Calcium in PDB 5f0e: Murine Endoplasmic Reticulum Alpha-Glucosidase II

All present enzymatic activity of Murine Endoplasmic Reticulum Alpha-Glucosidase II:
3.2.1.84;

The structure of Murine Endoplasmic Reticulum Alpha-Glucosidase II, PDB code: 5f0e 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)	59.09 / 1.74
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	104.144, 173.773, 62.836, 90.00, 90.00, 90.00
R / Rfree (%)	14.1 / 16.9

The binding sites of Calcium atom in the Murine Endoplasmic Reticulum Alpha-Glucosidase II (pdb code 5f0e). 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, PDB code: 5f0e:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:16.6 occ:1.00 O B:GLN50 2.3 18.4 1.0 OD1 B:ASP53 2.3 17.8 1.0 OD2 B:ASP63 2.3 18.4 1.0 O B:TYR55 2.3 18.6 1.0 OE2 B:GLU64 2.3 18.0 1.0 OD2 B:ASP57 2.3 18.8 1.0 H B:ASP53 3.3 12.4 1.0 H B:ASP57 3.3 16.4 1.0 H B:TYR55 3.3 18.8 1.0 HG2 B:GLU64 3.4 19.8 1.0 CD B:GLU64 3.4 22.8 1.0 C B:GLN50 3.4 21.4 1.0 HB3 B:GLN50 3.4 22.6 1.0 CG B:ASP57 3.5 21.3 1.0 HH11 A:ARG951 3.5 20.6 1.0 CG B:ASP53 3.5 21.4 1.0 HB2 B:ASP57 3.5 18.1 1.0 C B:TYR55 3.5 18.7 1.0 CG B:ASP63 3.5 16.2 1.0 HB2 B:ASP63 3.6 15.5 1.0 CG B:GLU64 3.9 18.7 1.0 HB3 B:TYR55 3.9 14.8 1.0 N B:ASP57 4.0 17.3 1.0 CB B:ASP57 4.0 17.7 1.0 HA B:CYS56 4.0 15.9 1.0 HA B:VAL51 4.0 18.9 1.0 HA B:GLN50 4.1 21.9 1.0 HG3 B:GLU64 4.1 19.0 1.0 HD12 B:ILE46 4.2 28.1 1.0 CB B:ASP63 4.2 15.9 1.0 CA B:GLN50 4.2 21.2 1.0 HD1 B:TYR55 4.2 19.1 1.0 N B:TYR55 4.2 17.4 1.0 OD2 B:ASP53 4.2 22.2 1.0 NH1 A:ARG951 4.2 19.9 1.0 N B:ASP53 4.3 15.2 1.0 CB B:GLN50 4.3 22.7 1.0 HH12 A:ARG951 4.3 19.2 1.0 CA B:TYR55 4.3 15.8 1.0 H B:ASN52 4.4 18.7 1.0 OE1 B:GLU64 4.4 16.8 1.0 N B:VAL51 4.4 19.6 1.0 N B:CYS56 4.5 15.3 1.0 CB B:ASP53 4.5 15.4 1.0 OD1 B:ASP57 4.5 19.9 1.0 OD1 B:ASP63 4.5 17.5 1.0 HB3 B:ASP53 4.5 15.8 1.0 O B:ASP63 4.5 17.9 1.0 CA B:CYS56 4.6 17.3 1.0 CB B:TYR55 4.6 14.6 1.0 C B:CYS56 4.6 19.8 1.0 CA B:ASP57 4.7 17.3 1.0 CA B:VAL51 4.7 19.4 1.0 N B:ASN52 4.7 17.7 1.0 HD11 B:ILE46 4.8 27.3 1.0 H B:ASP54 4.8 15.0 1.0 CA B:ASP53 4.8 14.1 1.0 CD1 B:ILE46 4.9 27.8 1.0 C B:ASP63 4.9 17.9 1.0 HB3 B:ASP63 4.9 16.9 1.0 HB3 B:ASP57 4.9 17.1 1.0 N B:ASP54 4.9 15.5 1.0 HB2 B:GLN50 4.9 23.5 1.0 C B:VAL51 4.9 19.1 1.0 C B:ASP53 4.9 18.3 1.0

Calcium binding site 2 out of 2 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:15.0 occ:1.00 OE2 B:GLU105 2.2 17.3 1.0 O B:ARG91 2.3 15.0 1.0 O B:VAL96 2.3 18.4 1.0 OD2 B:ASP98 2.3 18.4 1.0 OD2 B:ASP104 2.3 15.9 1.0 OD1 B:ASP94 2.4 13.3 1.0 H B:ASP98 3.2 18.0 1.0 H B:ASP94 3.2 15.3 1.0 H B:VAL96 3.3 16.6 1.0 CD B:GLU105 3.3 15.1 1.0 HG2 B:GLU105 3.3 15.9 1.0 CG B:ASP94 3.4 14.1 1.0 HB2 B:ASP104 3.4 16.6 1.0 HB3 B:ARG91 3.4 15.7 1.0 C B:VAL96 3.4 19.9 1.0 CG B:ASP104 3.4 20.8 1.0 CG B:ASP98 3.5 16.2 1.0 C B:ARG91 3.5 16.4 1.0 HB2 B:ASP98 3.5 14.8 1.0 HB B:VAL96 3.6 15.5 1.0 CG B:GLU105 3.8 16.9 1.0 OD2 B:ASP94 3.8 15.9 1.0 N B:ASP98 4.0 16.6 1.0 CB B:ASP98 4.0 14.9 1.0 CB B:ASP104 4.0 14.8 1.0 H B:ASN93 4.0 15.0 1.0 N B:VAL96 4.0 15.8 1.0 HA B:ARG91 4.1 14.5 1.0 HH21 A:ARG840 4.1 14.4 1.0 HA B:VAL92 4.1 14.4 1.0 CA B:VAL96 4.1 14.0 1.0 HG3 B:GLU105 4.2 18.7 1.0 HA B:CYS97 4.2 19.8 1.0 CA B:ARG91 4.2 12.9 1.0 N B:ASP94 4.2 14.9 1.0 CB B:ARG91 4.3 14.5 1.0 OE1 B:GLU105 4.3 18.3 1.0 CB B:VAL96 4.4 15.9 1.0 HD12 B:ILE87 4.4 16.2 1.0 N B:ASN93 4.5 14.0 1.0 OD1 B:ASP104 4.5 16.7 1.0 N B:CYS97 4.5 17.9 1.0 N B:VAL92 4.5 13.9 1.0 OD1 B:ASP98 4.5 15.1 1.0 HH22 A:ARG840 4.5 16.2 1.0 CB B:ASP94 4.5 13.6 1.0 H B:GLY95 4.6 16.3 1.0 HG12 B:VAL96 4.6 15.1 1.0 O B:ASP104 4.6 17.7 1.0 CA B:ASP98 4.6 15.8 1.0 NH2 A:ARG840 4.7 15.2 1.0 CA B:CYS97 4.7 20.5 1.0 C B:CYS97 4.7 23.4 1.0 CA B:VAL92 4.7 13.3 1.0 HB3 B:ASP104 4.7 13.7 1.0 C B:ASP104 4.7 17.5 1.0 CA B:ASP94 4.8 14.7 1.0 N B:GLY95 4.8 15.3 1.0 HB3 B:ASP94 4.8 14.3 1.0 HD11 B:ILE87 4.8 14.7 1.0 C B:VAL92 4.9 15.5 1.0 HB2 B:ARG91 4.9 13.0 1.0 HB3 B:ASP98 4.9 11.2 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