Magnesium in PDB 5y1w: Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc, PDB code: 5y1w was solved by A.K.Marapaka, A.Addlagatta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.67 / 1.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.421, 109.205, 112.477, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 20.6

The structure of Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc (pdb code 5y1w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc, PDB code: 5y1w:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1102 b:25.8 occ:1.00 O A:HOH1219 1.9 30.6 1.0 O A:HOH1238 1.9 14.7 1.0 O A:HOH1265 2.1 16.0 1.0 O A:HOH1703 2.1 26.4 1.0 O A:HOH1397 2.2 16.9 1.0 O A:HOH1346 2.4 18.7 1.0 O A:HOH1202 2.7 20.6 1.0 ZN A:ZN1101 3.2 14.8 1.0 OH A:TYR580 3.5 15.6 1.0 O A:ALA461 3.7 15.1 1.0 OE2 A:GLU519 3.8 14.7 1.0 OE1 A:GLU463 4.0 13.2 1.0 OE2 A:GLU497 4.1 16.5 1.0 OE1 A:GLU497 4.3 15.4 1.0 NE2 A:HIS496 4.4 12.3 1.0 O A:HOH1777 4.4 29.3 1.0 OE1 A:GLU519 4.5 13.7 1.0 CD A:GLU519 4.5 14.1 1.0 OE1 A:GLU319 4.5 17.4 1.0 NE2 A:HIS500 4.6 12.7 1.0 CZ A:TYR580 4.7 15.4 1.0 CD A:GLU497 4.7 14.6 1.0 C A:ALA461 4.7 12.1 1.0 CD2 A:HIS496 4.8 14.2 1.0 CE2 A:TYR580 4.9 14.2 1.0 O A:HOH1709 4.9 30.9 1.0 O A:HOH1817 4.9 26.0 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1103 b:25.1 occ:1.00 O A:HOH1380 2.0 22.3 1.0 O A:HOH1823 2.1 30.7 1.0 O A:HOH1883 2.1 26.8 1.0 O A:HOH1870 2.1 31.7 1.0 O A:HOH1508 2.1 24.6 1.0 O A:HOH1248 2.2 25.5 1.0 OE2 A:GLU957 3.7 18.2 1.0 ND2 A:ASN992 4.2 19.4 1.0 O A:HOH1381 4.2 27.2 1.0 O A:HOH1891 4.2 23.4 1.0 OD2 A:ASP995 4.2 21.1 1.0 O A:HOH1814 4.3 35.7 1.0 CD A:GLU957 4.5 19.3 1.0 O A:HOH1301 4.5 25.2 1.0 O A:HOH1465 4.6 21.2 1.0 CG A:GLU957 4.8 23.7 1.0 O A:HOH1836 4.9 34.1 1.0 CE A:LYS311 5.0 20.8 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1104 b:24.4 occ:1.00 O A:GLY250 2.1 16.3 1.0 O A:HOH1733 2.1 24.3 1.0 O A:HOH1731 2.1 25.1 1.0 C A:GLY250 3.2 16.9 1.0 CA A:GLY250 3.9 18.6 1.0 O A:HOH1434 4.0 20.3 1.0 N A:LEU251 4.3 15.6 1.0 CA A:LEU251 4.6 16.0 1.0 O A:ILE295 4.6 15.4 1.0 O A:HOH1773 4.8 20.3 1.0 CD2 A:HIS297 4.8 23.6 1.0 CA A:ILE296 4.8 15.0 1.0 C A:LEU251 5.0 16.8 1.0

A.K.Marapaka, A.Addlagatta. Crystal Structure of Plasmodium Falciparum Aminopeptidase N with Magnesium Bound to Active Site Zinc To Be Published.