Calcium in PDB 5y7f: Crystal Structure of Catalytic Domain of Uggt (Udp-Bound Form) From Thermomyces Dupontii

The structure of Crystal Structure of Catalytic Domain of Uggt (Udp-Bound Form) From Thermomyces Dupontii, PDB code: 5y7f was solved by T.Satoh, C.Song, T.Zhu, T.Toshimori, K.Murata, Y.Hayashi, H.Kamikubo, T.Uchihashi, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.410, 46.850, 131.990, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.8

The binding sites of Calcium atom in the Crystal Structure of Catalytic Domain of Uggt (Udp-Bound Form) From Thermomyces Dupontii (pdb code 5y7f). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Catalytic Domain of Uggt (Udp-Bound Form) From Thermomyces Dupontii, PDB code: 5y7f:

Calcium binding site 1 out of 1 in the Crystal Structure of Catalytic Domain of Uggt (Udp-Bound Form) From Thermomyces Dupontii


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 Catalytic Domain of Uggt (Udp-Bound Form) From Thermomyces Dupontii within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2003 b:9.0 occ:1.00 OD2 A:ASP1294 2.3 8.8 1.0 OD1 A:ASP1296 2.3 9.2 1.0 OD1 A:ASP1427 2.4 14.4 1.0 O2B A:UDP2001 2.4 13.7 1.0 O2A A:UDP2001 2.5 14.8 1.0 OD2 A:ASP1296 2.5 10.6 1.0 OD2 A:ASP1427 2.5 17.1 1.0 CG A:ASP1296 2.8 9.4 1.0 CG A:ASP1427 2.8 11.1 1.0 CG A:ASP1294 3.3 9.0 1.0 CB A:ASP1294 3.6 8.9 1.0 PB A:UDP2001 3.6 12.6 1.0 PA A:UDP2001 3.8 14.5 1.0 O3A A:UDP2001 3.9 13.2 1.0 O3' A:UDP2001 3.9 10.7 1.0 O1B A:UDP2001 4.0 14.3 1.0 CB A:ASP1296 4.3 9.5 1.0 CB A:ASP1427 4.3 10.9 1.0 O A:HOH2172 4.4 17.9 1.0 OD1 A:ASP1294 4.4 10.2 1.0 O A:HOH2152 4.4 12.5 1.0 NZ A:LYS1438 4.4 17.5 1.0 CA A:CYS1429 4.4 14.0 1.0 N A:CYS1429 4.4 12.3 1.0 CB A:ALA1352 4.4 8.6 1.0 C5' A:UDP2001 4.5 11.3 1.0 N A:LEU1428 4.6 11.2 1.0 O A:ASP1296 4.6 12.7 1.0 CB A:CYS1429 4.7 13.6 1.0 O5' A:UDP2001 4.7 13.7 1.0 C A:LEU1428 4.8 13.3 1.0 C3' A:UDP2001 4.8 9.8 1.0 O1A A:UDP2001 4.9 16.5 1.0 O3B A:UDP2001 4.9 15.1 1.0 CA A:ASP1296 5.0 9.5 1.0 C A:ASP1296 5.0 10.4 1.0

T.Satoh, C.Song, T.Zhu, T.Toshimori, K.Murata, Y.Hayashi, H.Kamikubo, T.Uchihashi, K.Kato. Visualisation of A Flexible Modular Structure of the Er Folding-Sensor Enzyme Uggt. Sci Rep V. 7 12142 2017.
ISSN: ESSN 2045-2322
PubMed: 28939828
DOI: 10.1038/S41598-017-12283-W