Magnesium 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:

Zinc

(Zn)

1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15, PDB code: 3q43:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1086 b:51.1 occ:1.00 O A:HOH1188 2.5 32.2 1.0 OE2 A:GLU957 3.8 20.3 1.0 ND2 A:ASN992 4.1 19.4 1.0 O A:HOH1402 4.1 23.5 1.0 OD2 A:ASP995 4.2 19.4 1.0 O A:HOH1128 4.4 21.8 1.0 O A:HOH1100 4.4 26.2 1.0 O A:HOH1096 4.5 16.0 1.0 CD A:GLU957 4.5 22.5 1.0 CG A:GLU957 4.8 20.0 1.0 O A:HOH1409 5.0 31.6 1.0

Magnesium binding site 2 out of 4 in the X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 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:Mg2 b:28.7 occ:1.00 O A:GLY250 2.1 13.8 1.0 C A:GLY250 3.2 13.5 1.0 CA A:GLY250 3.8 14.3 1.0 O A:HOH1123 4.1 9.9 1.0 O A:HOH1120 4.3 27.3 1.0 N A:LEU251 4.3 13.6 1.0 ND1 A:HIS297 4.3 16.0 1.0 O A:HOH1119 4.4 23.3 1.0 O A:ILE295 4.6 13.6 1.0 CA A:LEU251 4.6 13.1 1.0 C A:LEU251 4.9 14.6 1.0 CE1 A:HIS297 4.9 19.0 1.0 N A:LYS252 4.9 15.4 1.0 CA A:ILE296 4.9 14.2 1.0

Magnesium binding site 3 out of 4 in the X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 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:Mg3 b:51.6 occ:1.00 O A:HOH1747 2.4 19.3 1.0 O A:HOH1431 3.9 23.1 1.0 OD1 A:ASP438 4.0 22.5 1.0 OE1 A:GLU437 4.3 20.7 1.0 OD2 A:ASP438 4.3 20.4 1.0 OH A:TYR399 4.3 15.2 1.0 CB A:ALA434 4.5 13.4 1.0 CG A:ASP438 4.6 21.0 1.0 CD A:LYS402 4.8 24.9 1.0 CA A:ALA434 4.9 14.3 1.0

Magnesium binding site 4 out of 4 in the X-Ray Crystal Structure of Pfa-M1 Bound to Bestatin Derivative 15


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 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:Mg5 b:41.6 occ:1.00 NE2 A:HIS543 2.2 3.3 0.5 CD2 A:HIS543 2.4 10.4 0.5 CE1 A:HIS543 3.4 13.2 0.5 CG A:HIS543 3.7 12.8 0.5 ND1 A:HIS543 4.2 15.9 0.5 OG A:SER542 4.3 12.6 1.0 O A:HOH81 4.3 24.5 1.0 ND2 A:ASN527 4.3 17.4 1.0 O A:HOH1217 4.4 27.6 1.0 OE1 A:GLU526 4.4 15.5 1.0 O A:HOH1712 4.4 27.6 1.0 OE2 A:GLU526 4.5 18.6 1.0 ND1 A:HIS543 4.5 9.7 0.5 OG1 A:THR492 4.6 15.2 1.0 O A:THR539 4.7 14.3 1.0 O A:HOH1218 4.7 16.0 1.0 CB A:HIS543 4.8 9.7 0.5 CB A:HIS543 4.9 10.6 0.5 CD A:GLU526 4.9 17.6 1.0 O A:HOH1219 4.9 25.6 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