5 1.0 CA A:GLU572 4.7 23.9 1.0

Fluorine binding site 3 out of 3 in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6J) 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 (6J) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:F1102 b:15.8 occ:1.00 FAE A:J2D1102 0.0 15.8 1.0 CAW A:J2D1102 1.3 15.9 1.0 CBA A:J2D1102 2.3 17.6 1.0 CAL A:J2D1102 2.3 11.2 1.0 FAF A:J2D1102 2.8 20.4 1.0 O A:HOH1625 3.2 11.7 1.0 CA A:GLU572 3.4 23.9 1.0 N A:ALA320 3.5 9.8 1.0 CG A:GLU572 3.6 26.4 1.0 CAY A:J2D1102 3.6 10.8 1.0 CAV A:J2D1102 3.6 14.6 1.0 CE1 A:TYR575 3.7 11.2 1.0 N A:GLU572 3.9 21.0 1.0 O A:MET571 3.9 22.7 1.0 O A:GLU319 3.9 13.1 1.0 CB A:GLU572 4.0 23.3 1.0 CD1 A:TYR575 4.0 11.4 1.0 C A:MET571 4.0 19.4 1.0 C A:GLU319 4.1 12.2 1.0 CAK A:J2D1102 4.1 8.9 1.0 CB A:ALA320 4.1 12.0 1.0 CZ A:TYR575 4.4 8.9 1.0 CA A:ALA320 4.4 10.1 1.0 C A:GLU572 4.5 28.9 1.0 CE A:MET1034 4.6 21.5 1.0 FAD A:J2D1102 4.7 14.8 1.0 OH A:TYR575 4.7 11.0 1.0 O A:GLU572 4.8 30.8 1.0 CD A:GLU572 4.8 30.4 1.0 SD A:MET1034 4.8 18.6 1.0 CB A:MET571 4.8 22.1 0.5 CAX A:J2D1102 4.8 12.6 1.0 O A:HOH1604 4.9 17.4 1.0 CB A:MET571 4.9 21.9 0.5 CG A:TYR575 4.9 10.6 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