Magnesium in PDB 2bhd: Mg Substituted E. Coli Aminopeptidase P in Complex with Product

All present enzymatic activity of Mg Substituted E. Coli Aminopeptidase P in Complex with Product:
3.4.11.9;

The structure of Mg Substituted E. Coli Aminopeptidase P in Complex with Product, PDB code: 2bhd was solved by S.C.Graham, C.S.Bond, H.C.Freeman, J.M.Guss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.19 / 2.50
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	138.569, 138.569, 230.962, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 20.4

The binding sites of Magnesium atom in the Mg Substituted E. Coli Aminopeptidase P in Complex with Product (pdb code 2bhd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Mg Substituted E. Coli Aminopeptidase P in Complex with Product, PDB code: 2bhd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Mg Substituted E. Coli Aminopeptidase P in Complex with Product


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mg Substituted E. Coli Aminopeptidase P in Complex with Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1441 b:25.4 occ:1.00 OE2 A:GLU406 2.0 43.5 1.0 O A:HOH2085 2.0 42.9 1.0 OD2 A:ASP271 2.1 42.8 1.0 NE2 A:HIS354 2.1 42.8 1.0 OE2 A:GLU383 2.4 49.4 1.0 MG A:MG1442 2.9 35.1 1.0 CD A:GLU406 3.0 45.0 1.0 CE1 A:HIS354 3.0 45.1 1.0 CG A:ASP271 3.1 41.7 1.0 CD2 A:HIS354 3.1 42.8 1.0 CD A:GLU383 3.2 46.4 1.0 OE1 A:GLU383 3.3 49.8 1.0 OE1 A:GLU406 3.3 48.5 1.0 OD1 A:ASP271 3.4 44.7 1.0 CG2 A:THR381 3.7 43.4 1.0 OG1 A:THR381 3.8 43.5 1.0 CB A:THR381 4.0 43.3 1.0 ND1 A:HIS354 4.2 43.0 1.0 CG A:HIS354 4.2 42.4 1.0 N B:PRO1 4.3 70.8 1.0 CG A:GLU406 4.3 43.6 1.0 CB A:ASP271 4.4 41.4 1.0 CG A:GLU383 4.5 45.6 1.0 CA B:PRO1 4.7 70.8 1.0 NE2 A:HIS361 5.0 45.4 1.0

Magnesium binding site 2 out of 3 in the Mg Substituted E. Coli Aminopeptidase P in Complex with Product


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mg Substituted E. Coli Aminopeptidase P in Complex with Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1442 b:35.1 occ:1.00 O A:HOH2085 1.9 42.9 1.0 OD1 A:ASP271 2.0 44.7 1.0 OE1 A:GLU406 2.1 48.5 1.0 OD1 A:ASP260 2.3 42.4 1.0 OD2 A:ASP260 2.5 47.1 1.0 CG A:ASP260 2.8 44.6 1.0 CG A:ASP271 2.8 41.7 1.0 CD A:GLU406 2.9 45.0 1.0 MG A:MG1441 2.9 25.4 1.0 OD2 A:ASP271 2.9 42.8 1.0 OE2 A:GLU406 3.1 43.5 1.0 OG1 A:THR273 3.7 41.6 1.0 OH A:TYR229 3.8 41.1 1.0 OE1 A:GLU383 4.1 49.8 1.0 CZ A:TYR229 4.3 41.0 1.0 CB A:ASP271 4.3 41.4 1.0 CG A:GLU406 4.3 43.6 1.0 CB A:ASP260 4.3 43.5 1.0 N B:PRO1 4.5 70.8 1.0 CD B:PRO1 4.5 70.6 1.0 C A:ASP271 4.6 41.2 1.0 CE2 A:TYR229 4.6 41.2 1.0 OE2 A:GLU383 4.6 49.4 1.0 CD A:GLU383 4.7 46.4 1.0 CA A:ASP271 4.8 41.5 1.0 O A:ILE272 4.8 39.7 1.0 N A:ILE272 4.8 40.8 1.0 NE2 A:HIS354 4.9 42.8 1.0 O A:ASP271 4.9 41.5 1.0 CB A:GLU406 4.9 43.6 1.0 C A:ILE272 4.9 40.7 1.0 NE A:ARG404 4.9 40.9 1.0 CE1 A:TYR229 5.0 40.7 1.0

Magnesium binding site 3 out of 3 in the Mg Substituted E. Coli Aminopeptidase P in Complex with Product


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mg Substituted E. Coli Aminopeptidase P in Complex with Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1443 b:45.2 occ:1.00 O A:HOH2089 2.2 44.1 1.0 O A:HOH2090 2.2 47.6 1.0 O A:HOH2088 2.2 47.2 1.0 O A:ARG399 3.8 37.7 1.0 OE2 A:GLU396 4.1 40.6 1.0 O A:GLN397 4.4 37.1 1.0 O A:GLU396 4.6 36.4 1.0 O A:HOH2091 4.8 41.4 1.0 CD A:GLU396 4.9 40.5 1.0 C A:GLN397 4.9 37.2 1.0 C A:ARG399 5.0 38.0 1.0

S.C.Graham, C.S.Bond, H.C.Freeman, J.M.Guss. Structural and Functional Implications of Metal Ion Selection in Aminopeptidase P, A Metalloprotease with A Dinuclear Metal Center. Biochemistry V. 44 13820 2005.
ISSN: ISSN 0006-2960
PubMed: 16229471
DOI: 10.1021/BI0512849