Magnesium in PDB 3ebh: Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin

The structure of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin, PDB code: 3ebh 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)	27.47 / 1.65
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.651, 108.628, 117.964, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 20.2

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

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin (pdb code 3ebh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin, PDB code: 3ebh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg7 b:24.8 occ:1.00 O A:HOH26 2.0 19.3 1.0 O A:GLY250 2.1 14.7 1.0 O A:HOH1520 2.1 28.8 1.0 O A:HOH1099 2.1 25.6 1.0 O A:HOH1521 2.1 18.7 1.0 O A:HOH1212 2.2 17.5 1.0 C A:GLY250 3.2 13.7 1.0 CA A:GLY250 3.8 13.7 1.0 O A:HOH1191 4.2 13.4 1.0 ND1 A:HIS297 4.3 17.1 1.0 N A:LEU251 4.3 13.6 1.0 O A:HOH111 4.3 32.8 1.0 O A:HOH1459 4.6 14.4 1.0 O A:ILE295 4.6 14.6 1.0 CA A:LEU251 4.6 13.8 1.0 CA A:ILE296 4.9 12.3 1.0 CE1 A:HIS297 4.9 19.0 1.0 C A:LEU251 4.9 15.4 1.0 N A:LYS252 5.0 15.3 1.0

Magnesium binding site 2 out of 4 in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg8 b:30.8 occ:1.00 O A:HOH1523 1.9 22.8 1.0 O A:HOH1527 2.1 26.2 1.0 O A:HOH1176 2.2 21.1 1.0 O A:HOH1524 2.2 23.5 1.0 O A:HOH1525 2.2 28.3 1.0 O A:HOH1526 2.2 31.4 1.0 O A:HOH1421 4.0 35.6 1.0 O A:HOH1761 4.2 68.4 1.0 O A:HOH1222 4.2 27.9 1.0 OG A:SER542 4.3 12.5 1.0 OE1 A:GLU526 4.4 13.5 1.0 O A:HOH112 4.4 24.4 1.0 OD1 A:ASN527 4.4 15.7 1.0 CG2 A:THR492 4.5 9.6 0.5 ND1 A:HIS543 4.5 8.4 0.5 OE2 A:GLU526 4.5 14.1 1.0 OG1 A:THR492 4.6 7.6 0.5 O A:THR539 4.6 13.5 1.0 CB A:HIS543 4.7 5.7 0.5 O A:HOH1530 4.8 17.6 1.0 CD A:GLU526 4.9 13.8 1.0

Magnesium binding site 3 out of 4 in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg9 b:29.5 occ:1.00 O A:HOH1541 1.9 25.9 1.0 O A:HOH1543 2.1 29.1 1.0 O A:HOH1544 2.1 21.3 1.0 O A:HOH1542 2.2 27.5 1.0 OE2 A:GLU957 3.6 19.8 1.0 O A:HOH1725 3.8 44.0 1.0 ND2 A:ASN992 4.0 18.7 1.0 O A:HOH1410 4.2 21.5 1.0 OD2 A:ASP995 4.3 16.8 1.0 CD A:GLU957 4.3 16.8 1.0 CG A:GLU957 4.5 15.6 1.0 O A:HOH190 4.5 17.4 1.0 O A:HOH1307 4.5 29.4 1.0 O A:HOH1738 4.6 42.4 1.0 CD A:LYS311 4.7 24.3 1.0

Magnesium binding site 4 out of 4 in the Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of the M1 Alanylaminopeptidase From Malaria Complexed with Bestatin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg10 b:39.4 occ:1.00 O A:HOH1461 2.0 26.5 1.0 O A:HOH103 2.0 23.1 1.0 O A:HOH1566 2.1 36.5 1.0 O A:HOH1567 2.2 30.8 1.0 O A:HOH100 2.5 30.7 1.0 O A:HOH159 3.8 21.4 1.0 OD1 A:ASP438 3.9 21.4 1.0 OE1 A:GLU437 4.1 18.7 1.0 OH A:TYR399 4.2 17.2 1.0 OD2 A:ASP438 4.3 21.8 1.0 CB A:ALA434 4.4 13.7 1.0 CG A:ASP438 4.5 19.4 1.0 CD A:LYS402 4.7 23.3 1.0 CA A:ALA434 4.8 13.9 1.0 CG A:LYS402 4.9 23.6 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