Magnesium in PDB 4pv4: Proline Aminopeptidase P II From Yersinia Pestis

All present enzymatic activity of Proline Aminopeptidase P II From Yersinia Pestis:
3.4.11.9;

The structure of Proline Aminopeptidase P II From Yersinia Pestis, PDB code: 4pv4 was solved by J.Osipiuk, N.Maltseva, S.Shatsman, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.40 / 1.76
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	124.299, 82.865, 110.091, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 19.8

The binding sites of Magnesium atom in the Proline Aminopeptidase P II From Yersinia Pestis (pdb code 4pv4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Proline Aminopeptidase P II From Yersinia Pestis, PDB code: 4pv4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Proline Aminopeptidase P II From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:24.6 occ:1.00 OD1 A:ASP269 2.1 23.9 1.0 OE1 A:GLU405 2.2 21.2 1.0 O A:HOH1083 2.2 39.9 1.0 OD1 A:ASP258 2.3 18.4 1.0 OD2 A:ASP258 2.3 18.5 1.0 CG A:ASP258 2.7 17.5 1.0 CG A:ASP269 3.0 23.9 1.0 MG A:MG502 3.1 20.9 0.7 CD A:GLU405 3.1 21.6 1.0 OE2 A:GLU405 3.2 19.4 1.0 OD2 A:ASP269 3.3 29.7 1.0 OG1 A:THR271 3.5 17.7 1.0 OH A:TYR227 3.9 19.4 1.0 CB A:ASP258 4.2 16.5 1.0 OE1 A:GLU382 4.2 30.6 1.0 C24 A:1PE503 4.2 46.1 1.0 CZ A:TYR227 4.4 20.4 1.0 CB A:ASP269 4.4 17.8 1.0 CG A:GLU405 4.5 17.8 1.0 O A:HOH837 4.5 34.7 1.0 OH4 A:1PE503 4.6 47.1 1.0 NE A:ARG403 4.6 17.3 1.0 C A:ASP269 4.6 18.5 1.0 O A:ILE270 4.7 15.7 1.0 CE2 A:TYR227 4.7 20.4 1.0 C23 A:1PE503 4.7 36.2 1.0 C14 A:1PE503 4.8 48.3 1.0 C A:ILE270 4.8 16.9 1.0 OE2 A:GLU382 4.8 29.0 1.0 N A:ILE270 4.8 17.2 1.0 CA A:ASP269 4.8 17.0 1.0 CD A:GLU382 4.8 27.5 1.0 NH1 A:ARG403 4.8 21.6 1.0 CB A:THR271 4.9 17.7 1.0 O A:ASP269 4.9 18.6 1.0 CA A:ASP258 5.0 16.4 1.0 CB A:GLU405 5.0 18.4 1.0

Magnesium binding site 2 out of 4 in the Proline Aminopeptidase P II From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:20.9 occ:0.70 O A:HOH1083 2.0 39.9 1.0 OE2 A:GLU405 2.1 19.4 1.0 NE2 A:HIS352 2.2 20.1 1.0 OD2 A:ASP269 2.3 29.7 1.0 OE2 A:GLU382 2.4 29.0 1.0 MG A:MG501 3.1 24.6 1.0 CD A:GLU405 3.1 21.6 1.0 CE1 A:HIS352 3.1 20.3 1.0 CG A:ASP269 3.2 23.9 1.0 CD A:GLU382 3.2 27.5 1.0 CD2 A:HIS352 3.2 20.8 1.0 OE1 A:GLU382 3.3 30.6 1.0 OE1 A:GLU405 3.4 21.2 1.0 OD1 A:ASP269 3.4 23.9 1.0 O A:HOH837 3.5 34.7 1.0 CG2 A:THR380 3.7 18.8 1.0 OG1 A:THR380 3.8 19.9 1.0 CB A:THR380 4.0 17.8 1.0 OH2 A:1PE503 4.1 55.2 1.0 ND1 A:HIS352 4.2 19.7 1.0 CG A:HIS352 4.3 20.3 1.0 CB A:ASP269 4.3 17.8 1.0 CG A:GLU405 4.4 17.8 1.0 CG A:GLU382 4.5 20.2 1.0 CB A:GLU382 4.9 18.9 1.0 CG2 A:VAL358 5.0 21.6 1.0 NE2 A:HIS359 5.0 21.5 1.0

Magnesium binding site 3 out of 4 in the Proline Aminopeptidase P II From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:26.8 occ:1.00 OE2 B:GLU405 2.2 19.0 1.0 NE2 B:HIS352 2.2 20.2 1.0 OD2 B:ASP269 2.3 29.2 1.0 OE2 B:GLU382 2.5 26.7 1.0 O B:HOH844 2.5 38.8 1.0 MG B:MG502 3.1 24.8 1.0 CD B:GLU405 3.1 20.8 1.0 CD2 B:HIS352 3.1 19.8 1.0 CG B:ASP269 3.1 25.2 1.0 CD B:GLU382 3.2 27.7 1.0 CE1 B:HIS352 3.2 19.8 1.0 OE1 B:GLU382 3.3 29.7 1.0 OE1 B:GLU405 3.4 23.2 1.0 OD1 B:ASP269 3.5 23.8 1.0 O B:HOH781 3.6 33.7 1.0 CG2 B:THR380 3.6 17.8 1.0 OG1 B:THR380 3.8 18.9 1.0 CB B:THR380 4.0 18.4 1.0 ND1 B:HIS352 4.3 19.7 1.0 CG B:HIS352 4.3 19.1 1.0 CB B:ASP269 4.3 19.9 1.0 CG B:GLU405 4.5 18.9 1.0 CG B:GLU382 4.5 21.2 1.0 C11 B:P6G503 4.8 44.6 1.0 CB B:GLU382 4.9 20.1 1.0

Magnesium binding site 4 out of 4 in the Proline Aminopeptidase P II From Yersinia Pestis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Proline Aminopeptidase P II From Yersinia Pestis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:24.8 occ:1.00 OD1 B:ASP269 2.2 23.8 1.0 O B:HOH844 2.2 38.8 1.0 OE1 B:GLU405 2.2 23.2 1.0 OD2 B:ASP258 2.3 19.7 1.0 OD1 B:ASP258 2.4 20.4 1.0 CG B:ASP258 2.7 19.9 1.0 CG B:ASP269 3.0 25.2 1.0 CD B:GLU405 3.1 20.8 1.0 MG B:MG501 3.1 26.8 1.0 OE2 B:GLU405 3.2 19.0 1.0 OD2 B:ASP269 3.3 29.2 1.0 OG1 B:THR271 3.5 17.9 1.0 C12 B:P6G503 3.8 46.1 1.0 OH B:TYR227 3.9 17.8 1.0 C11 B:P6G503 4.1 44.6 1.0 O13 B:P6G503 4.1 36.2 1.0 CB B:ASP258 4.2 18.7 1.0 OE1 B:GLU382 4.2 29.7 1.0 CZ B:TYR227 4.4 20.0 1.0 CB B:ASP269 4.4 19.9 1.0 O B:HOH781 4.5 33.7 1.0 CG B:GLU405 4.5 18.9 1.0 C14 B:P6G503 4.5 41.0 1.0 NE B:ARG403 4.6 19.4 1.0 C B:ASP269 4.7 17.7 1.0 O B:ILE270 4.7 17.8 1.0 CE2 B:TYR227 4.7 19.7 1.0 C B:ILE270 4.8 17.0 1.0 O16 B:P6G503 4.8 40.7 1.0 CA B:ASP269 4.8 18.3 1.0 CD B:GLU382 4.9 27.7 1.0 N B:ILE270 4.9 17.3 1.0 OE2 B:GLU382 4.9 26.7 1.0 O B:ASP269 4.9 18.0 1.0 CB B:THR271 4.9 18.1 1.0 NH1 B:ARG403 4.9 23.3 1.0 CB B:GLU405 5.0 18.4 1.0 CA B:ASP258 5.0 18.1 1.0

J.Osipiuk, N.Maltseva, S.Shatsman, W.F.Anderson, A.Joachimiak. Proline Aminopeptidase P II From Yersinia Pestis To Be Published.