Calcium in PDB 5ief: Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-Butyl-1- Deoxynojirimycin

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

The structure of Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-Butyl-1- Deoxynojirimycin, PDB code: 5ief 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)	53.72 / 2.38
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.840, 172.890, 62.770, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.8

The binding sites of Calcium atom in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-Butyl-1- Deoxynojirimycin (pdb code 5ief). 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-Butyl-1- Deoxynojirimycin, PDB code: 5ief:
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-Butyl-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-Butyl-1- Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:23.6 occ:1.00 OD1 B:ASP53 2.2 23.2 1.0 OD2 B:ASP63 2.2 25.4 1.0 O B:GLN50 2.3 27.7 1.0 O B:TYR55 2.3 23.8 1.0 OE2 B:GLU64 2.3 26.6 1.0 OD2 B:ASP57 2.4 25.8 1.0 C B:GLN50 3.4 30.4 1.0 CG B:ASP53 3.4 26.9 1.0 CG B:ASP63 3.4 23.2 1.0 CD B:GLU64 3.4 34.5 1.0 CG B:ASP57 3.5 25.6 1.0 C B:TYR55 3.5 23.5 1.0 CG B:GLU64 3.9 18.5 1.0 CB B:ASP57 4.0 22.4 1.0 N B:ASP57 4.0 22.3 1.0 CB B:ASP63 4.0 23.0 1.0 CA B:GLN50 4.1 28.0 1.0 OD2 B:ASP53 4.1 31.9 1.0 CB B:GLN50 4.2 29.1 1.0 N B:TYR55 4.3 20.9 1.0 NH1 A:ARG951 4.3 27.3 1.0 N B:ASP53 4.3 27.2 1.0 CA B:TYR55 4.3 19.8 1.0 CB B:ASP53 4.4 27.4 1.0 OD1 B:ASP63 4.4 20.1 1.0 N B:VAL51 4.4 27.4 1.0 N B:CYS56 4.4 19.5 1.0 OE1 B:GLU64 4.5 23.9 1.0 OD1 B:ASP57 4.5 24.6 1.0 O B:ASP63 4.5 22.6 1.0 CA B:CYS56 4.6 19.5 1.0 C B:CYS56 4.6 24.9 1.0 CB B:TYR55 4.6 20.5 1.0 CA B:ASP57 4.7 22.7 1.0 N B:ASN52 4.7 27.8 1.0 CA B:VAL51 4.7 26.4 1.0 CA B:ASP53 4.8 26.6 1.0 C B:ASP63 4.8 24.3 1.0 CD1 B:ILE46 4.9 39.2 1.0 C B:VAL51 4.9 32.0 1.0 C B:ASP53 5.0 30.8 1.0 N B:ASP54 5.0 25.0 1.0

Calcium binding site 2 out of 2 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with N-Butyl-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-Butyl-1- Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:24.4 occ:1.00 OE2 B:GLU105 2.2 24.8 1.0 OD2 B:ASP104 2.3 30.0 1.0 O B:ARG91 2.3 22.6 1.0 O B:VAL96 2.3 30.4 1.0 OD2 B:ASP98 2.3 26.2 1.0 OD1 B:ASP94 2.4 24.2 1.0 CD B:GLU105 3.2 31.2 1.0 CG B:ASP104 3.4 28.3 1.0 CG B:ASP94 3.4 20.2 1.0 C B:VAL96 3.5 31.7 1.0 C B:ARG91 3.5 22.6 1.0 CG B:ASP98 3.5 28.1 1.0 CG B:GLU105 3.8 23.1 1.0 OD2 B:ASP94 3.8 24.6 1.0 N B:ASP98 3.9 27.3 1.0 CB B:ASP104 4.0 23.8 1.0 CB B:ASP98 4.0 27.3 1.0 N B:VAL96 4.1 27.4 1.0 CA B:VAL96 4.2 27.4 1.0 CA B:ARG91 4.2 19.3 1.0 N B:ASP94 4.2 22.4 1.0 OE1 B:GLU105 4.3 23.9 1.0 CB B:ARG91 4.3 14.2 1.0 CB B:VAL96 4.4 31.1 1.0 OD1 B:ASP104 4.4 26.7 1.0 N B:ASN93 4.5 24.2 1.0 N B:CYS97 4.5 29.4 1.0 N B:VAL92 4.5 21.4 1.0 OD1 B:ASP98 4.5 25.1 1.0 O B:ASP104 4.5 23.3 1.0 CB B:ASP94 4.6 21.0 1.0 CA B:ASP98 4.6 26.6 1.0 CA B:CYS97 4.6 30.6 1.0 C B:CYS97 4.6 31.6 1.0 C B:ASP104 4.7 26.6 1.0 CA B:VAL92 4.7 21.9 1.0 NH2 A:ARG840 4.7 24.2 1.0 N B:GLY95 4.8 25.0 1.0 CA B:ASP94 4.8 21.2 1.0 C B:VAL92 4.8 27.1 1.0 CA B:ASP104 5.0 23.1 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