Chlorine in PDB 5jxp: Crystal Structure of Porphyromonas Endodontalis DPP11 in Alternate Conformation

The structure of Crystal Structure of Porphyromonas Endodontalis DPP11 in Alternate Conformation, PDB code: 5jxp 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)	43.57 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	88.022, 103.990, 111.392, 90.00, 104.94, 90.00
R / Rfree (%)	20 / 24.1

The structure of Crystal Structure of Porphyromonas Endodontalis DPP11 in Alternate Conformation also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

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

Chlorine binding site 1 out of 2 in the Crystal Structure of Porphyromonas Endodontalis DPP11 in Alternate Conformation


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 in Alternate Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl802 b:37.3 occ:1.00 O A:HOH940 3.2 30.8 1.0 N A:MET637 3.3 48.8 1.0 N A:GLU599 3.3 38.6 1.0 N A:LEU598 3.7 35.0 1.0 CB A:SER636 3.7 42.4 1.0 CB A:THR597 3.7 34.3 1.0 CA A:SER636 3.8 47.1 1.0 CB A:GLU599 3.8 41.5 1.0 OG1 A:THR597 3.9 42.2 1.0 CB A:LEU598 4.0 27.1 1.0 CE1 A:TYR622 4.0 42.7 1.0 C A:SER636 4.0 48.6 1.0 CA A:GLU599 4.1 40.0 1.0 C A:LEU598 4.1 36.1 1.0 CA A:LEU598 4.1 28.5 1.0 OH A:TYR627 4.1 37.9 1.0 O A:MET637 4.2 57.9 1.0 CA A:MET637 4.3 45.4 1.0 CB A:MET637 4.4 42.5 1.0 CD1 A:TYR622 4.5 49.2 1.0 C A:THR597 4.5 29.6 1.0 CG2 A:THR597 4.6 27.8 1.0 C A:MET637 4.7 48.8 1.0 CA A:THR597 4.7 31.1 1.0 CZ A:TYR627 4.7 37.1 1.0 CE2 A:TYR627 4.7 35.4 1.0 OG A:SER636 4.9 39.1 1.0

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


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 in Alternate Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl803 b:80.4 occ:1.00 NZ A:LYS537 2.6 63.5 1.0 CE A:LYS537 3.4 65.3 1.0 CE1 A:TYR530 3.5 62.0 1.0 CZ A:TYR530 3.7 65.1 1.0 N A:LYS534 3.9 45.3 1.0 OH A:TYR530 4.0 67.9 1.0 CD1 A:TYR530 4.0 54.3 1.0 CA A:LYS534 4.1 45.2 1.0 O A:TYR530 4.1 51.0 1.0 CD A:LYS537 4.2 64.1 1.0 C A:GLN533 4.2 52.0 1.0 CB A:LYS534 4.3 47.4 1.0 CE2 A:TYR530 4.3 60.3 1.0 CB A:GLN533 4.6 49.9 1.0 O A:GLN533 4.6 56.2 1.0 CG A:TYR530 4.6 53.0 1.0 CD2 A:TYR530 4.7 56.6 1.0 CA A:GLN533 5.0 54.4 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