Calcium in PDB 5h9o: Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose

All present enzymatic activity of Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose:
3.2.1.84;

The structure of Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose, PDB code: 5h9o 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)	87.66 / 2.37
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	102.145, 170.741, 125.989, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.3

The binding sites of Calcium atom in the Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose (pdb code 5h9o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose, PDB code: 5h9o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:27.4 occ:1.00 OD1 B:ASP53 2.2 33.3 1.0 O B:TYR55 2.3 28.8 1.0 O B:GLN50 2.3 43.4 1.0 OD2 B:ASP57 2.3 20.3 1.0 OD2 B:ASP63 2.4 32.7 1.0 OE2 B:GLU64 2.4 18.6 1.0 H B:TYR55 3.3 24.0 1.0 H B:ASP53 3.3 25.6 1.0 H B:ASP57 3.3 30.0 1.0 HH11 A:ARG951 3.4 28.6 1.0 HG2 B:GLU64 3.4 27.2 1.0 CD B:GLU64 3.4 30.0 1.0 HB3 B:GLN50 3.4 44.7 1.0 C B:GLN50 3.4 43.9 1.0 CG B:ASP53 3.4 33.3 1.0 C B:TYR55 3.5 26.9 1.0 CG B:ASP57 3.5 29.9 1.0 HB2 B:ASP57 3.5 32.3 1.0 CG B:ASP63 3.6 29.1 1.0 HB2 B:ASP63 3.7 31.4 1.0 HB3 B:TYR55 3.8 22.3 1.0 CG B:GLU64 3.9 26.8 1.0 HA B:CYS56 4.0 27.7 1.0 N B:ASP57 4.0 30.1 1.0 HA B:GLN50 4.0 42.5 1.0 CB B:ASP57 4.0 30.6 1.0 HG3 B:GLU64 4.1 27.3 1.0 HA B:VAL51 4.1 37.1 1.0 NH1 A:ARG951 4.2 29.6 1.0 CA B:GLN50 4.2 42.7 1.0 OD2 B:ASP53 4.2 28.8 1.0 HD1 B:TYR55 4.2 24.4 1.0 N B:TYR55 4.2 22.7 1.0 HD12 B:ILE46 4.2 53.8 1.0 CB B:ASP63 4.2 30.9 1.0 HH12 A:ARG951 4.2 30.5 1.0 CB B:GLN50 4.3 43.9 1.0 CA B:TYR55 4.3 22.5 1.0 N B:ASP53 4.3 25.4 1.0 N B:CYS56 4.4 26.7 1.0 OE1 B:GLU64 4.4 27.4 1.0 H B:ASN52 4.4 28.7 1.0 CB B:ASP53 4.5 24.5 1.0 N B:VAL51 4.5 38.2 1.0 OD1 B:ASP57 4.5 28.0 1.0 HB3 B:ASP53 4.5 24.4 1.0 CA B:CYS56 4.5 27.2 1.0 OD1 B:ASP63 4.5 25.4 1.0 CB B:TYR55 4.6 22.1 1.0 C B:CYS56 4.6 33.3 1.0 O B:ASP63 4.6 32.9 1.0 CA B:ASP57 4.7 29.9 1.0 CA B:VAL51 4.7 36.3 1.0 N B:ASN52 4.8 28.1 1.0 H B:ASP54 4.8 27.8 1.0 CA B:ASP53 4.8 24.0 1.0 HD11 B:ILE46 4.8 53.3 1.0 CD1 B:ILE46 4.9 53.6 1.0 C B:ASP63 4.9 34.9 1.0 N B:ASP54 4.9 28.4 1.0 HB2 B:GLN50 4.9 44.1 1.0 HB3 B:ASP63 4.9 32.1 1.0 C B:ASP53 4.9 29.0 1.0 HB3 B:ASP57 5.0 28.8 1.0 HG2 B:GLN50 5.0 42.6 1.0

Calcium binding site 2 out of 4 in the Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:24.2 occ:1.00 OE2 B:GLU105 2.2 23.6 1.0 O B:ARG91 2.2 29.3 1.0 OD1 B:ASP94 2.3 13.5 1.0 O B:VAL96 2.3 32.2 1.0 OD2 B:ASP98 2.3 25.8 1.0 OD2 B:ASP104 2.3 31.3 1.0 H B:ASP94 3.1 15.8 1.0 H B:VAL96 3.2 25.9 1.0 CD B:GLU105 3.2 38.2 1.0 H B:ASP98 3.3 31.1 1.0 CG B:ASP94 3.3 21.0 1.0 HG2 B:GLU105 3.4 38.1 1.0 HB2 B:ASP104 3.4 32.1 1.0 C B:ARG91 3.4 27.5 1.0 HB3 B:ARG91 3.4 23.1 1.0 CG B:ASP104 3.5 35.3 1.0 C B:VAL96 3.5 32.4 1.0 CG B:ASP98 3.5 30.7 1.0 HB2 B:ASP98 3.6 31.7 1.0 HB B:VAL96 3.6 27.4 1.0 CG B:GLU105 3.8 38.1 1.0 OD2 B:ASP94 3.9 26.3 1.0 H B:ASN93 3.9 16.5 1.0 HA B:ARG91 4.0 22.7 1.0 CB B:ASP104 4.0 31.6 1.0 N B:VAL96 4.0 24.8 1.0 N B:ASP98 4.1 31.2 1.0 CB B:ASP98 4.1 31.6 1.0 HA B:VAL92 4.1 24.1 1.0 HH21 A:ARG840 4.1 24.4 1.0 N B:ASP94 4.1 15.4 1.0 CA B:ARG91 4.1 24.3 1.0 CA B:VAL96 4.2 23.6 1.0 HG3 B:GLU105 4.2 39.0 1.0 CB B:ARG91 4.2 23.8 1.0 OE1 B:GLU105 4.3 22.5 1.0 HA B:CYS97 4.3 32.3 1.0 CB B:VAL96 4.4 25.7 1.0 N B:ASN93 4.4 18.2 1.0 HD12 B:ILE87 4.4 32.8 1.0 N B:VAL92 4.4 22.6 1.0 CB B:ASP94 4.4 15.6 1.0 H B:GLY95 4.5 25.4 1.0 OD1 B:ASP104 4.5 33.5 1.0 OD1 B:ASP98 4.5 31.9 1.0 N B:CYS97 4.5 32.4 1.0 HH22 A:ARG840 4.6 25.2 1.0 O B:ASP104 4.6 25.8 1.0 HG12 B:VAL96 4.6 26.1 1.0 CA B:VAL92 4.6 23.7 1.0 NH2 A:ARG840 4.7 24.9 1.0 CA B:ASP94 4.7 14.5 1.0 C B:ASP104 4.7 31.0 1.0 CA B:ASP98 4.7 30.6 1.0 HB3 B:ASP94 4.7 15.5 1.0 HB3 B:ASP104 4.7 31.3 1.0 N B:GLY95 4.7 24.6 1.0 CA B:CYS97 4.8 33.1 1.0 C B:CYS97 4.8 34.7 1.0 C B:VAL92 4.8 25.8 1.0 HD11 B:ILE87 4.8 31.2 1.0 HB2 B:ARG91 4.9 22.8 1.0 HA B:ASN93 4.9 20.2 1.0 C B:ASP94 5.0 24.2 1.0

Calcium binding site 3 out of 4 in the Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca201 b:25.9 occ:1.00 OE2 D:GLU64 2.3 56.2 1.0 O D:TYR55 2.3 29.9 1.0 OD2 D:ASP63 2.3 39.8 1.0 O D:GLN50 2.4 37.0 1.0 OD1 D:ASP53 2.4 23.7 1.0 OD2 D:ASP57 2.8 41.1 1.0 HG2 D:GLU64 3.1 24.1 1.0 H D:ASP57 3.3 34.1 1.0 CD D:GLU64 3.3 47.9 1.0 H D:ASP53 3.3 23.6 1.0 HB2 D:ASP57 3.4 37.9 1.0 HB2 D:ASP63 3.4 35.6 1.0 H D:TYR55 3.4 26.6 1.0 CG D:ASP63 3.4 34.1 1.0 C D:GLN50 3.5 37.8 1.0 C D:TYR55 3.5 31.3 1.0 HH11 C:ARG951 3.5 19.9 1.0 HB3 D:GLN50 3.6 36.9 1.0 CG D:ASP53 3.7 27.2 1.0 CG D:GLU64 3.7 24.6 1.0 CG D:ASP57 3.8 40.8 1.0 HA D:CYS56 3.8 30.8 1.0 HG3 D:GLU64 3.9 25.2 1.0 N D:ASP57 3.9 34.2 1.0 CB D:ASP63 4.0 35.1 1.0 CB D:ASP57 4.0 37.0 1.0 HA D:VAL51 4.1 32.3 1.0 HA D:GLN50 4.1 36.0 1.0 HB3 D:TYR55 4.1 25.0 1.0 HD12 D:ILE46 4.1 42.8 1.0 CA D:GLN50 4.2 35.8 1.0 N D:ASP53 4.3 24.4 1.0 H D:ASN52 4.3 24.0 1.0 N D:TYR55 4.3 25.3 1.0 NH1 C:ARG951 4.3 20.7 1.0 OE1 D:GLU64 4.3 33.5 1.0 HD1 D:TYR55 4.3 25.0 1.0 N D:CYS56 4.4 30.8 1.0 CB D:GLN50 4.4 36.3 1.0 CA D:TYR55 4.4 24.9 1.0 CA D:CYS56 4.4 30.8 1.0 HH12 C:ARG951 4.4 20.6 1.0 OD2 D:ASP53 4.4 39.9 1.0 OD1 D:ASP63 4.4 30.1 1.0 N D:VAL51 4.5 33.2 1.0 O D:ASP63 4.5 33.5 1.0 C D:CYS56 4.5 34.6 1.0 CB D:ASP53 4.6 24.5 1.0 CA D:ASP57 4.6 36.0 1.0 HB3 D:ASP53 4.6 25.2 1.0 N D:ASN52 4.6 25.1 1.0 HD11 D:ILE46 4.7 43.2 1.0 HB3 D:ASP63 4.7 35.9 1.0 CA D:VAL51 4.7 31.2 1.0 C D:ASP63 4.7 35.5 1.0 CD1 D:ILE46 4.8 43.2 1.0 CB D:TYR55 4.8 25.1 1.0 H D:ASP54 4.8 27.6 1.0 HD13 D:ILE46 4.8 42.6 1.0 OD1 D:ASP57 4.8 43.1 1.0 CA D:ASP53 4.9 23.9 1.0 HB3 D:ASP57 5.0 37.0 1.0 C D:VAL51 5.0 31.6 1.0

Calcium binding site 4 out of 4 in the Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Complex of Murine Endoplasmic Reticulum Alpha-Glucosidase II with D- Glucose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:23.8 occ:1.00 OE2 D:GLU105 2.2 16.0 1.0 OD2 D:ASP104 2.2 32.3 1.0 O D:ARG91 2.3 32.5 1.0 OD2 D:ASP98 2.3 29.8 1.0 O D:VAL96 2.3 32.4 1.0 OD1 D:ASP94 2.4 23.3 1.0 H D:ASP98 3.2 33.4 1.0 H D:ASP94 3.3 27.6 1.0 CD D:GLU105 3.3 20.3 1.0 HB2 D:ASP104 3.3 32.1 1.0 H D:VAL96 3.3 27.7 1.0 HG2 D:GLU105 3.3 25.9 1.0 CG D:ASP104 3.4 35.5 1.0 HB3 D:ARG91 3.4 31.2 1.0 C D:ARG91 3.4 33.7 1.0 CG D:ASP98 3.4 29.9 1.0 HB2 D:ASP98 3.5 33.0 1.0 CG D:ASP94 3.5 24.8 1.0 C D:VAL96 3.5 32.3 1.0 HB D:VAL96 3.7 31.4 1.0 CG D:GLU105 3.8 26.2 1.0 CB D:ASP104 3.9 31.6 1.0 CB D:ASP98 4.0 32.0 1.0 N D:ASP98 4.0 33.4 1.0 H D:ASN93 4.0 25.6 1.0 OD2 D:ASP94 4.0 19.8 1.0 HA D:VAL92 4.1 28.5 1.0 HA D:ARG91 4.1 29.8 1.0 N D:VAL96 4.1 27.7 1.0 HH21 C:ARG840 4.1 28.4 1.0 CA D:ARG91 4.2 29.1 1.0 HG3 D:GLU105 4.2 26.1 1.0 HA D:CYS97 4.2 28.9 1.0 CA D:VAL96 4.2 27.0 1.0 N D:ASP94 4.2 26.5 1.0 CB D:ARG91 4.3 30.2 1.0 OE1 D:GLU105 4.3 27.1 1.0 HD12 D:ILE87 4.3 40.1 1.0 OD1 D:ASP104 4.4 38.2 1.0 N D:ASN93 4.4 25.6 1.0 CB D:VAL96 4.5 30.4 1.0 N D:VAL92 4.5 30.1 1.0 OD1 D:ASP98 4.5 28.4 1.0 N D:CYS97 4.5 30.4 1.0 HH22 C:ARG840 4.5 25.7 1.0 O D:ASP104 4.5 30.8 1.0 H D:GLY95 4.5 25.9 1.0 CB D:ASP94 4.6 24.6 1.0 CA D:ASP98 4.6 32.7 1.0 HB3 D:ASP104 4.6 31.3 1.0 HG12 D:VAL96 4.6 30.0 1.0 C D:ASP104 4.6 33.3 1.0 NH2 C:ARG840 4.7 26.2 1.0 CA D:VAL92 4.7 28.8 1.0 CA D:CYS97 4.7 30.5 1.0 C D:CYS97 4.7 34.1 1.0 HD11 D:ILE87 4.7 39.0 1.0 N D:GLY95 4.8 26.8 1.0 CA D:ASP94 4.8 24.5 1.0 HB3 D:ASP94 4.8 23.3 1.0 C D:VAL92 4.8 31.2 1.0 HB2 D:ARG91 4.9 30.6 1.0 HB3 D:ASP98 4.9 30.4 1.0 CD1 D:ILE87 4.9 39.6 1.0 CA D:ASP104 4.9 29.4 1.0 HA D:ASN93 5.0 27.2 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