Calcium in PDB 5iee: Murine Endoplasmic Reticulum Alpha-Glucosidase II with 1- Deoxynojirimycin

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

The structure of Murine Endoplasmic Reticulum Alpha-Glucosidase II with 1- Deoxynojirimycin, PDB code: 5iee 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)	88.90 / 1.92
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	103.480, 173.710, 62.910, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.6

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

Calcium binding site 1 out of 2 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with 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 1- Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:25.2 occ:1.00 O B:GLN50 2.1 27.2 1.0 OD1 B:ASP53 2.2 24.1 1.0 OE2 B:GLU64 2.3 26.1 1.0 OD2 B:ASP63 2.3 27.6 1.0 O B:TYR55 2.4 23.5 1.0 OD2 B:ASP57 2.5 23.8 1.0 C B:GLN50 3.3 30.6 1.0 H B:ASP53 3.3 21.6 1.0 H B:TYR55 3.3 22.6 1.0 CD B:GLU64 3.4 27.2 1.0 HG2 B:GLU64 3.4 22.6 1.0 CG B:ASP53 3.4 25.2 1.0 HB3 B:GLN50 3.4 33.1 1.0 HH11 A:ARG951 3.5 29.6 1.0 CG B:ASP63 3.5 26.4 1.0 H B:ASP57 3.5 25.8 1.0 HB2 B:ASP63 3.5 23.2 1.0 C B:TYR55 3.5 24.7 1.0 CG B:ASP57 3.6 25.8 1.0 HB2 B:ASP57 3.6 25.9 1.0 HB3 B:TYR55 3.8 24.1 1.0 CG B:GLU64 3.8 22.7 1.0 HA B:GLN50 3.9 32.9 1.0 HA B:VAL51 4.0 26.4 1.0 CA B:GLN50 4.0 32.0 1.0 HG3 B:GLU64 4.1 23.3 1.0 HD12 B:ILE46 4.1 39.2 1.0 OD2 B:ASP53 4.1 26.9 1.0 HA B:CYS56 4.1 23.2 1.0 CB B:ASP57 4.1 25.3 1.0 CB B:ASP63 4.1 23.2 1.0 N B:ASP57 4.1 25.8 1.0 HD1 B:TYR55 4.2 25.9 1.0 N B:TYR55 4.2 22.2 1.0 CB B:GLN50 4.2 33.1 1.0 NH1 A:ARG951 4.2 28.9 1.0 HH12 A:ARG951 4.3 28.6 1.0 N B:ASP53 4.3 21.4 1.0 CA B:TYR55 4.3 23.4 1.0 N B:VAL51 4.4 27.4 1.0 H B:ASN52 4.4 25.4 1.0 OE1 B:GLU64 4.4 21.1 1.0 HB3 B:ASP53 4.4 23.9 1.0 CB B:ASP53 4.4 22.9 1.0 OD1 B:ASP63 4.5 25.4 1.0 O B:ASP63 4.5 23.6 1.0 N B:CYS56 4.5 22.8 1.0 CB B:TYR55 4.6 23.2 1.0 OD1 B:ASP57 4.6 28.3 1.0 CA B:CYS56 4.6 23.0 1.0 CA B:VAL51 4.6 26.6 1.0 N B:ASN52 4.7 24.9 1.0 C B:CYS56 4.7 26.7 1.0 HD11 B:ILE46 4.7 38.9 1.0 H B:ASP54 4.7 21.9 1.0 CA B:ASP53 4.8 20.9 1.0 CA B:ASP57 4.8 25.3 1.0 HB3 B:ASP63 4.8 23.8 1.0 CD1 B:ILE46 4.8 39.4 1.0 C B:ASP63 4.9 24.2 1.0 HB2 B:GLN50 4.9 33.7 1.0 C B:VAL51 4.9 28.1 1.0 N B:ASP54 4.9 21.9 1.0 C B:ASP53 5.0 24.2 1.0

Calcium binding site 2 out of 2 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with 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 1- Deoxynojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:22.1 occ:1.00 OE2 B:GLU105 2.2 20.5 1.0 O B:VAL96 2.2 23.3 1.0 OD2 B:ASP104 2.3 24.7 1.0 O B:ARG91 2.3 23.2 1.0 OD2 B:ASP98 2.4 24.3 1.0 OD1 B:ASP94 2.4 19.9 1.0 H B:VAL96 3.2 22.6 1.0 CD B:GLU105 3.2 22.3 1.0 H B:ASP94 3.3 20.8 1.0 HG2 B:GLU105 3.3 16.4 1.0 H B:ASP98 3.3 20.3 1.0 C B:VAL96 3.4 25.2 1.0 CG B:ASP94 3.4 19.6 1.0 HB3 B:ARG91 3.4 19.6 1.0 HB2 B:ASP104 3.4 22.2 1.0 CG B:ASP104 3.4 24.2 1.0 C B:ARG91 3.5 23.4 1.0 CG B:ASP98 3.5 24.8 1.0 HB2 B:ASP98 3.6 23.2 1.0 HB B:VAL96 3.6 22.9 1.0 CG B:GLU105 3.8 17.6 1.0 OD2 B:ASP94 3.8 21.3 1.0 N B:VAL96 4.0 22.6 1.0 N B:ASP98 4.0 21.0 1.0 CB B:ASP104 4.0 22.5 1.0 CB B:ASP98 4.0 23.1 1.0 HA B:ARG91 4.1 22.2 1.0 H B:ASN93 4.1 20.6 1.0 CA B:VAL96 4.1 21.7 1.0 HG3 B:GLU105 4.1 18.3 1.0 HH21 A:ARG840 4.1 17.4 1.0 HA B:CYS97 4.2 24.5 1.0 HA B:VAL92 4.2 21.8 1.0 CA B:ARG91 4.2 20.1 1.0 CB B:ARG91 4.2 19.3 1.0 N B:ASP94 4.3 20.8 1.0 OE1 B:GLU105 4.3 22.9 1.0 HD12 B:ILE87 4.3 29.6 1.0 CB B:VAL96 4.3 23.8 1.0 N B:CYS97 4.4 22.8 1.0 OD1 B:ASP104 4.5 22.0 1.0 CB B:ASP94 4.5 20.6 1.0 HG12 B:VAL96 4.5 23.8 1.0 N B:VAL92 4.5 21.2 1.0 N B:ASN93 4.5 18.7 1.0 HH22 A:ARG840 4.5 17.4 1.0 OD1 B:ASP98 4.6 21.8 1.0 H B:GLY95 4.6 21.9 1.0 CA B:CYS97 4.6 23.4 1.0 CA B:ASP98 4.7 21.8 1.0 C B:CYS97 4.7 25.6 1.0 NH2 A:ARG840 4.7 17.1 1.0 HB3 B:ASP94 4.7 20.8 1.0 O B:ASP104 4.7 22.6 1.0 HB3 B:ASP104 4.7 22.2 1.0 CA B:VAL92 4.7 21.2 1.0 C B:ASP104 4.8 23.9 1.0 HB2 B:ARG91 4.8 19.4 1.0 HD11 B:ILE87 4.8 30.1 1.0 CA B:ASP94 4.8 20.6 1.0 N B:GLY95 4.8 21.6 1.0 C B:VAL92 4.9 20.4 1.0 CD1 B:ILE87 5.0 29.9 1.0 HB3 B:ASP98 5.0 23.3 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