Zinc in PDB 4icr: Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps

The structure of Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps, PDB code: 4icr was solved by S.Lee, K.K.Kim, M.H.Ta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.32 / 2.17
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	94.278, 185.277, 59.237, 90.00, 90.00, 90.00
R / Rfree (%)	22.9 / 30

The structure of Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps also contains other interesting chemical elements:

Arsenic

(As)

4 atoms

The binding sites of Zinc atom in the Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps (pdb code 4icr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps, PDB code: 4icr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:27.3 occ:1.00 O2 A:CAC503 1.7 28.2 1.0 OE2 A:GLU253 1.9 24.2 1.0 OE2 A:GLU319 2.0 28.4 1.0 NE2 A:HIS348 2.1 24.2 1.0 CD A:GLU253 2.9 22.9 1.0 CD A:GLU319 3.0 30.3 1.0 OE1 A:GLU253 3.1 25.1 1.0 CE1 A:HIS348 3.1 24.6 1.0 CD2 A:HIS348 3.1 29.9 1.0 AS A:CAC503 3.2 30.6 1.0 OE1 A:GLU319 3.3 30.3 1.0 C1 A:CAC503 3.7 26.4 1.0 OD1 A:ASP383 3.7 28.4 1.0 ZN A:ZN502 3.7 30.5 1.0 CB A:ALA321 3.8 29.4 1.0 O A:ASP343 4.1 28.1 1.0 O1 A:CAC503 4.2 32.0 1.0 ND1 A:HIS348 4.2 23.5 1.0 CG A:GLU253 4.3 23.2 1.0 CG A:HIS348 4.3 23.5 1.0 CG A:ASP383 4.3 28.1 1.0 CG A:GLU319 4.3 29.7 1.0 CB A:PHE255 4.5 26.3 1.0 OD2 A:ASP383 4.6 28.9 1.0 C2 A:CAC503 4.6 30.3 1.0 CB A:ASP343 4.7 27.9 1.0 CG A:PHE255 4.7 28.3 1.0 CB A:GLU253 4.7 24.5 1.0 O1 A:CAC504 4.8 51.2 1.0 CD2 A:PHE255 4.9 28.6 1.0

Zinc binding site 2 out of 4 in the Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:30.5 occ:1.00 OE1 A:GLU319 1.9 30.3 1.0 OD2 A:ASP383 2.0 28.9 1.0 O1 A:CAC503 2.0 32.0 1.0 NE2 A:HIS381 2.1 34.4 1.0 OD1 A:ASP383 2.2 28.4 1.0 CG A:ASP383 2.4 28.1 1.0 O2 A:CAC503 2.8 28.2 1.0 CE1 A:HIS381 2.8 32.0 1.0 AS A:CAC503 3.0 30.6 1.0 O1 A:CAC504 3.0 51.2 1.0 CD A:GLU319 3.0 30.3 1.0 CD2 A:HIS381 3.3 31.9 1.0 OE2 A:GLU319 3.6 28.4 1.0 ZN A:ZN501 3.7 27.3 1.0 CB A:ASP383 4.0 30.1 1.0 ND1 A:HIS381 4.0 34.9 1.0 CB A:ALA350 4.0 29.9 1.0 OH A:TYR355 4.1 29.4 1.0 CE2 A:TYR355 4.2 28.9 1.0 CG A:GLU319 4.2 29.7 1.0 AS A:CAC504 4.2 45.9 1.0 C1 A:CAC503 4.3 26.4 1.0 CG A:HIS381 4.3 32.7 1.0 C2 A:CAC504 4.4 42.4 1.0 CB A:GLU319 4.4 30.7 1.0 CZ A:TYR355 4.6 31.5 1.0 C2 A:CAC503 4.6 30.3 1.0 OD2 A:ASP343 4.8 30.4 1.0 NE2 A:HIS348 4.8 24.2 1.0 CA A:ASP383 4.9 30.9 1.0 CD2 A:HIS348 4.9 29.9 1.0

Zinc binding site 3 out of 4 in the Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:37.1 occ:1.00 OE1 B:GLU319 1.9 35.5 1.0 NE2 B:HIS381 2.0 34.7 1.0 O2 B:CAC503 2.1 31.4 1.0 OD1 B:ASP383 2.2 42.2 1.0 OD2 B:ASP383 2.5 31.8 1.0 O1 B:CAC503 2.7 26.4 1.0 CG B:ASP383 2.7 36.9 1.0 CE1 B:HIS381 2.9 35.6 1.0 AS B:CAC503 2.9 34.9 1.0 CD2 B:HIS381 3.1 40.2 1.0 CD B:GLU319 3.1 35.6 1.0 O1 B:CAC504 3.6 49.6 1.0 C2 B:CAC504 3.6 45.4 1.0 ZN B:ZN502 3.8 31.9 1.0 OE2 B:GLU319 3.8 33.7 1.0 OH B:TYR355 3.9 36.1 1.0 CE2 B:TYR355 4.0 34.7 1.0 ND1 B:HIS381 4.0 39.2 1.0 CB B:ALA350 4.1 39.0 1.0 C2 B:CAC503 4.1 32.6 1.0 CB B:ASP383 4.2 37.4 1.0 CG B:HIS381 4.2 38.8 1.0 AS B:CAC504 4.2 49.1 1.0 CG B:GLU319 4.3 38.6 1.0 CB B:GLU319 4.4 41.2 1.0 CZ B:TYR355 4.5 33.1 1.0 C1 B:CAC503 4.6 33.5 1.0 NE2 B:HIS348 4.8 31.8 1.0 CD2 B:HIS348 4.9 34.6 1.0 O2 B:CAC504 5.0 52.4 1.0 N B:ASP383 5.0 38.6 1.0 OD2 B:ASP343 5.0 34.6 1.0 CA B:ASP383 5.0 38.5 1.0

Zinc binding site 4 out of 4 in the Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For Substrate Recognition and Reaction Mechanism of Bacterial Aminopeptidase Peps within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:31.9 occ:1.00 O1 B:CAC503 1.7 26.4 1.0 OE2 B:GLU253 1.9 25.3 1.0 OE2 B:GLU319 2.0 33.7 1.0 NE2 B:HIS348 2.2 31.8 1.0 CD B:GLU253 2.8 30.4 1.0 CD B:GLU319 2.9 35.6 1.0 CE1 B:HIS348 3.0 29.5 1.0 OE1 B:GLU319 3.0 35.5 1.0 OE1 B:GLU253 3.0 32.3 1.0 AS B:CAC503 3.2 34.9 1.0 CD2 B:HIS348 3.3 34.6 1.0 OD1 B:ASP383 3.4 42.2 1.0 C2 B:CAC503 3.7 32.6 1.0 CB B:ALA321 3.7 37.0 1.0 ZN B:ZN501 3.8 37.1 1.0 O B:ASP343 4.0 34.0 1.0 ND1 B:HIS348 4.2 32.1 1.0 CG B:GLU253 4.2 29.0 1.0 CG B:ASP383 4.3 36.9 1.0 CG B:HIS348 4.3 34.6 1.0 O2 B:CAC503 4.3 31.4 1.0 CG B:GLU319 4.4 38.6 1.0 C1 B:CAC503 4.5 33.5 1.0 CB B:PHE255 4.6 34.2 1.0 CB B:GLU253 4.7 29.7 1.0 CB B:ASP343 4.8 30.6 1.0 O1 B:CAC504 4.8 49.6 1.0 CG B:PHE255 4.8 33.3 1.0 OD2 B:ASP383 5.0 31.8 1.0 C B:ASP343 5.0 32.0 1.0

H.M.Ta, S.Bae, S.Han, J.Song, T.K.Ahn, S.Hohng, S.Lee, K.K.Kim. Structure-Based Elucidation of the Regulatory Mechanism For Aminopeptidase Activity. Acta Crystallogr.,Sect.D V. 69 1738 2013.
ISSN: ISSN 0907-4449
PubMed: 23999297
DOI: 10.1107/S0907444913012651