Calcium 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:

Chlorine

(Cl)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Porphyromonas Endodontalis DPP11 in Alternate Conformation, PDB code: 5jxp:

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


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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:Ca801 b:54.9 occ:1.00 NH1 A:ARG694 3.5 29.1 1.0 OD1 A:ASN632 3.7 39.5 1.0 OG A:SER633 3.8 68.9 1.0 NZ A:LYS595 3.8 44.6 1.0 N A:SER633 3.8 39.7 1.0 O A:VAL263 3.9 54.8 1.0 O A:GLN261 4.0 40.3 1.0 CA A:GLY262 4.1 47.0 1.0 CA A:ASN632 4.1 33.6 1.0 N A:VAL263 4.2 41.0 1.0 CB A:ASN632 4.4 31.2 1.0 CG A:ASN632 4.4 34.6 1.0 CZ A:ARG694 4.4 32.1 1.0 CB A:SER633 4.5 54.9 1.0 C A:GLY262 4.5 47.3 1.0 C A:ASN632 4.5 39.9 1.0 NH2 A:ARG694 4.6 32.8 1.0 C A:VAL263 4.8 48.8 1.0 CA A:SER633 4.8 41.6 1.0 O A:HOH1050 4.9 49.3 1.0 C A:GLN261 4.9 45.4 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