Zinc in PDB 2bhb: Zn Substituted E. Coli Aminopeptidase P

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

The structure of Zn Substituted E. Coli Aminopeptidase P, PDB code: 2bhb 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 / 2.41
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	138.814, 138.814, 230.914, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 19

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

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Zn Substituted E. Coli Aminopeptidase P (pdb code 2bhb). 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, PDB code: 2bhb:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:44.4 occ:1.00 O A:HOH2209 2.1 42.0 1.0 NE2 A:HIS354 2.1 48.9 1.0 OE2 A:GLU406 2.2 47.9 1.0 OD2 A:ASP271 2.2 50.3 1.0 OE2 A:GLU383 2.4 55.8 1.0 CE1 A:HIS354 3.0 50.3 1.0 ZN A:ZN1002 3.1 45.1 1.0 CD A:GLU383 3.1 52.3 1.0 CD2 A:HIS354 3.1 48.5 1.0 CG A:ASP271 3.1 51.0 1.0 CD A:GLU406 3.1 49.2 1.0 OE1 A:GLU383 3.2 50.3 1.0 OD1 A:ASP271 3.5 55.6 1.0 OE1 A:GLU406 3.5 50.3 1.0 CG2 A:THR381 3.6 48.8 1.0 OG1 A:THR381 3.7 48.0 1.0 O A:HOH2210 3.8 44.6 1.0 CB A:THR381 3.9 48.9 1.0 ND1 A:HIS354 4.1 47.8 1.0 CG A:HIS354 4.2 47.6 1.0 CB A:ASP271 4.4 48.7 1.0 CG A:GLU383 4.4 51.4 1.0 CG A:GLU406 4.5 48.2 1.0 C3 A:MRD1009 4.6 78.8 1.0 NE2 A:HIS361 4.6 59.8 1.0 CD2 A:HIS361 4.8 58.1 1.0 CB A:GLU383 5.0 51.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:45.1 occ:1.00 O A:HOH2209 1.9 42.0 1.0 OD1 A:ASP260 2.1 48.8 1.0 OE1 A:GLU406 2.1 50.3 1.0 OD1 A:ASP271 2.1 55.6 1.0 OD2 A:ASP260 2.6 50.3 1.0 CG A:ASP260 2.6 49.2 1.0 CD A:GLU406 2.9 49.2 1.0 CG A:ASP271 3.0 51.0 1.0 ZN A:ZN1001 3.1 44.4 1.0 OE2 A:GLU406 3.1 47.9 1.0 OD2 A:ASP271 3.2 50.3 1.0 OG1 A:THR273 3.6 48.1 1.0 OH A:TYR229 3.7 48.3 1.0 OE1 A:GLU383 4.0 50.3 1.0 O A:HOH2210 4.1 44.6 1.0 CB A:ASP260 4.2 48.8 1.0 CZ A:TYR229 4.3 47.4 1.0 CG A:GLU406 4.3 48.2 1.0 CB A:ASP271 4.3 48.7 1.0 C A:ASP271 4.4 48.1 1.0 O A:ILE272 4.4 45.8 1.0 C A:ILE272 4.6 47.5 1.0 N A:ILE272 4.6 47.7 1.0 O A:ASP271 4.6 47.8 1.0 CE2 A:TYR229 4.6 48.2 1.0 CD A:GLU383 4.7 52.3 1.0 CA A:ASP271 4.7 48.8 1.0 OE2 A:GLU383 4.7 55.8 1.0 CB A:GLU406 4.8 49.9 1.0 CA A:ASP260 4.8 49.2 1.0 N A:THR273 4.8 48.5 1.0 NE A:ARG404 4.9 52.2 1.0 CB A:THR273 4.9 48.3 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1006 b:51.0 occ:0.30 NE2 A:HIS170 2.0 48.4 1.0 OD2 A:ASP48 2.1 51.9 1.0 CE1 A:HIS170 2.6 48.6 1.0 O A:HOH2091 3.1 51.8 1.0 CG A:ASP48 3.2 50.3 1.0 CD2 A:HIS170 3.3 48.3 1.0 O A:HOH2029 3.6 49.1 1.0 OD1 A:ASP48 3.7 51.3 1.0 ND1 A:HIS170 3.8 49.6 1.0 CG A:ARG166 4.0 49.4 1.0 CG A:HIS170 4.2 48.7 1.0 NH1 A:ARG173 4.2 48.8 1.0 CD A:ARG166 4.2 49.8 1.0 CG1 A:VAL363 4.4 44.4 1.0 CB A:ASP48 4.5 48.0 1.0 CB A:ARG166 4.7 48.7 1.0 OE2 A:GLU133 4.7 72.0 1.0 CZ3 A:TRP165 4.8 50.1 1.0 OE1 A:GLU133 4.8 66.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:0.0 occ:0.50 NE2 A:HIS71 2.0 78.7 1.0 CE1 A:HIS71 2.9 77.9 1.0 CD2 A:HIS71 3.0 76.6 1.0 ND1 A:HIS71 4.0 77.6 1.0 CG A:HIS71 4.1 73.0 1.0 ND1 A:HIS73 4.4 68.5 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