Potassium in PDB 4y04: Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) From Porphyromonas Gingivalis (Space)

The structure of Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) From Porphyromonas Gingivalis (Space), PDB code: 4y04 was solved by Y.Sakamoto, Y.Suzuki, I.Iizuka, C.Tateoka, S.Roppongi, M.Fujimoto, K.Inaka, H.Tanaka, M.Yamada, K.Ohta, T.Nonaka, W.Ogasawara, N.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 1.66
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	99.140, 103.280, 175.310, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 22.5

The binding sites of Potassium atom in the Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) From Porphyromonas Gingivalis (Space) (pdb code 4y04). 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) From Porphyromonas Gingivalis (Space), PDB code: 4y04:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) 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) From Porphyromonas Gingivalis (Space) within 5.0Å range: probe atom residue distance (Å) B Occ A:K801 b:31.2 occ:1.00 O A:HOH1587 2.5 39.7 1.0 OD1 A:ASP672 2.6 21.9 1.0 OD1 A:ASN218 2.8 25.1 1.0 CG A:ASP672 3.3 24.6 1.0 OD2 A:ASP672 3.3 25.9 1.0 O A:HOH1583 3.3 43.5 1.0 CD2 A:TRP219 3.4 22.1 1.0 CE3 A:TRP219 3.5 26.2 1.0 CE2 A:TRP219 3.5 23.7 1.0 CZ3 A:TRP219 3.6 25.7 1.0 CZ2 A:TRP219 3.7 27.1 1.0 CH2 A:TRP219 3.7 26.4 1.0 CG A:ASN218 3.9 28.5 1.0 CG A:TRP219 4.1 23.1 1.0 N A:TRP219 4.2 23.1 1.0 NE1 A:TRP219 4.2 22.7 1.0 O A:HOH1581 4.2 38.2 1.0 O A:HOH1322 4.4 43.2 1.0 CD1 A:TRP219 4.5 27.2 1.0 ND2 A:ASN218 4.5 26.9 1.0 OD1 A:ASN333 4.5 35.8 1.0 CA A:TRP219 4.6 22.8 1.0 CB A:ASP672 4.7 22.4 1.0 O A:HOH1588 4.9 42.4 1.0 O A:HOH1582 4.9 40.5 1.0 CB A:TRP219 4.9 25.2 1.0 C A:ASN218 5.0 22.3 1.0

Potassium binding site 2 out of 2 in the Crystal Structure of Dipeptidyl Peptidase 11 (DPP11) 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) From Porphyromonas Gingivalis (Space) within 5.0Å range: probe atom residue distance (Å) B Occ A:K802 b:28.2 occ:1.00 O A:THR278 2.7 24.4 1.0 OG1 A:THR651 2.7 22.5 1.0 OD2 A:ASP681 2.8 30.1 1.0 O A:HOH1059 2.8 29.0 1.0 O A:HOH1429 3.1 38.0 1.0 OG1 A:THR278 3.1 32.1 1.0 CG A:ASP681 3.6 33.7 1.0 C A:THR278 3.8 21.1 1.0 OD1 A:ASP681 3.9 29.1 1.0 CB A:THR651 3.9 19.1 1.0 CG2 A:THR651 4.0 18.7 1.0 N A:THR278 4.2 23.2 1.0 CB A:THR278 4.3 28.4 1.0 CA A:THR278 4.3 23.2 1.0 NH2 A:ARG673 4.4 24.8 0.5 N A:GLY652 4.4 19.1 1.0 CB A:ASP681 4.7 29.7 1.0 N A:THR279 4.8 19.7 1.0 NH2 A:ARG673 4.8 22.7 0.5

Y.Sakamoto, Y.Suzuki, I.Iizuka, C.Tateoka, S.Roppongi, M.Fujimoto, K.Inaka, H.Tanaka, M.Yamada, K.Ohta, H.Gouda, T.Nonaka, W.Ogasawara, N.Tanaka. Structural and Mutational Analyses of Dipeptidyl Peptidase 11 From Porphyromonas Gingivalis Reveal the Molecular Basis For Strict Substrate Specificity. Sci Rep V. 5 11151 2015.
ISSN: ESSN 2045-2322
PubMed: 26057589
DOI: 10.1038/SREP11151