Calcium in PDB 5ieg: Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-9'- Methoxynonyl-1-Deoxynojirimycin

All present enzymatic activity of Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-9'- Methoxynonyl-1-Deoxynojirimycin:
3.2.1.84;

The structure of Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-9'- Methoxynonyl-1-Deoxynojirimycin, PDB code: 5ieg was solved by A.T.Caputo, P.Roversi, D.S.Alonzi, J.L.Kiappes, N.Zitzmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	89.38 / 1.82
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.321, 173.311, 63.032, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.5

The binding sites of Calcium atom in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-9'- Methoxynonyl-1-Deoxynojirimycin (pdb code 5ieg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-9'- Methoxynonyl-1-Deoxynojirimycin, PDB code: 5ieg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-9'- Methoxynonyl-1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-9'- Methoxynonyl-1-Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:21.1 occ:1.00 OD1 B:ASP53 2.3 21.7 1.0 OD2 B:ASP63 2.3 21.6 1.0 O B:GLN50 2.3 24.3 1.0 O B:TYR55 2.3 20.6 1.0 OE2 B:GLU64 2.3 19.5 1.0 OD2 B:ASP57 2.4 22.0 1.0 CD B:GLU64 3.4 23.4 1.0 C B:GLN50 3.4 26.6 1.0 CG B:ASP57 3.5 25.7 1.0 CG B:ASP63 3.5 16.2 1.0 CG B:ASP53 3.5 23.7 1.0 C B:TYR55 3.5 20.4 1.0 CG B:GLU64 3.9 20.7 1.0 CB B:ASP57 4.0 23.6 1.0 N B:ASP57 4.0 23.2 1.0 CB B:ASP63 4.1 21.9 1.0 CA B:GLN50 4.1 25.6 1.0 OD2 B:ASP53 4.2 27.8 1.0 N B:TYR55 4.2 18.6 1.0 CB B:GLN50 4.2 27.3 1.0 NH1 A:ARG951 4.3 27.3 1.0 N B:ASP53 4.3 18.9 1.0 CA B:TYR55 4.3 18.0 1.0 N B:VAL51 4.4 24.1 1.0 OD1 B:ASP63 4.5 19.3 1.0 OE1 B:GLU64 4.5 19.1 1.0 CB B:ASP53 4.5 21.0 1.0 N B:CYS56 4.5 17.2 1.0 OD1 B:ASP57 4.5 24.5 1.0 O B:ASP63 4.5 21.1 1.0 CA B:CYS56 4.6 18.1 1.0 C B:CYS56 4.6 24.0 1.0 CB B:TYR55 4.6 18.1 1.0 CA B:ASP57 4.7 23.3 1.0 N B:ASN52 4.7 20.0 1.0 CA B:VAL51 4.7 23.4 1.0 CA B:ASP53 4.8 18.9 1.0 CD1 B:ILE46 4.8 41.0 1.0 C B:ASP63 4.8 20.9 1.0 C B:VAL51 5.0 24.6 1.0 N B:ASP54 5.0 18.9 1.0 C B:ASP53 5.0 20.4 1.0

Calcium binding site 2 out of 2 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-9'- Methoxynonyl-1-Deoxynojirimycin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-9'- Methoxynonyl-1-Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:18.5 occ:1.00 OE2 B:GLU105 2.2 20.5 1.0 O B:VAL96 2.3 20.3 1.0 OD2 B:ASP98 2.3 18.8 1.0 O B:ARG91 2.3 17.5 1.0 OD2 B:ASP104 2.3 19.3 1.0 OD1 B:ASP94 2.4 16.9 1.0 CD B:GLU105 3.3 16.8 1.0 CG B:ASP94 3.4 14.8 1.0 CG B:ASP98 3.4 18.1 1.0 CG B:ASP104 3.4 21.6 1.0 C B:VAL96 3.4 21.8 1.0 C B:ARG91 3.5 18.1 1.0 CG B:GLU105 3.8 17.8 1.0 OD2 B:ASP94 3.8 19.7 1.0 N B:ASP98 3.9 20.0 1.0 CB B:ASP98 4.0 20.0 1.0 CB B:ASP104 4.0 17.9 1.0 N B:VAL96 4.0 18.0 1.0 CA B:VAL96 4.2 17.1 1.0 CA B:ARG91 4.2 15.9 1.0 N B:ASP94 4.2 17.6 1.0 CB B:ARG91 4.3 16.4 1.0 OE1 B:GLU105 4.3 21.9 1.0 CB B:VAL96 4.4 19.5 1.0 OD1 B:ASP104 4.5 20.8 1.0 N B:CYS97 4.5 20.1 1.0 OD1 B:ASP98 4.5 18.8 1.0 N B:ASN93 4.5 15.1 1.0 N B:VAL92 4.5 15.6 1.0 CB B:ASP94 4.5 16.2 1.0 O B:ASP104 4.6 19.3 1.0 CA B:ASP98 4.6 20.4 1.0 NH2 A:ARG840 4.6 16.9 1.0 CA B:CYS97 4.7 21.1 1.0 C B:CYS97 4.7 24.5 1.0 C B:ASP104 4.7 20.8 1.0 CA B:VAL92 4.7 14.8 1.0 CA B:ASP94 4.8 16.6 1.0 N B:GLY95 4.8 17.4 1.0 C B:VAL92 4.9 18.8 1.0 CD1 B:ILE87 5.0 20.6 1.0

A.T.Caputo, D.S.Alonzi, L.Marti, I.B.Reca, J.L.Kiappes, W.B.Struwe, A.Cross, S.Basu, E.D.Lowe, B.Darlot, A.Santino, P.Roversi, N.Zitzmann. Structures of Mammalian Er Alpha-Glucosidase II Capture the Binding Modes of Broad-Spectrum Iminosugar Antivirals. Proc.Natl.Acad.Sci.Usa V. 113 E4630 2016.
ISSN: ESSN 1091-6490
PubMed: 27462106
DOI: 10.1073/PNAS.1604463113