Zinc in PDB 2bh3: Zn Substituted E. Coli Aminopeptidase P in Complex with Product

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

The structure of Zn Substituted E. Coli Aminopeptidase P in Complex with Product, PDB code: 2bh3 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 / 2.40
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	138.012, 138.012, 230.734, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 20.1

The structure of Zn Substituted E. Coli Aminopeptidase P in Complex with Product also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Zn Substituted E. Coli Aminopeptidase P in Complex with Product (pdb code 2bh3). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Zn Substituted E. Coli Aminopeptidase P in Complex with Product, PDB code: 2bh3:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Zn Substituted E. Coli Aminopeptidase P in Complex with Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Zn Substituted E. Coli Aminopeptidase P in Complex with Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:47.3 occ:1.00 O A:HOH2145 2.0 43.4 1.0 OD1 A:ASP260 2.1 48.0 1.0 OD1 A:ASP271 2.1 52.3 1.0 OE1 A:GLU406 2.1 45.5 1.0 OD2 A:ASP260 2.6 45.0 1.0 CG A:ASP260 2.7 46.8 1.0 CG A:ASP271 3.0 47.2 1.0 CD A:GLU406 3.0 44.8 1.0 ZN A:ZN1002 3.1 46.2 1.0 OD2 A:ASP271 3.1 49.2 1.0 OE2 A:GLU406 3.1 44.5 1.0 OG1 A:THR273 3.6 45.7 1.0 OH A:TYR229 3.7 42.5 1.0 O A:HOH2146 3.9 59.4 1.0 OE1 A:GLU383 4.1 51.2 1.0 CB A:ASP260 4.2 45.8 1.0 CZ A:TYR229 4.2 43.0 1.0 CG A:GLU406 4.3 45.5 1.0 CB A:ASP271 4.3 45.8 1.0 C A:ASP271 4.5 45.2 1.0 O A:ILE272 4.5 43.7 1.0 OE2 A:GLU383 4.6 54.3 1.0 C A:ILE272 4.6 44.6 1.0 CE2 A:TYR229 4.6 44.7 1.0 CD A:GLU383 4.6 51.1 1.0 N A:ILE272 4.6 44.8 1.0 N A:PRO501 4.6 56.2 1.0 O A:ASP271 4.6 44.3 1.0 CD A:PRO501 4.7 55.5 1.0 CA A:ASP271 4.7 46.3 1.0 CA A:ASP260 4.8 46.3 1.0 CB A:GLU406 4.9 45.7 1.0 N A:THR273 4.9 44.6 1.0 NE A:ARG404 4.9 46.5 1.0 CB A:THR273 5.0 44.3 1.0 NE2 A:HIS354 5.0 44.3 1.0

Zinc binding site 2 out of 4 in the Zn Substituted E. Coli Aminopeptidase P in Complex with Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Zn Substituted E. Coli Aminopeptidase P in Complex with Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:46.2 occ:1.00 O A:HOH2145 2.1 43.4 1.0 NE2 A:HIS354 2.1 44.3 1.0 OE2 A:GLU406 2.2 44.5 1.0 OD2 A:ASP271 2.2 49.2 1.0 OE2 A:GLU383 2.2 54.3 1.0 CE1 A:HIS354 3.0 48.5 1.0 CD A:GLU383 3.1 51.1 1.0 ZN A:ZN1001 3.1 47.3 1.0 CD2 A:HIS354 3.1 49.0 1.0 CD A:GLU406 3.1 44.8 1.0 CG A:ASP271 3.2 47.2 1.0 OE1 A:GLU383 3.3 51.2 1.0 OE1 A:GLU406 3.4 45.5 1.0 OD1 A:ASP271 3.5 52.3 1.0 CG2 A:THR381 3.6 43.6 1.0 OG1 A:THR381 3.7 42.9 1.0 CB A:THR381 3.9 45.3 1.0 ND1 A:HIS354 4.1 43.1 1.0 CG A:HIS354 4.2 43.9 1.0 N A:PRO501 4.3 56.2 1.0 CG A:GLU383 4.4 49.7 1.0 CB A:ASP271 4.4 45.8 1.0 CG A:GLU406 4.5 45.5 1.0 O A:HOH2146 4.5 59.4 1.0 CA A:PRO501 4.7 55.6 1.0 O A:HOH2117 4.9 48.0 1.0 CB A:GLU383 4.9 49.0 1.0 NE2 A:HIS361 5.0 58.8 1.0

Zinc binding site 3 out of 4 in the Zn Substituted E. Coli Aminopeptidase P in Complex with Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Zn Substituted E. Coli Aminopeptidase P in Complex with Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:0.8 occ:0.50 NE2 A:HIS71 2.0 87.4 1.0 CE1 A:HIS71 3.0 86.9 1.0 CD2 A:HIS71 3.0 84.4 1.0 ND1 A:HIS71 4.1 85.5 1.0 CG A:HIS71 4.2 79.2 1.0 ND1 A:HIS73 4.5 73.9 1.0

Zinc binding site 4 out of 4 in the Zn Substituted E. Coli Aminopeptidase P in Complex with Product


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Zn Substituted E. Coli Aminopeptidase P in Complex with Product within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1008 b:75.4 occ:1.00 NE2 A:HIS361 2.5 58.8 1.0 N A:PRO501 2.5 56.2 1.0 O A:HOH2146 2.6 59.4 1.0 NE2 A:HIS243 2.6 57.1 1.0 O A:PRO501 2.6 55.2 1.0 CE1 A:HIS361 2.8 62.7 1.0 C A:PRO501 3.2 56.2 1.0 CD2 A:HIS243 3.3 60.1 1.0 CA A:PRO501 3.3 55.6 1.0 CD A:PRO501 3.5 55.5 1.0 CE1 A:HIS243 3.7 58.9 1.0 O A:HOH2025 3.7 45.6 1.0 CD2 A:HIS361 3.8 56.3 1.0 O A:HOH2145 3.9 43.4 1.0 ND1 A:HIS361 4.1 62.2 1.0 N A:LEU502 4.3 57.2 1.0 CB A:PRO501 4.4 55.9 1.0 CG A:HIS243 4.6 57.4 1.0 CG A:HIS361 4.6 52.3 1.0 CG A:PRO501 4.6 55.0 1.0 ND1 A:HIS243 4.7 62.2 1.0 NE2 A:HIS354 5.0 44.3 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