Zinc in PDB 4ics: Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate

The structure of Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate, PDB code: 4ics 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)	41.20 / 1.97
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.365, 126.365, 139.328, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 25.7

The binding sites of Zinc atom in the Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate (pdb code 4ics). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate, PDB code: 4ics:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:44.6 occ:1.00 O A:TRP503 2.3 39.3 1.0 O A:HOH601 2.3 26.9 1.0 OD1 A:ASP383 2.3 33.2 1.0 OE1 A:GLU319 2.3 26.8 1.0 OD2 A:ASP383 2.4 30.2 1.0 NE2 A:HIS381 2.5 31.0 1.0 CG A:ASP383 2.7 26.2 1.0 C A:TRP503 2.8 37.7 1.0 N A:GLY504 3.0 38.9 1.0 O A:HOH798 3.2 46.9 1.0 CD A:GLU319 3.3 23.2 1.0 CD2 A:HIS381 3.3 28.1 1.0 CE1 A:HIS381 3.5 28.3 1.0 OE2 A:GLU319 3.7 22.0 1.0 ZN A:ZN502 3.8 27.2 1.0 CA A:TRP503 4.1 36.9 1.0 CB A:ASP383 4.2 23.2 1.0 N A:TRP503 4.2 35.7 1.0 CB A:ALA350 4.2 20.8 1.0 OH A:TYR355 4.2 41.0 1.0 OD2 A:ASP343 4.2 26.8 1.0 CE2 A:TYR355 4.4 37.0 1.0 CA A:GLY504 4.4 39.7 1.0 CD2 A:HIS348 4.4 19.1 1.0 CG A:HIS381 4.5 27.1 1.0 CG A:GLU319 4.5 22.1 1.0 ND1 A:HIS381 4.6 28.2 1.0 NE2 A:HIS348 4.6 19.7 1.0 CB A:GLU319 4.6 20.9 1.0 CZ A:TYR355 4.8 37.4 1.0 CB A:TRP503 4.9 36.2 1.0 CA A:ASP383 5.0 23.3 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:27.2 occ:1.00 O A:HOH601 2.0 26.9 1.0 OE2 A:GLU319 2.0 22.0 1.0 OE1 A:GLU253 2.1 24.5 1.0 NE2 A:HIS348 2.2 19.7 1.0 N A:TRP503 2.3 35.7 1.0 OE2 A:GLU253 2.4 21.9 1.0 CD A:GLU253 2.5 25.0 1.0 CD A:GLU319 3.1 23.2 1.0 CE1 A:HIS348 3.1 21.9 1.0 CA A:TRP503 3.2 36.9 1.0 CD2 A:HIS348 3.2 19.1 1.0 OE1 A:GLU319 3.4 26.8 1.0 C A:TRP503 3.4 37.7 1.0 ZN A:ZN501 3.8 44.6 1.0 O A:TRP503 3.8 39.3 1.0 CB A:ALA321 3.9 20.6 1.0 N A:GLY504 4.0 38.9 1.0 CG A:GLU253 4.1 22.1 1.0 ND1 A:HIS348 4.3 21.3 1.0 OD2 A:ASP343 4.3 26.8 1.0 CG A:HIS348 4.3 20.2 1.0 CG A:GLU319 4.4 22.1 1.0 CG A:PHE255 4.4 25.5 1.0 CB A:PHE255 4.4 23.4 1.0 CB A:TRP503 4.6 36.2 1.0 CD2 A:PHE255 4.7 25.9 1.0 CA A:GLY504 4.7 39.7 1.0 CG A:ASP343 4.8 25.7 1.0 CB A:GLU253 4.8 22.8 1.0 O A:HOH613 4.8 20.7 1.0 OD2 A:ASP383 4.8 30.2 1.0 CD1 A:PHE255 4.9 26.5 1.0 OD1 A:ASP383 5.0 33.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:37.1 occ:1.00 O B:TRP503 2.1 35.3 1.0 OD1 B:ASP383 2.2 27.3 1.0 NE2 B:HIS381 2.2 24.7 1.0 OE1 B:GLU319 2.2 22.9 1.0 O B:HOH603 2.3 24.7 1.0 OD2 B:ASP383 2.3 33.5 1.0 C B:TRP503 2.6 33.0 1.0 CG B:ASP383 2.6 27.7 1.0 N B:GLY504 2.9 36.5 1.0 CD2 B:HIS381 3.2 20.8 1.0 CD B:GLU319 3.2 21.8 1.0 CE1 B:HIS381 3.2 24.6 1.0 OE2 B:GLU319 3.5 21.3 1.0 CA B:TRP503 3.7 32.6 1.0 ZN B:ZN502 3.8 25.5 1.0 CB B:ASP383 4.1 22.3 1.0 CB B:ALA350 4.1 19.5 1.0 N B:TRP503 4.1 29.9 1.0 OH B:TYR355 4.2 21.2 1.0 CA B:GLY504 4.2 36.9 1.0 CE2 B:TYR355 4.3 25.2 1.0 ND1 B:HIS381 4.3 25.1 1.0 CG B:HIS381 4.3 25.1 1.0 CD2 B:HIS348 4.4 17.6 1.0 OD2 B:ASP343 4.4 24.0 1.0 CG B:GLU319 4.5 21.0 1.0 NE2 B:HIS348 4.5 16.5 1.0 CB B:GLU319 4.6 22.0 1.0 CZ B:TYR355 4.7 24.8 1.0 CB B:TRP503 4.8 32.2 1.0 CA B:ASP383 4.9 23.1 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Peps From Streptococcus Pneumoniae in Complex with A Substrate within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn502 b:25.5 occ:1.00 OE2 B:GLU319 2.0 21.3 1.0 OE1 B:GLU253 2.1 25.5 1.0 O B:HOH603 2.1 24.7 1.0 NE2 B:HIS348 2.1 16.5 1.0 OE2 B:GLU253 2.1 24.1 1.0 N B:TRP503 2.2 29.9 1.0 CD B:GLU253 2.4 26.3 1.0 CA B:TRP503 2.9 32.6 1.0 CE1 B:HIS348 3.0 19.7 1.0 CD B:GLU319 3.1 21.8 1.0 CD2 B:HIS348 3.2 17.6 1.0 OE1 B:GLU319 3.4 22.9 1.0 C B:TRP503 3.4 33.0 1.0 ZN B:ZN501 3.8 37.1 1.0 CB B:ALA321 3.9 21.1 1.0 CG B:GLU253 3.9 24.8 1.0 O B:TRP503 4.0 35.3 1.0 N B:GLY504 4.1 36.5 1.0 ND1 B:HIS348 4.2 15.9 1.0 CG B:HIS348 4.3 17.1 1.0 CB B:TRP503 4.3 32.2 1.0 OD2 B:ASP343 4.4 24.0 1.0 CG B:GLU319 4.4 21.0 1.0 CG B:PHE255 4.5 22.6 1.0 CB B:PHE255 4.5 22.5 1.0 OD1 B:ASP383 4.6 27.3 1.0 CD2 B:PHE255 4.6 25.6 1.0 CA B:GLY504 4.7 36.9 1.0 CB B:GLU253 4.7 23.4 1.0 O B:HOH666 4.8 21.9 1.0 CG B:ASP343 4.9 25.4 1.0 CD1 B:PHE255 5.0 26.7 1.0 CG B:TRP503 5.0 33.0 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