Potassium in PDB 6jtb: Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) with Citrate From Porphyromonas Gingivalis (Space)

The structure of Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) with Citrate From Porphyromonas Gingivalis (Space), PDB code: 6jtb was solved by Y.Sakamoto, Y.Suzuki, I.Iizuka, S.Roppongi, C.Kushibiki, A.Nakamura, W.Ogasawara, N.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.56 / 1.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.130, 103.350, 176.520, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 19.4

The binding sites of Potassium atom in the Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) with Citrate From Porphyromonas Gingivalis (Space) (pdb code 6jtb). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) with Citrate From Porphyromonas Gingivalis (Space), PDB code: 6jtb:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) with Citrate From Porphyromonas Gingivalis (Space)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) with Citrate From Porphyromonas Gingivalis (Space) within 5.0Å range: probe atom residue distance (Å) B Occ A:K809 b:20.8 occ:1.00 OD1 A:ASP672 2.6 16.3 1.0 O A:HOH1057 2.7 26.0 1.0 OD1 A:ASN218 2.7 20.6 1.0 O7 A:CIT802 2.9 22.2 1.0 CD2 A:TRP219 3.4 18.1 1.0 CE2 A:TRP219 3.4 18.5 1.0 CG A:ASP672 3.4 16.4 1.0 O2 A:CIT802 3.4 29.7 1.0 CE3 A:TRP219 3.4 17.5 1.0 CZ2 A:TRP219 3.5 18.7 1.0 CZ3 A:TRP219 3.5 18.4 1.0 CH2 A:TRP219 3.5 17.6 1.0 OD2 A:ASP672 3.6 17.3 1.0 C2 A:CIT802 3.8 22.8 1.0 C1 A:CIT802 3.8 27.6 1.0 CG A:ASN218 3.8 21.4 1.0 C3 A:CIT802 3.9 22.1 1.0 CG A:TRP219 4.1 18.1 1.0 NE1 A:TRP219 4.1 18.4 1.0 O A:HOH1305 4.3 22.7 1.0 ND2 A:ASN218 4.3 22.6 1.0 N A:TRP219 4.3 16.9 1.0 C4 A:CIT802 4.4 23.8 1.0 CD1 A:TRP219 4.4 18.3 1.0 O4 A:PEG801 4.5 18.0 1.0 OD1 A:ASN333 4.5 27.0 1.0 O A:HOH1566 4.7 44.2 1.0 O1 A:CIT802 4.7 27.9 1.0 CB A:ASP672 4.8 16.0 1.0 CA A:TRP219 4.8 17.0 1.0 O4 A:CIT802 5.0 21.4 1.0 O A:HOH1166 5.0 42.4 1.0 CB A:TRP219 5.0 17.6 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) with Citrate From Porphyromonas Gingivalis (Space)


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) with Citrate From Porphyromonas Gingivalis (Space) within 5.0Å range: probe atom residue distance (Å) B Occ A:K810 b:20.1 occ:1.00 O2 A:CIT804 2.6 42.0 1.0 O A:HOH1287 2.7 17.9 1.0 O A:THR278 2.7 18.9 1.0 OD2 A:ASP681 2.7 23.3 1.0 O1 A:PEG801 2.7 33.1 1.0 OG1 A:THR651 2.8 16.8 1.0 OG1 A:THR278 3.0 21.9 1.0 CG A:ASP681 3.5 25.3 1.0 C1 A:CIT804 3.6 48.2 1.0 C A:THR278 3.7 16.4 1.0 O A:HOH927 3.8 29.9 1.0 O1 A:CIT804 3.8 52.3 1.0 OD1 A:ASP681 3.9 21.3 1.0 CB A:THR651 4.0 15.5 1.0 C1 A:PEG801 4.0 38.8 1.0 CG2 A:THR651 4.1 15.1 1.0 N A:THR278 4.1 15.8 1.0 CB A:THR278 4.2 19.8 1.0 CA A:THR278 4.2 16.4 1.0 N A:GLY652 4.4 15.1 1.0 CB A:ASP681 4.6 22.4 1.0 O5 A:CIT804 4.7 47.7 1.0 N A:THR279 4.8 16.2 1.0 C6 A:CIT804 4.8 42.0 1.0 C2 A:CIT804 4.9 44.7 1.0 O A:HOH1396 4.9 29.7 1.0 NH2 A:ARG673 5.0 24.9 1.0

Y.Sakamoto, Y.Suzuki, A.Nakamura, Y.Watanabe, M.Sekiya, S.Roppongi, C.Kushibiki, I.Iizuka, O.Tani, H.Sakashita, K.Inaka, H.Tanaka, M.Yamada, K.Ohta, N.Honma, Y.Shida, W.Ogasawara, M.Nakanishi-Matsui, T.Nonaka, H.Gouda, N.Tanaka. Fragment-Based Discovery of the First Nonpeptidyl Inhibitor of An S46 Family Peptidase. Sci Rep V. 9 13587 2019.
ISSN: ESSN 2045-2322
PubMed: 31537874
DOI: 10.1038/S41598-019-49984-3