Arsenic 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:

Zinc	(Zn)	6 atoms
Sodium	(Na)	1 atom

The binding sites of Arsenic 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 Arsenic atom.
In total 3 binding sites of Arsenic where determined in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12, PDB code: 5cnx:
Jump to Arsenic binding site number: 1; 2; 3;

Arsenic binding site 1 out of 3 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As 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:As403 b:55.7 occ:1.00 AS A:CAC403 0.0 55.7 1.0 O2 A:CAC403 1.7 62.0 1.0 O1 A:CAC403 1.7 46.9 1.0 C2 A:CAC403 2.0 55.3 1.0 C1 A:CAC403 2.0 49.6 1.0 ZN A:ZN401 3.2 44.1 1.0 ZN A:ZN402 3.3 37.6 1.0 OD2 A:ASP223 3.7 41.7 1.0 NE2 A:HIS299 3.7 50.5 1.0 OD2 A:ASP212 4.1 39.1 1.0 NE2 A:HIS292 4.2 41.5 1.0 OD1 A:ASP223 4.2 43.8 1.0 OE1 A:GLU321 4.3 44.5 1.0 OD1 A:ASP212 4.3 38.9 1.0 CE1 A:HIS299 4.3 48.9 1.0 CG A:ASP223 4.3 42.5 1.0 CE1 A:HIS195 4.5 60.8 1.0 CG A:ASP212 4.5 39.4 1.0 OE2 A:GLU321 4.6 41.7 1.0 OE2 A:GLU335 4.7 40.4 1.0 CZ A:PHE181 4.7 33.2 1.0 CE1 A:PHE181 4.7 32.9 1.0 CD2 A:HIS299 4.8 50.1 1.0 OE1 A:GLU335 4.8 40.1 1.0 CD A:GLU321 4.9 42.9 1.0 NE2 A:HIS195 4.9 60.3 1.0 CD2 A:HIS292 4.9 41.7 1.0 CG1 A:VAL298 5.0 32.4 1.0

Arsenic binding site 2 out of 3 in the Crystal Structure of Xaa-Pro Aminopeptidase From Escherichia Coli K12


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As 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 B:As403 b:62.6 occ:1.00 AS B:CAC403 0.0 62.6 1.0 O2 B:CAC403 1.7 69.8 1.0 O1 B:CAC403 1.8 59.6 1.0 C2 B:CAC403 2.0 56.7 1.0 C1 B:CAC403 2.0 65.4 1.0 ZN B:ZN401 3.2 42.6 1.0 ZN B:ZN402 3.3 36.7 1.0 NE2 B:HIS299 3.6 45.8 1.0 OD2 B:ASP223 3.6 38.3 1.0 NE2 B:HIS292 4.1 34.2 1.0 OD2 B:ASP212 4.1 38.6 1.0 OE1 B:GLU321 4.2 42.0 1.0 CE1 B:HIS299 4.2 46.2 1.0 OD1 B:ASP223 4.3 37.9 1.0 O B:HOH516 4.3 31.1 1.0 CG B:ASP223 4.4 38.4 1.0 OE2 B:GLU321 4.4 41.8 1.0 OD1 B:ASP212 4.6 38.9 1.0 CG B:ASP212 4.7 38.7 1.0 CD2 B:HIS299 4.7 46.2 1.0 CD B:GLU321 4.7 41.6 1.0 CZ B:PHE181 4.8 33.8 1.0 CE2 B:PHE181 4.8 33.6 1.0 OE2 B:GLU335 4.8 41.4 1.0 CD2 B:HIS292 4.8 34.6 1.0 CE1 B:HIS292 4.9 34.8 1.0 OE1 B:GLU335 4.9 40.0 1.0 CG1 B:VAL298 5.0 40.6 1.0

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


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As 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 C:As403 b:51.0 occ:0.68 AS C:CAC403 0.0 51.0 0.7 O2 C:CAC403 1.7 45.5 0.7 O1 C:CAC403 1.7 46.6 0.7 C2 C:CAC403 2.0 49.1 0.7 C1 C:CAC403 2.0 47.2 0.7 ZN C:ZN401 3.2 49.8 1.0 ZN C:ZN402 3.4 43.3 1.0 NE2 C:HIS299 3.7 54.9 1.0 OD2 C:ASP223 3.8 44.4 1.0 OD2 C:ASP212 4.0 40.5 1.0 NE2 C:HIS292 4.2 40.2 1.0 OE1 C:GLU321 4.2 49.7 1.0 CE1 C:HIS299 4.3 53.4 1.0 OD1 C:ASP223 4.3 44.3 1.0 OE2 C:GLU321 4.4 50.3 1.0 CG C:ASP223 4.4 45.0 1.0 OD1 C:ASP212 4.5 41.9 1.0 CG C:ASP212 4.6 41.2 1.0 CD C:GLU321 4.8 50.2 1.0 CD2 C:HIS299 4.8 55.0 1.0 CZ C:PHE181 4.8 36.6 1.0 CD2 C:HIS292 4.9 40.2 1.0 CE2 C:PHE181 4.9 34.8 1.0 CE1 C:HIS292 4.9 41.1 1.0 CG1 C:VAL298 5.0 45.1 1.0 OE1 C:GLU335 5.0 53.8 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