Zinc in PDB 3q43: X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15

The structure of X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15, PDB code: 3q43 was solved by S.Mcgowan, D.C.Greenbaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.07 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.772, 108.814, 118.683, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 20.7

The structure of X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15 also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15 (pdb code 3q43). 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 Pfa-M1 Bound to Bestatin Derivative 15, PDB code: 3q43:

Zinc binding site 1 out of 1 in the X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15


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 Pfa-M1 Bound to Bestatin Derivative 15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:13.5 occ:1.00 O2 A:D661087 2.0 16.0 1.0 OE1 A:GLU519 2.0 10.4 1.0 NE2 A:HIS496 2.0 13.4 1.0 NE2 A:HIS500 2.1 9.4 1.0 CD A:GLU519 2.7 12.0 1.0 OE2 A:GLU519 2.8 14.4 1.0 CD2 A:HIS496 3.0 12.8 1.0 CD2 A:HIS500 3.0 9.5 1.0 CE1 A:HIS496 3.1 13.0 1.0 C8 A:D661087 3.1 17.2 1.0 CE1 A:HIS500 3.1 11.3 1.0 C9 A:D661087 3.5 19.5 1.0 N1 A:D661087 3.6 18.5 1.0 C7 A:D661087 3.7 13.3 1.0 O3 A:D661087 4.0 22.9 1.0 OE1 A:GLU497 4.0 13.4 1.0 N2 A:D661087 4.1 19.2 1.0 CG A:HIS496 4.1 10.7 1.0 ND1 A:HIS496 4.1 12.7 1.0 ND1 A:HIS500 4.2 10.3 1.0 CG A:HIS500 4.2 9.2 1.0 CG A:GLU519 4.2 10.4 1.0 OE1 A:GLU463 4.4 12.6 1.0 OH A:TYR580 4.4 16.5 1.0 CE1 A:TYR580 4.4 14.8 1.0 OE2 A:GLU497 4.7 13.2 1.0 CG2 A:THR522 4.7 10.7 1.0 CA A:GLU519 4.7 11.1 1.0 CD A:GLU497 4.7 14.9 1.0 CB A:GLU519 4.8 10.8 1.0 CZ A:TYR580 4.8 15.2 1.0 CD A:GLU463 4.9 11.9 1.0 CB A:THR522 4.9 9.3 1.0 OE2 A:GLU463 4.9 15.7 1.0 NZ A:LYS518 5.0 13.3 1.0

G.Velmourougane, M.B.Harbut, S.Dalal, S.Mcgowan, C.A.Oellig, N.Meinhardt, J.C.Whisstock, M.Klemba, D.C.Greenbaum. Synthesis of New (-)-Bestatin-Based Inhibitor Libraries Reveals A Novel Binding Mode in the S1 Pocket of the Essential Malaria M1 Metalloaminopeptidase. J.Med.Chem. V. 54 1655 2011.
ISSN: ISSN 0022-2623
PubMed: 21366301
DOI: 10.1021/JM101227T