Zinc in PDB 3ebi: Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog

The structure of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog, PDB code: 3ebi was solved by S.Mcgowan, C.J.Porter, A.M.Buckle, J.C.Whisstock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.61 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.852, 108.633, 118.325, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.1

The structure of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog (pdb code 3ebi). 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 Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog, PDB code: 3ebi:

Zinc binding site 1 out of 1 in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with the Phosphinate Dipeptide Analog within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1 b:14.2 occ:1.00 O3 A:BEY1085 1.9 25.0 1.0 NE2 A:HIS500 2.0 8.0 1.0 NE2 A:HIS496 2.0 16.7 1.0 OE1 A:GLU519 2.1 6.0 1.0 CD A:GLU519 2.9 10.5 1.0 P A:BEY1085 2.9 17.5 1.0 CD2 A:HIS500 3.0 9.0 1.0 CD2 A:HIS496 3.0 11.2 1.0 OE2 A:GLU519 3.0 9.9 1.0 CE1 A:HIS500 3.1 4.0 1.0 CE1 A:HIS496 3.1 13.1 1.0 O4 A:BEY1085 3.1 20.3 1.0 C19 A:BEY1085 3.7 18.9 1.0 OH A:TYR580 4.0 17.9 1.0 CE1 A:TYR580 4.1 11.4 1.0 N A:BEY1085 4.1 16.2 1.0 CG A:HIS500 4.1 3.3 1.0 ND1 A:HIS500 4.1 7.6 1.0 CG A:HIS496 4.2 11.9 1.0 ND1 A:HIS496 4.2 15.9 1.0 CG A:GLU519 4.3 9.0 1.0 C17 A:BEY1085 4.4 25.2 1.0 OE1 A:GLU463 4.5 9.1 1.0 CZ A:TYR580 4.5 11.6 1.0 CG2 A:THR522 4.6 6.1 1.0 C8 A:BEY1085 4.6 26.8 1.0 CA A:GLU519 4.8 10.4 1.0 CB A:GLU519 4.8 10.3 1.0 CB A:THR522 4.8 10.3 1.0 OE2 A:GLU463 4.9 14.8 1.0 CD A:GLU463 4.9 7.3 1.0 OE2 A:GLU497 4.9 13.2 1.0

S.Mcgowan, C.J.Porter, J.Lowther, C.M.Stack, S.J.Golding, T.S.Skinner-Adams, K.R.Trenholme, F.Teuscher, S.M.Donnelly, J.Grembecka, A.Mucha, P.Kafarski, R.Degori, A.M.Buckle, D.L.Gardiner, J.C.Whisstock, J.P.Dalton. Structural Basis For the Inhibition of the Essential Plasmodium Falciparum M1 Neutral Aminopeptidase Proc.Natl.Acad.Sci.Usa V. 106 2537 2009.
ISSN: ISSN 0027-8424
PubMed: 19196988
DOI: 10.1073/PNAS.0807398106