Chlorine in PDB 5jwi: Crystal Structure of Porphyromonas Endodontalis DPP11 in Complex with Dipeptide Arg-Glu

The structure of Crystal Structure of Porphyromonas Endodontalis DPP11 in Complex with Dipeptide Arg-Glu, PDB code: 5jwi was solved by G.A.Bezerra, S.Fedosyuk, Y.Ohara-Nemoto, T.K.Nemoto, K.Djinovic-Carugo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.57 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	111.441, 112.534, 148.260, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.9

The binding sites of Chlorine atom in the Crystal Structure of Porphyromonas Endodontalis DPP11 in Complex with Dipeptide Arg-Glu (pdb code 5jwi). 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 Complex with Dipeptide Arg-Glu, PDB code: 5jwi:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Porphyromonas Endodontalis DPP11 in Complex with Dipeptide Arg-Glu


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 Complex with Dipeptide Arg-Glu within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl801 b:56.4 occ:1.00 NZ B:LYS595 3.4 36.7 1.0 NH1 B:ARG694 3.4 30.9 1.0 O B:VAL263 3.5 38.1 1.0 OD1 B:ASN632 3.5 35.0 1.0 N B:VAL263 3.9 34.8 1.0 CA B:GLY262 4.0 33.9 1.0 C B:GLY262 4.2 34.4 1.0 CZ B:ARG694 4.2 33.0 1.0 NH2 B:ARG694 4.3 33.7 1.0 CG B:ASN632 4.3 34.9 1.0 C B:VAL263 4.4 38.2 1.0 CA B:ASN632 4.4 39.3 1.0 N B:SER633 4.4 37.4 1.0 O B:HOH1025 4.4 44.1 1.0 CB B:ASN632 4.4 32.3 1.0 OG B:SER633 4.4 74.7 1.0 O B:GLN261 4.5 47.9 1.0 CA B:VAL263 4.7 35.4 1.0 CE B:LYS595 4.8 36.5 1.0 C B:ASN632 4.9 37.6 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Porphyromonas Endodontalis DPP11 in Complex with Dipeptide Arg-Glu


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 Complex with Dipeptide Arg-Glu within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl802 b:46.2 occ:1.00 N B:ASN684 3.3 38.3 1.0 C B:LEU682 3.5 43.3 1.0 N B:PRO683 3.6 37.0 1.0 CA B:LEU682 3.7 47.9 1.0 CB B:LEU682 3.7 40.2 1.0 CD B:PRO683 3.8 31.7 1.0 CB B:ASN684 3.8 46.8 1.0 CD1 B:TYR685 3.8 44.2 1.0 O B:LEU682 4.0 36.2 1.0 CA B:ASN684 4.0 43.0 1.0 CG B:PRO683 4.3 34.3 1.0 N B:TYR685 4.3 34.6 1.0 CD2 B:LEU682 4.3 35.4 1.0 C B:PRO683 4.3 40.9 1.0 CE1 B:TYR685 4.4 42.6 1.0 CA B:PRO683 4.4 39.1 1.0 ND2 B:ASN684 4.5 56.1 1.0 CG B:ASN684 4.5 58.1 1.0 C B:ASN684 4.5 40.8 1.0 CG B:LEU682 4.6 42.6 1.0 CD B:ARG347 4.8 55.4 1.0 CG B:TYR685 4.9 43.6 1.0 CB B:PRO683 4.9 33.0 1.0 CB B:TYR685 5.0 42.0 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