Calcium in PDB 5jqp: Crystal Structure of Er Glucosidase II Heterodimeric Complex Consisting of Catalytic Subunit and the Binding Domain of Regulatory Subunit

The structure of Crystal Structure of Er Glucosidase II Heterodimeric Complex Consisting of Catalytic Subunit and the Binding Domain of Regulatory Subunit, PDB code: 5jqp was solved by T.Satoh, T.Toshimori, M.Noda, S.Uchiyama, K.Kato, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.20
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.716, 88.712, 173.103, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 20.6

The binding sites of Calcium atom in the Crystal Structure of Er Glucosidase II Heterodimeric Complex Consisting of Catalytic Subunit and the Binding Domain of Regulatory Subunit (pdb code 5jqp). 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 Er Glucosidase II Heterodimeric Complex Consisting of Catalytic Subunit and the Binding Domain of Regulatory Subunit, PDB code: 5jqp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Er Glucosidase II Heterodimeric Complex Consisting of Catalytic Subunit and the Binding Domain of Regulatory Subunit


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 Er Glucosidase II Heterodimeric Complex Consisting of Catalytic Subunit and the Binding Domain of Regulatory Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1001 b:22.6 occ:1.00 O B:GLN56 2.2 26.9 1.0 O B:SER61 2.3 24.6 1.0 OE2 B:GLU70 2.3 18.4 1.0 OD2 B:ASP63 2.3 22.1 1.0 OD2 B:ASP69 2.3 25.2 1.0 OD1 B:ASP59 2.5 31.9 1.0 CD B:GLU70 3.3 19.1 1.0 CG B:ASP63 3.4 22.3 1.0 CG B:ASP59 3.4 28.6 1.0 C B:GLN56 3.4 26.6 1.0 CG B:ASP69 3.4 22.7 1.0 C B:SER61 3.5 24.7 1.0 OD2 B:ASP59 3.7 28.9 1.0 CG B:GLU70 3.9 19.9 1.0 N B:SER61 4.0 25.6 1.0 CB B:ASP69 4.0 21.0 1.0 CB B:ASP63 4.1 22.9 1.0 N B:ASP63 4.1 22.1 1.0 CA B:SER61 4.1 25.0 1.0 N B:ASP59 4.1 24.7 1.0 CA B:GLN56 4.2 26.1 1.0 O B:ASP69 4.2 20.8 1.0 CB B:GLN56 4.2 26.8 1.0 O B:HOH1102 4.2 23.5 1.0 OD1 B:ASP63 4.3 26.4 1.0 OE1 B:GLU70 4.3 17.7 1.0 CB B:SER61 4.4 25.9 1.0 N B:ILE57 4.4 27.7 1.0 OD1 B:ASP69 4.4 21.3 1.0 N B:ASN58 4.5 24.6 1.0 CB B:ASP59 4.5 27.8 1.0 N B:CYS62 4.5 23.5 1.0 CA B:ILE57 4.6 25.2 1.0 C B:ASP69 4.6 19.2 1.0 CA B:ASP59 4.7 27.1 1.0 C B:ILE57 4.7 24.5 1.0 CA B:ASP63 4.7 22.8 1.0 CA B:CYS62 4.7 24.6 1.0 OG B:SER61 4.8 28.7 1.0 C B:ASP59 4.8 26.5 1.0 N B:ASN60 4.8 27.0 1.0 C B:CYS62 4.9 23.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Er Glucosidase II Heterodimeric Complex Consisting of Catalytic Subunit and the Binding Domain of Regulatory Subunit


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 Er Glucosidase II Heterodimeric Complex Consisting of Catalytic Subunit and the Binding Domain of Regulatory Subunit within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1002 b:18.6 occ:1.00 O B:VAL126 2.3 20.6 1.0 O B:TYR121 2.3 15.5 1.0 OD2 B:ASP128 2.3 18.1 1.0 OD2 B:ASP137 2.3 19.0 1.0 OD1 B:ASP124 2.4 21.1 1.0 OE2 B:GLU138 2.4 18.4 1.0 CG B:ASP124 3.5 21.4 1.0 CG B:ASP128 3.5 20.8 1.0 C B:VAL126 3.5 24.2 1.0 C B:TYR121 3.5 16.5 1.0 CG B:ASP137 3.5 18.7 1.0 CD B:GLU138 3.5 20.6 1.0 CG B:GLU138 3.9 20.9 1.0 OD2 B:ASP124 3.9 22.3 1.0 CB B:ASP137 4.1 18.2 1.0 N B:VAL126 4.1 22.8 1.0 CB B:ASP128 4.1 22.8 1.0 N B:ASP128 4.2 25.0 1.0 CA B:VAL126 4.2 23.0 1.0 CA B:TYR121 4.2 17.1 1.0 N B:ASP124 4.3 18.9 1.0 CB B:TYR121 4.3 17.5 1.0 NH2 A:ARG835 4.3 18.1 1.0 CB B:VAL126 4.3 24.1 1.0 OD1 B:ASP128 4.4 20.5 1.0 N B:CYS127 4.5 24.2 1.0 N B:VAL122 4.5 16.2 1.0 OD1 B:ASP137 4.5 18.2 1.0 N B:ASN123 4.5 17.5 1.0 OE1 B:GLU138 4.6 21.0 1.0 O B:ASP137 4.6 20.2 1.0 CA B:CYS127 4.7 25.8 1.0 CA B:VAL122 4.7 16.0 1.0 CB B:ASP124 4.7 21.0 1.0 C B:CYS127 4.7 27.1 1.0 CG1 B:VAL126 4.8 28.2 1.0 CA B:ASP128 4.8 23.6 1.0 C B:ASP137 4.9 20.0 1.0 C B:VAL122 4.9 16.8 1.0 CA B:ASP124 4.9 21.3 1.0 N B:GLY125 4.9 20.6 1.0

T.Satoh, T.Toshimori, M.Noda, S.Uchiyama, K.Kato. Interaction Mode Between Catalytic and Regulatory Subunits in Glucosidase II Involved in Er Glycoprotein Quality Control. Protein Sci. V. 25 2095 2016.
ISSN: ISSN 0961-8368
PubMed: 27576940
DOI: 10.1002/PRO.3031