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

The structure of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion, PDB code: 6eed 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)	35.80 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.149, 109.230, 117.920, 90.00, 90.00, 90.00
R / Rfree (%)	15.4 / 18

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

Fluorine	(F)	3 atoms
Magnesium	(Mg)	4 atoms

The binding sites of Zinc atom in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion (pdb code 6eed). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion, PDB code: 6eed:

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Crystal Structure of Pf-M1 in Complex with Inhibitor (6P) and Catalytic Zinc Ion within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:12.8 occ:0.80 OE1 A:GLU519 2.0 10.7 1.0 O A:J6A1102 2.0 10.2 1.0 NE2 A:HIS500 2.1 10.7 1.0 NE2 A:HIS496 2.1 10.4 1.0 OAC A:J6A1102 2.2 11.0 1.0 CD A:GLU519 2.8 12.0 1.0 C A:J6A1102 2.8 9.2 1.0 OE2 A:GLU519 2.8 13.5 1.0 NAS A:J6A1102 2.9 10.7 1.0 CD2 A:HIS496 3.0 9.1 1.0 CE1 A:HIS500 3.1 10.8 1.0 CD2 A:HIS500 3.1 9.5 1.0 CE1 A:HIS496 3.2 11.2 1.0 O A:HOH1277 3.4 12.4 1.0 OE1 A:GLU463 4.1 11.5 1.0 OH A:TYR580 4.1 10.7 1.0 CE2 A:TYR580 4.1 11.0 1.0 ND1 A:HIS500 4.2 11.0 1.0 CG A:HIS496 4.2 9.4 1.0 CG A:HIS500 4.2 10.3 1.0 CG A:GLU519 4.2 11.6 1.0 CA A:J6A1102 4.3 10.9 1.0 ND1 A:HIS496 4.3 9.8 1.0 OE1 A:GLU497 4.4 11.6 1.0 CZ A:TYR580 4.6 11.1 1.0 CD A:GLU463 4.7 11.0 1.0 N A:J6A1102 4.7 11.8 1.0 OE2 A:GLU463 4.8 12.9 1.0 CG2 A:THR522 4.8 11.8 1.0 OE2 A:GLU497 4.8 11.2 1.0 O2 A:PO41115 4.9 49.4 0.8 CB A:GLU519 4.9 11.6 1.0 CA A:GLU519 4.9 11.1 1.0 NZ A:LYS518 4.9 11.6 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