Calcium in PDB 5b5t: Crystal Structure of Escherichia Coli Gamma-Glutamyltranspeptidase in Complex with Peptidyl Phosphonate Inhibitor 1B

All present enzymatic activity of Crystal Structure of Escherichia Coli Gamma-Glutamyltranspeptidase in Complex with Peptidyl Phosphonate Inhibitor 1B:
2.3.2.2; 3.4.19.13;

The structure of Crystal Structure of Escherichia Coli Gamma-Glutamyltranspeptidase in Complex with Peptidyl Phosphonate Inhibitor 1B, PDB code: 5b5t was solved by K.Wada, K.Fukuyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.33 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.990, 126.388, 129.075, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.4

The binding sites of Calcium atom in the Crystal Structure of Escherichia Coli Gamma-Glutamyltranspeptidase in Complex with Peptidyl Phosphonate Inhibitor 1B (pdb code 5b5t). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Escherichia Coli Gamma-Glutamyltranspeptidase in Complex with Peptidyl Phosphonate Inhibitor 1B, PDB code: 5b5t:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Escherichia Coli Gamma-Glutamyltranspeptidase in Complex with Peptidyl Phosphonate Inhibitor 1B


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 Escherichia Coli Gamma-Glutamyltranspeptidase in Complex with Peptidyl Phosphonate Inhibitor 1B within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:18.1 occ:1.00 O B:SER572 2.2 21.0 1.0 OD1 B:ASP575 2.3 22.1 1.0 O B:ASP569 2.4 18.4 1.0 O B:HOH839 2.4 19.2 1.0 O B:HOH768 2.4 28.9 1.0 O B:HOH836 2.5 25.0 1.0 O B:HOH843 2.6 26.9 1.0 OD2 B:ASP575 2.9 18.0 1.0 CG B:ASP575 2.9 19.7 1.0 C B:SER572 3.4 20.9 1.0 C B:ASP569 3.5 14.9 1.0 CA B:PRO570 4.0 17.6 1.0 O B:HOH830 4.1 23.4 1.0 N B:PRO570 4.2 17.3 1.0 C B:PRO570 4.2 17.0 1.0 N B:SER572 4.2 17.2 1.0 O B:HOH864 4.2 30.9 1.0 O B:PRO570 4.3 17.1 1.0 CA B:SER572 4.3 22.4 1.0 N B:VAL573 4.4 17.9 1.0 CA B:VAL573 4.4 19.6 1.0 N B:ASP569 4.4 18.1 1.0 CB B:ASP575 4.4 17.6 1.0 CA B:ASP569 4.5 17.0 1.0 CB B:SER568 4.6 15.1 1.0 C B:SER568 4.6 17.8 1.0 CB B:SER572 4.7 24.8 1.0 O C:HOH655 4.8 30.8 1.0 N B:ASP575 4.8 18.2 1.0 O B:HOH790 4.8 32.3 1.0 O B:SER568 4.8 21.4 1.0 C B:VAL573 4.9 18.4 1.0 N B:ARG571 4.9 18.3 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Escherichia Coli Gamma-Glutamyltranspeptidase in Complex with Peptidyl Phosphonate Inhibitor 1B


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Escherichia Coli Gamma-Glutamyltranspeptidase in Complex with Peptidyl Phosphonate Inhibitor 1B within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:19.0 occ:1.00 O D:SER572 2.3 22.7 1.0 O D:ASP569 2.3 16.6 1.0 OD1 D:ASP575 2.4 21.4 1.0 O D:HOH803 2.4 24.8 1.0 O D:HOH769 2.4 24.2 1.0 O D:HOH837 2.5 20.7 1.0 O D:HOH840 2.6 26.0 1.0 OD2 D:ASP575 2.8 18.2 1.0 CG D:ASP575 2.9 19.6 1.0 C D:ASP569 3.4 16.2 1.0 C D:SER572 3.4 20.4 1.0 CA D:PRO570 4.0 18.8 1.0 O D:HOH808 4.1 22.7 1.0 N D:PRO570 4.1 15.8 1.0 N D:SER572 4.2 17.3 1.0 C D:PRO570 4.2 18.0 1.0 O D:PRO570 4.3 17.4 1.0 N D:ASP569 4.3 17.7 1.0 CA D:SER572 4.3 20.4 1.0 N D:VAL573 4.4 16.7 1.0 CA D:VAL573 4.4 19.8 1.0 CB D:ASP575 4.4 18.1 1.0 O D:HOH858 4.5 33.1 1.0 CA D:ASP569 4.5 17.5 1.0 CB D:SER572 4.6 20.7 1.0 CB D:SER568 4.6 16.4 1.0 C D:SER568 4.7 17.2 1.0 N D:ASP575 4.7 18.4 1.0 O D:HOH721 4.8 28.9 1.0 C D:VAL573 4.8 20.5 1.0 N D:ARG571 4.9 18.5 1.0

A.Kamiyama, M.Nakajima, L.Han, K.Wada, M.Mizutani, Y.Tabuchi, A.Kojima-Yuasa, I.Matsui-Yuasa, H.Suzuki, K.Fukuyama, B.Watanabe, J.Hiratake. Phosphonate-Based Irreversible Inhibitors of Human Gamma-Glutamyl Transpeptidase (Ggt). Ggstop Is A Non-Toxic and Highly Selective Inhibitor with Critical Electrostatic Interaction with An Active-Site Residue LYS562 For Enhanced Inhibitory Activity Bioorg.Med.Chem. V. 24 5340 2016.
ISSN: ESSN 1464-3391
PubMed: 27622749
DOI: 10.1016/J.BMC.2016.08.050