Chlorine in PDB 5jxf: Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp

The structure of Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp, PDB code: 5jxf 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)	46.83 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	126.051, 70.689, 191.598, 90.00, 97.26, 90.00
R / Rfree (%)	19.6 / 24.4

The structure of Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp also contains other interesting chemical elements:

Sodium

(Na)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp (pdb code 5jxf). 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 Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp, PDB code: 5jxf:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in the Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp


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 Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl801 b:53.7 occ:1.00 N C:GLY627 3.1 63.0 1.0 CA C:GLY627 3.4 54.0 1.0 CA C:GLY624 3.8 46.1 1.0 C C:GLY624 3.9 52.9 1.0 N C:GLU625 3.9 51.4 1.0 CD2 C:TYR620 4.2 28.2 1.0 C C:GLY627 4.2 51.0 1.0 CB C:TYR620 4.3 32.2 1.0 C C:ASN626 4.3 62.6 1.0 N C:ASN626 4.3 61.7 1.0 O C:GLY624 4.5 56.6 1.0 N C:LYS628 4.5 42.8 1.0 C C:GLU625 4.5 60.0 1.0 CA C:ASN626 4.7 61.8 1.0 CG C:TYR620 4.7 31.7 1.0 CA C:GLU625 4.7 60.8 1.0 O C:GLY621 4.7 39.3 1.0 N C:GLY624 4.8 40.6 1.0 O C:LYS628 4.9 37.4 1.0

Chlorine binding site 2 out of 3 in the Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp


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 Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl801 b:81.7 occ:1.00 N D:GLY627 3.3 82.9 1.0 CA D:GLY627 3.5 85.1 1.0 CA D:GLY624 3.8 82.5 1.0 CD2 D:TYR620 4.0 65.6 1.0 CB D:TYR620 4.0 73.2 1.0 N D:GLU625 4.1 87.5 1.0 C D:GLY624 4.1 88.3 1.0 C D:GLY627 4.2 84.2 1.0 N D:LYS628 4.4 79.5 1.0 CG D:TYR620 4.4 69.3 1.0 N D:ASN626 4.5 86.8 1.0 C D:ASN626 4.5 82.5 1.0 O D:LYS618 4.5 79.7 1.0 O D:LYS628 4.8 76.6 1.0 C D:GLU625 4.8 85.7 1.0 N D:GLY624 4.8 77.8 1.0 O D:GLY621 4.8 78.2 1.0 O D:GLY624 4.9 92.5 1.0 CA D:ASN626 4.9 85.3 1.0 O D:GLY627 5.0 82.7 1.0 CA D:GLU625 5.0 84.4 1.0

Chlorine binding site 3 out of 3 in the Crystal Structure of Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp


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 Flavobacterium Psychrophilum DPP11 in Complex with Dipeptide Arg-Asp within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl802 b:41.4 occ:1.00 O D:HOH905 2.8 46.0 1.0 OG1 D:THR639 3.2 48.0 1.0 ND2 D:ASN659 3.6 62.3 1.0 O D:THR640 3.7 49.8 1.0 CG D:ARG662 3.7 56.4 1.0 CB D:THR639 3.7 46.5 1.0 C D:ASP661 3.9 47.7 1.0 O D:ASP661 3.9 45.7 1.0 C D:THR640 4.0 46.4 1.0 N D:THR640 4.0 46.4 1.0 CB D:ASN643 4.1 48.6 1.0 CA D:THR640 4.2 49.6 1.0 CA D:ASP661 4.3 44.0 1.0 N D:ARG662 4.3 48.8 1.0 NE D:ARG662 4.3 50.6 1.0 CD D:ARG662 4.4 56.4 1.0 C D:THR639 4.4 47.4 1.0 N D:ASP661 4.5 47.0 1.0 CG D:ASN659 4.6 61.0 1.0 CB D:ARG662 4.7 51.8 1.0 N D:GLY641 4.7 42.7 1.0 CA D:THR639 4.7 51.0 1.0 OD1 D:ASN659 4.8 57.5 1.0 CG2 D:THR639 4.8 41.9 1.0 C D:ASN643 4.8 44.8 1.0 N D:SER644 4.8 50.9 1.0 CA D:ARG662 4.9 48.6 1.0 CA D:ASN643 4.9 46.9 1.0 O D:THR639 5.0 51.3 1.0 C D:PHE660 5.0 47.8 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