Zinc in PDB 1wbq: Znmg Substituted Aminopeptidase P From E. Coli

All present enzymatic activity of Znmg Substituted Aminopeptidase P From E. Coli:
3.4.11.9;

The structure of Znmg Substituted Aminopeptidase P From E. Coli, PDB code: 1wbq 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)	29.97 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	111.974, 236.703, 137.637, 90.00, 106.14, 90.00
R / Rfree (%)	16.7 / 19.7

The structure of Znmg Substituted Aminopeptidase P From E. Coli also contains other interesting chemical elements:

Magnesium	(Mg)	6 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Zinc atom in the Znmg Substituted Aminopeptidase P From E. Coli (pdb code 1wbq). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Znmg Substituted Aminopeptidase P From E. Coli, PDB code: 1wbq:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1440 b:53.9 occ:1.00 OE2 A:GLU406 2.2 44.6 1.0 OD2 A:ASP271 2.2 35.7 1.0 NE2 A:HIS354 2.2 30.8 1.0 O A:HOH2191 2.4 37.8 1.0 OE2 A:GLU383 2.5 41.5 1.0 CG A:ASP271 3.0 32.7 1.0 CE1 A:HIS354 3.2 31.0 1.0 CD A:GLU406 3.2 33.5 1.0 O A:HOH2155 3.2 45.7 1.0 CD A:GLU383 3.2 36.4 1.0 CD2 A:HIS354 3.2 28.8 1.0 OD1 A:ASP271 3.2 29.9 1.0 OE1 A:GLU383 3.3 40.1 1.0 MG A:MG1441 3.3 32.0 1.0 OE1 A:GLU406 3.5 32.2 1.0 CG2 A:THR381 3.7 30.5 1.0 OG1 A:THR381 3.8 30.6 1.0 O A:HOH2134 3.8 34.0 1.0 CB A:THR381 4.0 30.7 1.0 ND1 A:HIS354 4.3 32.6 1.0 CB A:ASP271 4.3 32.7 1.0 CG A:HIS354 4.3 34.6 1.0 CG A:GLU406 4.5 35.0 1.0 CG A:GLU383 4.5 36.9 1.0 NE2 A:HIS361 4.8 39.6 1.0 CD2 A:HIS361 5.0 42.4 1.0 CG2 A:VAL360 5.0 35.5 1.0

Zinc binding site 2 out of 4 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1440 b:44.1 occ:1.00 OE2 B:GLU406 2.2 43.0 1.0 OD2 B:ASP271 2.2 32.5 1.0 NE2 B:HIS354 2.3 30.6 1.0 O B:HOH2285 2.3 24.2 1.0 OE2 B:GLU383 2.5 43.3 1.0 CG B:ASP271 3.0 31.2 1.0 CD B:GLU406 3.1 34.9 1.0 CD B:GLU383 3.2 37.3 1.0 OE1 B:GLU383 3.2 40.6 1.0 CD2 B:HIS354 3.2 26.5 1.0 MG B:MG1441 3.2 26.7 1.0 CE1 B:HIS354 3.3 29.1 1.0 OD1 B:ASP271 3.3 32.0 1.0 O B:HOH2235 3.3 34.9 1.0 OE1 B:GLU406 3.4 31.6 1.0 CG2 B:THR381 3.7 31.9 1.0 O B:HOH2198 3.8 25.8 1.0 OG1 B:THR381 3.8 28.7 1.0 CB B:THR381 4.0 30.6 1.0 CB B:ASP271 4.3 33.8 1.0 CG B:HIS354 4.4 33.7 1.0 ND1 B:HIS354 4.4 30.2 1.0 CG B:GLU406 4.5 34.7 1.0 CG B:GLU383 4.5 37.2 1.0 NE2 B:HIS361 4.8 38.7 1.0 CG2 B:VAL360 4.9 36.0 1.0 CD2 B:HIS361 5.0 41.2 1.0

Zinc binding site 3 out of 4 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1440 b:67.0 occ:1.00 OD2 C:ASP271 2.1 30.5 1.0 OE2 C:GLU406 2.2 43.1 1.0 NE2 C:HIS354 2.3 31.4 1.0 OE2 C:GLU383 2.4 42.3 1.0 CD C:GLU383 3.0 36.5 1.0 CG C:ASP271 3.1 31.8 1.0 CD C:GLU406 3.1 33.7 1.0 MG C:MG1441 3.1 60.4 1.0 OE1 C:GLU383 3.2 42.8 1.0 CD2 C:HIS354 3.2 28.1 1.0 CE1 C:HIS354 3.2 30.6 1.0 OE1 C:GLU406 3.3 31.2 1.0 OD1 C:ASP271 3.4 32.6 1.0 CG2 C:THR381 3.7 30.8 1.0 OG1 C:THR381 3.7 28.3 1.0 CB C:THR381 3.9 29.4 1.0 CB C:ASP271 4.3 30.9 1.0 ND1 C:HIS354 4.3 32.5 1.0 CG C:GLU383 4.4 36.3 1.0 CG C:HIS354 4.4 34.2 1.0 CG C:GLU406 4.4 34.8 1.0 NE2 C:HIS361 4.9 36.6 1.0 CB C:GLU383 5.0 35.6 1.0

Zinc binding site 4 out of 4 in the Znmg Substituted Aminopeptidase P From E. Coli


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Znmg Substituted Aminopeptidase P From E. Coli within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1440 b:46.7 occ:1.00 OE2 D:GLU406 2.1 44.5 1.0 OD2 D:ASP271 2.1 35.8 1.0 NE2 D:HIS354 2.3 31.5 1.0 O D:HOH2256 2.3 25.0 1.0 OE2 D:GLU383 2.5 43.2 1.0 CG D:ASP271 3.0 31.1 1.0 CD D:GLU406 3.1 35.4 1.0 CD D:GLU383 3.2 34.8 1.0 CD2 D:HIS354 3.2 26.4 1.0 OE1 D:GLU383 3.2 40.9 1.0 CE1 D:HIS354 3.2 31.3 1.0 OD1 D:ASP271 3.3 30.4 1.0 MG D:MG1441 3.3 29.7 1.0 OE1 D:GLU406 3.4 31.3 1.0 CG2 D:THR381 3.7 31.1 1.0 OG1 D:THR381 3.9 28.8 1.0 CB D:THR381 4.0 29.1 1.0 O D:HOH2172 4.1 25.5 1.0 CB D:ASP271 4.3 32.3 1.0 ND1 D:HIS354 4.3 33.1 1.0 CG D:HIS354 4.3 35.9 1.0 CG D:GLU406 4.4 33.9 1.0 CG D:GLU383 4.5 37.7 1.0 NE2 D:HIS361 4.9 40.6 1.0 CG2 D:VAL360 4.9 36.3 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