Calcium in PDB 5hjo: Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Substrate Analogue

All present enzymatic activity of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Substrate Analogue:
3.2.1.84;

The structure of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Substrate Analogue, PDB code: 5hjo 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)	103.10 / 2.29
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	127.050, 176.440, 103.480, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 23.6

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

Calcium binding site 1 out of 4 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Substrate Analogue


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 Bound Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:39.9 occ:1.00 O B:TYR55 2.3 38.9 1.0 O B:GLN50 2.3 34.2 1.0 OE2 B:GLU64 2.3 35.7 1.0 OD1 B:ASP53 2.3 38.9 1.0 OD2 B:ASP57 2.3 42.2 1.0 OD2 B:ASP63 2.4 37.3 1.0 H B:ASP53 3.3 35.8 1.0 H B:ASP57 3.3 34.7 1.0 HH21 A:ARG951 3.4 43.2 1.0 HG2 B:GLU64 3.4 36.2 1.0 H B:TYR55 3.4 35.6 1.0 CD B:GLU64 3.4 33.7 1.0 C B:GLN50 3.4 36.9 1.0 HB3 B:GLN50 3.4 39.9 1.0 CG B:ASP57 3.5 44.2 1.0 C B:TYR55 3.5 38.7 1.0 CG B:ASP53 3.5 42.3 1.0 HB2 B:ASP57 3.5 36.5 1.0 CG B:ASP63 3.6 32.5 1.0 HB2 B:ASP63 3.7 29.9 1.0 CG B:GLU64 3.9 34.4 1.0 HB3 B:TYR55 3.9 33.8 1.0 HA B:CYS56 3.9 32.1 1.0 N B:ASP57 4.0 34.6 1.0 HA B:GLN50 4.0 39.0 1.0 CB B:ASP57 4.0 37.5 1.0 HA B:VAL51 4.1 34.2 1.0 HG3 B:GLU64 4.1 33.6 1.0 CA B:GLN50 4.2 38.2 1.0 NH2 A:ARG951 4.2 42.3 1.0 HD2 B:TYR55 4.2 32.6 1.0 CB B:ASP63 4.2 30.1 1.0 OD2 B:ASP53 4.3 40.4 1.0 HH22 A:ARG951 4.3 41.6 1.0 HD12 B:ILE46 4.3 36.9 1.0 N B:TYR55 4.3 34.2 1.0 CB B:GLN50 4.3 39.7 1.0 N B:ASP53 4.3 35.3 1.0 CA B:TYR55 4.3 32.8 1.0 H B:ASN52 4.4 36.6 1.0 N B:VAL51 4.4 32.8 1.0 N B:CYS56 4.4 34.3 1.0 OE1 B:GLU64 4.5 36.8 1.0 O B:ASP63 4.5 35.8 1.0 OD1 B:ASP57 4.5 42.9 1.0 HB3 B:ASP53 4.5 33.2 1.0 CB B:ASP53 4.5 34.4 1.0 CA B:CYS56 4.5 33.7 1.0 OD1 B:ASP63 4.6 30.6 1.0 C B:CYS56 4.6 36.5 1.0 CB B:TYR55 4.6 34.5 1.0 CA B:VAL51 4.7 33.2 1.0 CA B:ASP57 4.7 36.5 1.0 N B:ASN52 4.7 37.2 1.0 CA B:ASP53 4.8 34.4 1.0 H B:ASP54 4.8 38.5 1.0 HD11 B:ILE46 4.8 36.5 1.0 C B:ASP63 4.9 34.7 1.0 CD1 B:ILE46 4.9 37.6 1.0 C B:VAL51 5.0 37.5 1.0 HB3 B:ASP63 5.0 30.6 1.0 HB2 B:GLN50 5.0 40.0 1.0 HB3 B:ASP57 5.0 37.5 1.0 C B:ASP53 5.0 39.0 1.0

Calcium binding site 2 out of 4 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Substrate Analogue


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 Bound Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:36.3 occ:1.00 OD1 B:ASP98 2.3 34.2 1.0 O B:VAL96 2.3 37.9 1.0 OE2 B:GLU105 2.3 30.7 1.0 O B:ARG91 2.3 42.7 1.0 OD1 B:ASP94 2.3 31.6 1.0 OD2 B:ASP104 2.3 30.7 1.0 H B:ASP94 3.2 35.3 1.0 H B:ASP98 3.2 43.6 1.0 H B:VAL96 3.3 34.4 1.0 CG B:ASP94 3.3 36.6 1.0 CD B:GLU105 3.3 36.2 1.0 HG2 B:GLU105 3.4 33.1 1.0 HB3 B:ARG91 3.4 32.2 1.0 CG B:ASP98 3.4 33.2 1.0 C B:VAL96 3.4 39.0 1.0 HB2 B:ASP104 3.4 42.8 1.0 C B:ARG91 3.5 40.2 1.0 CG B:ASP104 3.5 40.9 1.0 HB2 B:ASP98 3.5 42.2 1.0 HB B:VAL96 3.6 37.2 1.0 OD2 B:ASP94 3.8 34.0 1.0 CG B:GLU105 3.9 32.9 1.0 N B:ASP98 4.0 44.4 1.0 CB B:ASP98 4.0 41.7 1.0 HA B:ARG91 4.0 33.1 1.0 H B:ASN93 4.0 39.0 1.0 CB B:ASP104 4.0 41.0 1.0 N B:VAL96 4.1 33.1 1.0 HH11 A:ARG840 4.1 48.3 1.0 HA B:VAL92 4.1 34.3 1.0 CA B:ARG91 4.2 33.1 1.0 CA B:VAL96 4.2 32.5 1.0 HA B:CYS97 4.2 42.6 1.0 HG3 B:GLU105 4.2 32.4 1.0 N B:ASP94 4.2 34.8 1.0 CB B:ARG91 4.2 31.8 1.0 OE1 B:GLU105 4.3 35.5 1.0 CB B:VAL96 4.3 36.9 1.0 HD12 B:ILE87 4.4 41.5 1.0 OD2 B:ASP98 4.4 36.5 1.0 N B:CYS97 4.5 39.8 1.0 N B:VAL92 4.5 38.0 1.0 N B:ASN93 4.5 37.2 1.0 CB B:ASP94 4.5 36.0 1.0 H B:GLY95 4.5 37.6 1.0 OD1 B:ASP104 4.5 39.5 1.0 HH12 A:ARG840 4.5 48.9 1.0 HG12 B:VAL96 4.5 37.1 1.0 O B:ASP104 4.6 34.7 1.0 CA B:ASP98 4.6 42.9 1.0 NH1 A:ARG840 4.7 48.4 1.0 CA B:CYS97 4.7 41.5 1.0 C B:CYS97 4.7 48.6 1.0 CA B:VAL92 4.7 35.6 1.0 HB3 B:ASP104 4.8 41.1 1.0 C B:ASP104 4.8 39.4 1.0 HB3 B:ASP94 4.8 37.4 1.0 CA B:ASP94 4.8 34.5 1.0 N B:GLY95 4.8 37.1 1.0 HD11 B:ILE87 4.8 42.3 1.0 HB2 B:ARG91 4.9 31.1 1.0 C B:VAL92 4.9 38.1 1.0 HB3 B:ASP98 4.9 40.4 1.0 CD1 B:ILE87 5.0 41.8 1.0

Calcium binding site 3 out of 4 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Substrate Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca202 b:37.0 occ:1.00 OE2 D:GLU64 2.1 44.0 1.0 O D:GLN50 2.3 39.4 1.0 O D:TYR55 2.3 38.3 1.0 OD2 D:ASP63 2.3 39.7 1.0 OD1 D:ASP53 2.3 37.2 1.0 OD2 D:ASP57 2.3 43.2 1.0 CD D:GLU64 3.2 57.1 1.0 H D:TYR55 3.3 31.5 1.0 H D:ASP53 3.3 37.9 1.0 HH21 C:ARG951 3.3 54.6 1.0 C D:GLN50 3.4 39.0 1.0 CG D:ASP53 3.5 38.8 1.0 CG D:ASP57 3.5 40.6 1.0 C D:TYR55 3.5 39.0 1.0 H D:ASP57 3.5 33.0 1.0 HB3 D:GLN50 3.5 38.3 1.0 CG D:ASP63 3.5 35.6 1.0 HG2 D:GLU64 3.5 40.8 1.0 HB2 D:ASP57 3.7 37.6 1.0 HB3 D:TYR55 3.9 32.8 1.0 HB2 D:ASP63 3.9 31.9 1.0 CG D:GLU64 3.9 40.6 1.0 HA D:GLN50 3.9 36.6 1.0 HA D:VAL51 3.9 33.9 1.0 H D:ASN52 4.1 43.0 1.0 N D:ASP57 4.1 34.3 1.0 NH2 C:ARG951 4.1 54.6 1.0 CA D:GLN50 4.1 37.2 1.0 CB D:ASP57 4.1 36.9 1.0 HH22 C:ARG951 4.1 54.9 1.0 N D:TYR55 4.1 32.8 1.0 HA D:CYS56 4.2 34.3 1.0 HG3 D:GLU64 4.2 40.1 1.0 O D:ASP63 4.2 36.8 1.0 OE1 D:GLU64 4.2 36.8 1.0 OD2 D:ASP53 4.3 40.5 1.0 N D:ASP53 4.3 38.5 1.0 CA D:TYR55 4.3 33.2 1.0 HB3 D:ASP53 4.3 37.2 1.0 N D:VAL51 4.3 35.5 1.0 CB D:ASP63 4.3 32.9 1.0 CB D:GLN50 4.3 38.3 1.0 HD2 D:TYR55 4.4 32.2 1.0 CB D:ASP53 4.4 37.9 1.0 OD1 D:ASP57 4.4 40.0 1.0 OD1 D:ASP63 4.4 34.1 1.0 HD12 D:ILE46 4.5 38.5 1.0 N D:CYS56 4.5 35.1 1.0 N D:ASN52 4.5 43.2 1.0 CA D:VAL51 4.5 34.5 1.0 C D:CYS56 4.6 36.3 1.0 CB D:TYR55 4.6 33.2 1.0 H D:ASP54 4.6 37.5 1.0 CA D:CYS56 4.7 34.5 1.0 CA D:ASP53 4.7 37.7 1.0 HD11 D:ILE46 4.7 38.5 1.0 CA D:ASP57 4.7 36.6 1.0 C D:ASP63 4.8 34.4 1.0 C D:VAL51 4.8 45.0 1.0 N D:ASP54 4.8 37.6 1.0 C D:ASP53 4.9 40.6 1.0

Calcium binding site 4 out of 4 in the Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Substrate Analogue


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Murine Endoplasmic Reticulum Alpha-Glucosidase II with Bound Substrate Analogue within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca203 b:36.6 occ:1.00 OD2 D:ASP104 2.2 40.2 1.0 O D:VAL96 2.2 37.3 1.0 OE2 D:GLU105 2.3 31.7 1.0 OD1 D:ASP98 2.3 34.9 1.0 O D:ARG91 2.3 39.7 1.0 OD1 D:ASP94 2.4 33.5 1.0 H D:ASP98 3.2 41.2 1.0 CD D:GLU105 3.3 32.9 1.0 H D:ASP94 3.3 35.3 1.0 HG2 D:GLU105 3.3 41.3 1.0 H D:VAL96 3.3 32.4 1.0 CG D:ASP104 3.4 40.6 1.0 CG D:ASP94 3.4 37.0 1.0 C D:VAL96 3.4 39.4 1.0 CG D:ASP98 3.4 38.8 1.0 HB3 D:ARG91 3.4 31.8 1.0 HB2 D:ASP98 3.5 43.7 1.0 C D:ARG91 3.5 37.8 1.0 HB2 D:ASP104 3.5 40.5 1.0 HB D:VAL96 3.6 35.0 1.0 CG D:GLU105 3.8 41.8 1.0 OD2 D:ASP94 3.9 31.6 1.0 H D:ASN93 3.9 35.6 1.0 N D:ASP98 3.9 42.3 1.0 CB D:ASP98 4.0 42.9 1.0 CB D:ASP104 4.1 38.9 1.0 N D:VAL96 4.1 31.4 1.0 HA D:CYS97 4.1 42.6 1.0 HA D:ARG91 4.1 32.3 1.0 HG3 D:GLU105 4.1 41.6 1.0 CA D:VAL96 4.2 31.4 1.0 CA D:ARG91 4.2 31.4 1.0 HH11 C:ARG840 4.3 43.9 1.0 HA D:VAL92 4.3 36.9 1.0 N D:ASP94 4.3 34.9 1.0 CB D:ARG91 4.3 31.4 1.0 OE1 D:GLU105 4.3 30.5 1.0 O D:ASP104 4.4 35.2 1.0 OD1 D:ASP104 4.4 40.7 1.0 CB D:VAL96 4.4 35.0 1.0 N D:CYS97 4.4 40.8 1.0 HD12 D:ILE87 4.4 31.6 1.0 N D:ASN93 4.5 34.9 1.0 OD2 D:ASP98 4.5 40.2 1.0 H D:GLY95 4.5 35.2 1.0 HG12 D:VAL96 4.6 33.1 1.0 CB D:ASP94 4.6 36.7 1.0 N D:VAL92 4.6 36.3 1.0 CA D:CYS97 4.6 42.7 1.0 C D:ASP104 4.6 40.0 1.0 CA D:ASP98 4.6 41.8 1.0 C D:CYS97 4.6 47.0 1.0 HD11 D:ILE87 4.7 31.8 1.0 HH12 C:ARG840 4.8 43.9 1.0 CA D:VAL92 4.8 36.0 1.0 NH1 C:ARG840 4.8 43.8 1.0 HB3 D:ASP104 4.8 38.0 1.0 N D:GLY95 4.8 33.6 1.0 CA D:ASP94 4.9 35.5 1.0 HB3 D:ASP94 4.9 37.4 1.0 HB2 D:ARG91 4.9 31.5 1.0 HA D:ASN93 4.9 34.8 1.0 HB3 D:ASP98 4.9 43.6 1.0 C D:VAL92 5.0 38.8 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