Calcium in PDB 5n2j: Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum (Closed Form)

The structure of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum (Closed Form), PDB code: 5n2j was solved by P.Roversi, A.T.Caputo, J.Hill, D.S.Alonzi, N.Zitzmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	114.59 / 4.40
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	148.600, 148.600, 179.970, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 25.9

The binding sites of Calcium atom in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum (Closed Form) (pdb code 5n2j). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum (Closed Form), PDB code: 5n2j:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum (Closed Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1613 b:0.4 occ:0.62 OD2 A:ASP1302 2.5 0.7 1.0 OD1 A:ASP1435 2.7 0.2 1.0 OD2 A:ASP1304 2.7 0.0 1.0 OD2 A:ASP1435 3.0 0.6 1.0 OD1 A:ASP1304 3.2 0.4 1.0 CG A:ASP1435 3.2 0.5 1.0 CG A:ASP1304 3.3 0.8 1.0 CG A:ASP1302 3.3 0.3 1.0 HB3 A:ASP1302 3.6 0.4 1.0 HB1 A:ALA1360 3.7 0.4 1.0 HZ1 A:LYS1446 3.8 0.3 1.0 HH A:TYR1211 3.9 0.7 1.0 CB A:ASP1302 4.0 0.5 1.0 HB2 A:ALA1360 4.0 0.4 1.0 HB2 A:ASP1302 4.1 0.4 1.0 OD1 A:ASP1302 4.2 0.4 1.0 CB A:ALA1360 4.4 0.5 1.0 H A:LEU1436 4.5 0.2 1.0 HA A:ALA1360 4.5 0.7 1.0 HA A:CYS1437 4.6 0.7 1.0 OH A:TYR1211 4.6 0.3 1.0 HZ3 A:LYS1446 4.6 0.1 1.0 NZ A:LYS1446 4.6 0.3 1.0 O A:LEU1436 4.7 1.0 1.0 CB A:ASP1435 4.8 0.0 1.0 CB A:ASP1304 4.8 0.1 1.0 H A:ASP1304 4.8 1.0 1.0 HE21 A:GLN1305 4.9 0.7 1.0 HE2 A:LYS1446 4.9 0.8 1.0

Calcium binding site 2 out of 2 in the Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum (Closed Form)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Udp-Glucose Glycoprotein Glucosyltransferase From Chaetomium Thermophilum (Closed Form) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1613 b:0.3 occ:1.00 OD2 B:ASP1302 2.5 0.2 1.0 OD2 B:ASP1304 2.7 0.8 1.0 OD1 B:ASP1435 2.7 0.3 1.0 OD2 B:ASP1435 3.1 0.8 1.0 OD1 B:ASP1304 3.2 0.3 1.0 CG B:ASP1435 3.2 0.4 1.0 CG B:ASP1304 3.3 0.3 1.0 CG B:ASP1302 3.3 0.9 1.0 HB3 B:ASP1302 3.6 0.5 1.0 HB1 B:ALA1360 3.7 0.4 1.0 HZ1 B:LYS1446 3.8 0.9 1.0 CB B:ASP1302 3.9 0.0 1.0 HH B:TYR1211 3.9 0.7 1.0 HB2 B:ASP1302 4.0 0.3 1.0 HB2 B:ALA1360 4.0 0.9 1.0 OD1 B:ASP1302 4.2 0.8 1.0 CB B:ALA1360 4.3 0.8 1.0 H B:LEU1436 4.5 0.4 1.0 HA B:ALA1360 4.5 0.3 1.0 HA B:CYS1437 4.6 0.5 1.0 HZ3 B:LYS1446 4.6 0.4 1.0 OH B:TYR1211 4.6 0.1 1.0 NZ B:LYS1446 4.6 0.7 1.0 O B:LEU1436 4.6 0.5 1.0 CB B:ASP1435 4.8 0.4 1.0 CB B:ASP1304 4.8 0.7 1.0 H B:ASP1304 4.8 0.4 1.0 HE2 B:LYS1446 4.9 0.9 1.0 HE21 B:GLN1305 4.9 0.3 1.0

P.Roversi, L.Marti, A.T.Caputo, D.S.Alonzi, J.C.Hill, K.C.Dent, A.Kumar, M.D.Levasseur, A.Lia, T.Waksman, S.Basu, Y.Soto Albrecht, K.Qian, J.P.Mcivor, C.B.Lipp, D.Siliqi, S.Vasiljevic, S.Mohammed, P.Lukacik, M.A.Walsh, A.Santino, N.Zitzmann. Interdomain Conformational Flexibility Underpins the Activity of Uggt, the Eukaryotic Glycoprotein Secretion Checkpoint. Proc. Natl. Acad. Sci. V. 114 8544 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28739903
DOI: 10.1073/PNAS.1703682114