Zinc in PDB 5cnx: Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12

The structure of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12, PDB code: 5cnx was solved by A.Kumar, V.Are, B.Ghosh, S.Jamdar, R.D.Makde, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.90 / 2.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	224.202, 224.202, 74.636, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 24

The structure of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 also contains other interesting chemical elements:

Arsenic	(As)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 (pdb code 5cnx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12, PDB code: 5cnx:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


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 Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:44.1 occ:1.00 O1 A:CAC403 2.0 46.9 1.0 OE2 A:GLU335 2.1 40.4 1.0 OE2 A:GLU321 2.1 41.7 1.0 NE2 A:HIS292 2.2 41.5 1.0 OD2 A:ASP223 2.3 41.7 1.0 CD A:GLU321 2.8 42.9 1.0 OE1 A:GLU321 3.0 44.5 1.0 CD2 A:HIS292 3.1 41.7 1.0 CE1 A:HIS292 3.1 41.4 1.0 CD A:GLU335 3.1 41.1 1.0 CG A:ASP223 3.2 42.5 1.0 AS A:CAC403 3.2 55.7 1.0 ZN A:ZN402 3.2 37.6 1.0 OD1 A:ASP223 3.6 43.8 1.0 OE1 A:GLU335 3.6 40.1 1.0 C1 A:CAC403 3.6 49.6 1.0 OG1 A:THR319 3.6 34.2 1.0 O2 A:CAC403 3.9 62.0 1.0 CG2 A:THR319 3.9 33.7 1.0 CB A:THR319 4.1 34.4 1.0 CG A:GLU321 4.2 43.8 1.0 ND1 A:HIS292 4.2 41.8 1.0 CG A:HIS292 4.2 41.7 1.0 CB A:ASP223 4.3 42.5 1.0 CG A:GLU335 4.4 42.3 1.0 NE2 A:HIS299 4.8 50.5 1.0 C2 A:CAC403 4.9 55.3 1.0 CB A:GLU321 5.0 44.2 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


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 Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:37.6 occ:1.00 OE1 A:GLU335 1.9 40.1 1.0 O1 A:CAC403 1.9 46.9 1.0 OD1 A:ASP212 2.1 38.9 1.0 OD1 A:ASP223 2.1 43.8 1.0 CD A:GLU335 2.7 41.1 1.0 CG A:ASP212 2.8 39.4 1.0 OD2 A:ASP212 2.8 39.1 1.0 OE2 A:GLU335 2.9 40.4 1.0 CG A:ASP223 3.0 42.5 1.0 ZN A:ZN401 3.2 44.1 1.0 OD2 A:ASP223 3.3 41.7 1.0 AS A:CAC403 3.3 55.7 1.0 OG1 A:THR225 3.6 43.1 1.0 OE1 A:GLU321 3.8 44.5 1.0 C2 A:CAC403 3.8 55.3 1.0 CZ A:PHE181 3.9 33.2 1.0 O2 A:CAC403 4.0 62.0 1.0 CG A:GLU335 4.1 42.3 1.0 CB A:ASP212 4.2 40.0 1.0 CB A:ASP223 4.3 42.5 1.0 O A:MET224 4.3 46.3 1.0 N A:MET224 4.4 45.3 1.0 C A:MET224 4.4 46.6 1.0 C A:ASP223 4.5 44.1 1.0 CD A:GLU321 4.5 42.9 1.0 CE1 A:PHE181 4.6 32.9 1.0 CE2 A:PHE181 4.6 32.7 1.0 CB A:GLU335 4.7 43.3 1.0 OE2 A:GLU321 4.7 41.7 1.0 CA A:ASP223 4.7 43.1 1.0 CA A:ASP212 4.7 40.5 1.0 N A:PHE213 4.8 37.3 1.0 N A:THR225 4.8 44.3 1.0 CA A:MET224 4.8 46.5 1.0 C1 A:CAC403 4.9 49.6 1.0 CB A:THR225 4.9 44.3 1.0 O A:ASP223 4.9 44.3 1.0 O A:PHE213 4.9 37.2 1.0 C A:ASP212 5.0 40.1 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


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 Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn401 b:42.6 occ:1.00 OE2 B:GLU321 2.1 41.8 1.0 OE2 B:GLU335 2.1 41.4 1.0 O1 B:CAC403 2.1 59.6 1.0 NE2 B:HIS292 2.2 34.2 1.0 OD2 B:ASP223 2.2 38.3 1.0 CD B:GLU321 2.8 41.6 1.0 OE1 B:GLU321 3.0 42.0 1.0 CE1 B:HIS292 3.1 34.8 1.0 CG B:ASP223 3.1 38.4 1.0 CD2 B:HIS292 3.1 34.6 1.0 ZN B:ZN402 3.2 36.7 1.0 CD B:GLU335 3.2 40.8 1.0 AS B:CAC403 3.2 62.6 1.0 OD1 B:ASP223 3.6 37.9 1.0 OE1 B:GLU335 3.6 40.0 1.0 C1 B:CAC403 3.6 65.4 1.0 OG1 B:THR319 3.7 28.9 1.0 CG2 B:THR319 3.7 28.6 1.0 O2 B:CAC403 3.8 69.8 1.0 CB B:THR319 4.0 28.6 1.0 CG B:GLU321 4.1 41.4 1.0 ND1 B:HIS292 4.2 35.6 1.0 CG B:HIS292 4.2 35.5 1.0 CB B:ASP223 4.2 39.2 1.0 CG B:GLU335 4.4 41.0 1.0 NE2 B:HIS299 4.8 45.8 1.0 O B:HOH516 4.9 31.1 1.0 CB B:GLU321 5.0 40.4 1.0 C2 B:CAC403 5.0 56.7 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


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 Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:36.7 occ:1.00 O1 B:CAC403 1.9 59.6 1.0 OE1 B:GLU335 1.9 40.0 1.0 OD1 B:ASP223 2.0 37.9 1.0 OD1 B:ASP212 2.0 38.9 1.0 CG B:ASP212 2.7 38.7 1.0 OD2 B:ASP212 2.7 38.6 1.0 CD B:GLU335 2.7 40.8 1.0 CG B:ASP223 2.8 38.4 1.0 OE2 B:GLU335 2.8 41.4 1.0 OD2 B:ASP223 3.1 38.3 1.0 ZN B:ZN401 3.2 42.6 1.0 AS B:CAC403 3.3 62.6 1.0 OG1 B:THR225 3.5 37.0 1.0 OE1 B:GLU321 3.6 42.0 1.0 CZ B:PHE181 3.9 33.8 1.0 O2 B:CAC403 4.0 69.8 1.0 C2 B:CAC403 4.0 56.7 1.0 CG B:GLU335 4.2 41.0 1.0 CB B:ASP212 4.2 38.3 1.0 CB B:ASP223 4.2 39.2 1.0 O B:MET224 4.3 36.5 1.0 CD B:GLU321 4.4 41.6 1.0 N B:MET224 4.4 37.4 1.0 C B:MET224 4.5 36.6 1.0 C B:ASP223 4.5 38.8 1.0 OE2 B:GLU321 4.5 41.8 1.0 CE2 B:PHE181 4.5 33.6 1.0 CA B:ASP223 4.7 39.0 1.0 CE1 B:PHE181 4.7 34.4 1.0 CB B:GLU335 4.7 40.1 1.0 CA B:ASP212 4.8 38.1 1.0 N B:PHE213 4.8 35.2 1.0 N B:THR225 4.9 37.2 1.0 CA B:MET224 4.9 37.2 1.0 C1 B:CAC403 4.9 65.4 1.0 CB B:THR225 4.9 36.8 1.0 O B:PHE213 4.9 36.3 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn401 b:49.8 occ:1.00 O1 C:CAC403 2.1 46.6 0.7 OD2 C:ASP223 2.1 44.4 1.0 NE2 C:HIS292 2.1 40.2 1.0 OE2 C:GLU321 2.1 50.3 1.0 OE2 C:GLU335 2.2 55.1 1.0 CD C:GLU321 2.9 50.2 1.0 CG C:ASP223 3.0 45.0 1.0 ZN C:ZN402 3.0 43.3 1.0 CE1 C:HIS292 3.1 41.1 1.0 OE1 C:GLU321 3.1 49.7 1.0 CD C:GLU335 3.1 54.8 1.0 CD2 C:HIS292 3.2 40.2 1.0 AS C:CAC403 3.2 51.0 0.7 OD1 C:ASP223 3.4 44.3 1.0 OE1 C:GLU335 3.5 53.8 1.0 C1 C:CAC403 3.6 47.2 0.7 O2 C:CAC403 3.8 45.5 0.7 CG2 C:THR319 3.9 49.0 1.0 OG1 C:THR319 3.9 47.9 1.0 CB C:THR319 4.1 49.1 1.0 CB C:ASP223 4.2 47.0 1.0 ND1 C:HIS292 4.2 41.8 1.0 CG C:GLU321 4.2 51.5 1.0 CG C:HIS292 4.3 41.3 1.0 CG C:GLU335 4.5 56.9 1.0 OD2 C:ASP212 4.9 40.5 1.0 NE2 C:HIS299 4.9 54.9 1.0 C2 C:CAC403 4.9 49.1 0.7 OD1 C:ASP212 5.0 41.9 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:43.3 occ:1.00 O1 C:CAC403 1.9 46.6 0.7 OD1 C:ASP223 2.0 44.3 1.0 OD1 C:ASP212 2.0 41.9 1.0 OE1 C:GLU335 2.0 53.8 1.0 OD2 C:ASP212 2.5 40.5 1.0 CG C:ASP212 2.6 41.2 1.0 CG C:ASP223 2.8 45.0 1.0 CD C:GLU335 2.9 54.8 1.0 ZN C:ZN401 3.0 49.8 1.0 OE2 C:GLU335 3.1 55.1 1.0 OD2 C:ASP223 3.1 44.4 1.0 AS C:CAC403 3.4 51.0 0.7 OG1 C:THR225 3.6 45.7 1.0 OE1 C:GLU321 3.7 49.7 1.0 CZ C:PHE181 3.9 36.6 1.0 O2 C:CAC403 4.0 45.5 0.7 C2 C:CAC403 4.0 49.1 0.7 CB C:ASP212 4.1 40.4 1.0 CB C:ASP223 4.2 47.0 1.0 CG C:GLU335 4.3 56.9 1.0 N C:MET224 4.3 55.5 1.0 O C:MET224 4.3 53.5 1.0 CD C:GLU321 4.4 50.2 1.0 C C:ASP223 4.4 48.5 1.0 C C:MET224 4.5 55.0 1.0 OE2 C:GLU321 4.5 50.3 1.0 CE1 C:PHE181 4.6 37.6 1.0 CA C:ASP223 4.6 47.7 1.0 CE2 C:PHE181 4.7 34.8 1.0 CA C:ASP212 4.7 41.9 1.0 CB C:GLU335 4.7 56.1 1.0 N C:PHE213 4.8 46.7 1.0 CA C:MET224 4.9 56.7 1.0 O C:ASP223 4.9 50.1 1.0 C1 C:CAC403 4.9 47.2 0.7 N C:THR225 4.9 49.2 1.0 CB C:THR225 5.0 47.0 1.0 O C:PHE213 5.0 49.5 1.0 C C:ASP212 5.0 41.8 1.0

V.N.Are, A.Kumar, V.D.Goyal, S.S.Gotad, B.Ghosh, R.Gadre, S.N.Jamdar, R.D.Makde. Structures and Activities of Widely Conserved Small Prokaryotic Aminopeptidases-P Clarify Classification of M24B Peptidases Proteins 2018.
ISSN: ESSN 1097-0134
PubMed: 30536999
DOI: 10.1002/PROT.25641