Chlorine in PDB 5jxk: Crystal Structure of Porphyromonas Endodontalis DPP11

The structure of Crystal Structure of Porphyromonas Endodontalis DPP11, PDB code: 5jxk was solved by G.A.Bezerra, I.Cornaciu, G.Hoffmann, K.Djinovic-Carugo, J.A.Marquez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.70 / 2.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.752, 91.831, 229.917, 90.00, 90.00, 90.00
R / Rfree (%)	24 / 27.3

The binding sites of Chlorine atom in the Crystal Structure of Porphyromonas Endodontalis DPP11 (pdb code 5jxk). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Crystal Structure of Porphyromonas Endodontalis DPP11, PDB code: 5jxk:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Porphyromonas Endodontalis DPP11


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Porphyromonas Endodontalis DPP11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl801 b:12.7 occ:1.00 O A:VAL263 3.5 26.7 1.0 NZ A:LYS595 3.6 22.4 1.0 NH1 A:ARG694 3.7 23.5 1.0 OD1 A:ASN632 3.8 22.8 1.0 N A:SER633 4.0 30.9 1.0 OG A:SER633 4.1 42.7 1.0 N A:VAL263 4.1 23.7 1.0 CA A:ASN632 4.3 26.9 1.0 CA A:GLY262 4.3 24.3 1.0 NH2 A:ARG694 4.4 20.5 1.0 CB A:ASN632 4.4 26.1 1.0 CG A:ASN632 4.4 23.7 1.0 CZ A:ARG694 4.4 21.5 1.0 C A:VAL263 4.5 25.9 1.0 C A:GLY262 4.6 23.4 1.0 CB A:SER633 4.6 35.1 1.0 C A:ASN632 4.6 29.8 1.0 O A:GLN261 4.7 26.4 1.0 CA A:SER633 4.9 34.0 1.0 CA A:VAL263 5.0 23.7 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Porphyromonas Endodontalis DPP11


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Porphyromonas Endodontalis DPP11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:13.3 occ:1.00 O A:HOH912 3.1 20.1 1.0 N A:MET637 3.4 24.8 1.0 N A:GLU599 3.5 24.8 1.0 N A:LEU598 3.7 24.8 1.0 CB A:THR597 3.7 22.8 1.0 CB A:SER636 3.8 27.4 1.0 CA A:SER636 3.9 28.1 1.0 OG1 A:THR597 4.0 24.1 1.0 CB A:LEU598 4.0 22.4 1.0 CB A:GLU599 4.1 28.5 1.0 CA A:LEU598 4.2 21.9 1.0 C A:SER636 4.2 26.1 1.0 C A:LEU598 4.2 23.5 1.0 O A:MET637 4.3 20.9 1.0 CA A:GLU599 4.3 26.7 1.0 OH A:TYR627 4.4 31.9 1.0 CA A:MET637 4.4 23.2 1.0 CB A:MET637 4.4 23.2 1.0 C A:THR597 4.4 21.1 1.0 CE1 A:TYR622 4.5 30.0 1.0 CG2 A:THR597 4.6 23.0 1.0 CA A:THR597 4.7 20.9 1.0 C A:MET637 4.8 21.4 1.0 CD1 A:TYR622 4.9 28.9 1.0 CE2 A:TYR627 4.9 28.8 1.0 CZ A:TYR627 5.0 27.9 1.0 OE1 A:GLU599 5.0 48.4 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Porphyromonas Endodontalis DPP11


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Porphyromonas Endodontalis DPP11 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:36.4 occ:1.00 N B:MET637 3.2 31.8 1.0 CA B:SER636 3.6 30.0 1.0 N B:GLU599 3.6 25.5 1.0 CB B:SER636 3.6 28.6 1.0 CB B:THR597 3.9 23.4 1.0 C B:SER636 3.9 28.9 1.0 N B:LEU598 3.9 23.8 1.0 CB B:GLU599 4.0 26.5 1.0 OH B:TYR627 4.1 32.8 1.0 CB B:LEU598 4.2 27.3 1.0 CA B:MET637 4.2 27.2 1.0 O B:MET637 4.2 25.0 1.0 OG1 B:THR597 4.3 23.6 1.0 CB B:MET637 4.3 28.6 1.0 CA B:GLU599 4.3 26.6 1.0 CA B:LEU598 4.4 25.3 1.0 C B:LEU598 4.4 25.9 1.0 CE2 B:TYR627 4.5 33.0 1.0 CZ B:TYR627 4.6 33.3 1.0 CG2 B:THR597 4.6 23.8 1.0 C B:MET637 4.6 25.5 1.0 C B:THR597 4.7 22.2 1.0 CE1 B:TYR622 4.7 32.4 1.0 OE1 B:GLU599 4.7 30.2 1.0 CA B:THR597 4.8 22.0 1.0 N B:SER636 4.9 32.2 1.0 OG B:SER636 4.9 28.4 1.0 CD1 B:TYR622 4.9 32.5 1.0

G.A.Bezerra, Y.Ohara-Nemoto, I.Cornaciu, S.Fedosyuk, G.Hoffmann, A.Round, J.A.Marquez, T.K.Nemoto, K.Djinovic-Carugo. Bacterial Protease Uses Distinct Thermodynamic Signatures For Substrate Recognition. Sci Rep V. 7 2848 2017.
ISSN: ESSN 2045-2322
PubMed: 28588213
DOI: 10.1038/S41598-017-03220-Y