Calcium in PDB 7l9e: Crystal Structure of Apo-Alpha Glucosidase

All present enzymatic activity of Crystal Structure of Apo-Alpha Glucosidase:
3.2.1.207;

The structure of Crystal Structure of Apo-Alpha Glucosidase, PDB code: 7l9e was solved by S.S.Karade, R.A.Mariuzza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.33 / 2.29
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	102.966, 102.966, 240.596, 90, 90, 120
R / Rfree (%)	18 / 20.6

The binding sites of Calcium atom in the Crystal Structure of Apo-Alpha Glucosidase (pdb code 7l9e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Apo-Alpha Glucosidase, PDB code: 7l9e:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Apo-Alpha Glucosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Apo-Alpha Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:49.5 occ:1.00 O B:TYR55 2.3 50.4 1.0 OD1 B:ASP53 2.4 55.0 1.0 O B:GLN50 2.4 57.9 1.0 OE2 B:GLU64 2.4 56.3 1.0 OD2 B:ASP57 2.4 52.5 1.0 OD2 B:ASP63 2.4 54.4 1.0 CD B:GLU64 3.4 43.6 1.0 CG B:ASP57 3.5 56.1 1.0 C B:GLN50 3.5 63.1 1.0 CG B:ASP53 3.5 57.2 1.0 C B:TYR55 3.5 42.1 1.0 CG B:ASP63 3.6 61.5 1.0 CG B:GLU64 3.9 47.9 1.0 CB B:ASP57 4.0 45.9 1.0 N B:ASP57 4.0 46.0 1.0 NH1 A:ARG951 4.1 46.3 1.0 OD2 B:ASP53 4.2 56.0 1.0 CA B:GLN50 4.2 65.0 1.0 CB B:ASP63 4.2 54.6 1.0 CB B:GLN50 4.3 60.8 1.0 N B:TYR55 4.3 49.4 1.0 O B:ASP63 4.4 43.8 1.0 CA B:TYR55 4.4 44.7 1.0 N B:ASP53 4.4 42.5 1.0 OE1 B:GLU64 4.5 40.5 1.0 OD1 B:ASP57 4.5 56.7 1.0 N B:CYS56 4.5 43.1 1.0 N B:VAL51 4.5 56.7 1.0 OD1 B:ASP63 4.5 55.1 1.0 CB B:ASP53 4.6 49.2 1.0 CA B:CYS56 4.6 57.3 1.0 C B:CYS56 4.6 52.9 1.0 CB B:TYR55 4.7 40.0 1.0 CA B:VAL51 4.7 45.4 1.0 CA B:ASP57 4.7 52.6 1.0 N B:ASN52 4.7 53.0 1.0 C B:ASP63 4.8 48.0 1.0 CA B:ASP53 4.9 49.7 1.0 C B:VAL51 5.0 60.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Apo-Alpha Glucosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Apo-Alpha Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:41.2 occ:1.00 O B:VAL96 2.2 41.9 1.0 O B:ARG91 2.3 41.7 1.0 OE2 B:GLU105 2.3 38.4 1.0 OD1 B:ASP94 2.5 43.5 1.0 OD2 B:ASP104 2.5 47.7 1.0 OD2 B:ASP98 2.5 42.2 1.0 CD B:GLU105 3.4 42.4 1.0 C B:VAL96 3.4 37.4 1.0 CG B:ASP94 3.4 35.7 1.0 C B:ARG91 3.5 38.5 1.0 CG B:ASP98 3.6 50.8 1.0 CG B:ASP104 3.6 51.3 1.0 OD2 B:ASP94 3.7 44.5 1.0 CG B:GLU105 3.9 47.4 1.0 N B:VAL96 3.9 37.1 1.0 CA B:VAL96 4.1 44.3 1.0 CB B:ASP98 4.1 40.2 1.0 N B:ASP98 4.1 44.8 1.0 CB B:ASP104 4.2 45.1 1.0 N B:ASP94 4.2 45.9 1.0 CA B:ARG91 4.2 40.2 1.0 CB B:ARG91 4.3 35.9 1.0 CB B:VAL96 4.3 42.2 1.0 OE1 B:GLU105 4.4 31.0 1.0 N B:ASN93 4.4 44.7 1.0 N B:CYS97 4.4 41.1 1.0 N B:VAL92 4.5 43.3 1.0 O B:ASP104 4.5 46.9 1.0 CB B:ASP94 4.6 35.3 1.0 CA B:VAL92 4.7 40.9 1.0 OD1 B:ASP104 4.7 52.5 1.0 CA B:CYS97 4.7 43.7 1.0 NH2 A:ARG840 4.7 35.0 1.0 OD1 B:ASP98 4.7 53.0 1.0 C B:CYS97 4.7 38.0 1.0 CA B:ASP98 4.8 44.3 1.0 C B:ASP104 4.8 39.7 1.0 C B:VAL92 4.8 40.0 1.0 N B:GLY95 4.8 40.7 1.0 CA B:ASP94 4.8 29.9 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Apo-Alpha Glucosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Apo-Alpha Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:48.1 occ:1.00 OD1 D:ASP53 2.3 50.5 1.0 O D:TYR55 2.3 44.6 1.0 OD2 D:ASP63 2.4 53.9 1.0 OD2 D:ASP57 2.4 45.9 1.0 OE2 D:GLU64 2.4 52.7 1.0 O D:GLN50 2.4 56.5 1.0 CD D:GLU64 3.4 45.8 1.0 CG D:ASP53 3.5 52.0 1.0 CG D:ASP57 3.5 43.7 1.0 C D:TYR55 3.5 43.5 1.0 C D:GLN50 3.5 66.0 1.0 CG D:ASP63 3.6 59.6 1.0 CG D:GLU64 3.9 39.3 1.0 CB D:ASP57 4.0 40.2 1.0 N D:ASP57 4.1 50.1 1.0 OD2 D:ASP53 4.1 55.7 1.0 CA D:GLN50 4.2 65.5 1.0 N D:TYR55 4.2 38.4 1.0 CB D:ASP63 4.2 55.4 1.0 CB D:GLN50 4.2 55.7 1.0 CA D:TYR55 4.3 37.3 1.0 O D:ASP63 4.3 54.2 1.0 NH1 C:ARG951 4.3 54.1 1.0 N D:ASP53 4.4 37.9 1.0 N D:CYS56 4.5 39.9 1.0 OE1 D:GLU64 4.5 47.8 1.0 N D:VAL51 4.5 55.5 1.0 OD1 D:ASP57 4.5 56.6 1.0 CB D:ASP53 4.5 52.1 1.0 OD1 D:ASP63 4.6 56.4 1.0 CB D:TYR55 4.6 45.5 1.0 CA D:CYS56 4.6 43.0 1.0 C D:CYS56 4.6 45.6 1.0 N D:ASN52 4.7 46.0 1.0 CA D:ASP57 4.7 48.6 1.0 CA D:VAL51 4.7 43.4 1.0 C D:ASP63 4.8 52.6 1.0 CA D:ASP53 4.8 49.6 1.0 C D:ASP53 5.0 47.8 1.0 N D:ASP54 5.0 47.4 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Apo-Alpha Glucosidase


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Apo-Alpha Glucosidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca602 b:41.0 occ:1.00 O D:VAL96 2.3 42.6 1.0 OE2 D:GLU105 2.3 39.2 1.0 O D:ARG91 2.3 34.9 1.0 OD2 D:ASP98 2.4 35.6 1.0 OD2 D:ASP104 2.5 47.5 1.0 OD1 D:ASP94 2.5 40.5 1.0 CG D:ASP94 3.3 41.0 1.0 CD D:GLU105 3.4 44.2 1.0 C D:VAL96 3.4 37.7 1.0 C D:ARG91 3.5 37.5 1.0 CG D:ASP98 3.5 50.2 1.0 CG D:ASP104 3.6 50.8 1.0 OD2 D:ASP94 3.7 37.7 1.0 CG D:GLU105 3.9 43.8 1.0 CB D:ASP98 4.0 46.2 1.0 N D:VAL96 4.0 37.5 1.0 N D:ASP98 4.1 47.0 1.0 CA D:VAL96 4.1 40.5 1.0 CB D:ASP104 4.2 44.5 1.0 CB D:ARG91 4.2 45.1 1.0 CA D:ARG91 4.2 43.2 1.0 N D:ASP94 4.2 42.0 1.0 CB D:VAL96 4.4 43.3 1.0 OE1 D:GLU105 4.4 41.2 1.0 N D:ASN93 4.4 37.9 1.0 N D:CYS97 4.5 44.2 1.0 O D:ASP104 4.5 39.5 1.0 N D:VAL92 4.5 42.3 1.0 CB D:ASP94 4.6 40.8 1.0 OD1 D:ASP98 4.6 49.2 1.0 NH2 C:ARG840 4.6 41.4 1.0 OD1 D:ASP104 4.6 50.2 1.0 CA D:ASP98 4.7 45.6 1.0 C D:CYS97 4.7 41.0 1.0 CA D:CYS97 4.7 44.4 1.0 CA D:VAL92 4.7 40.2 1.0 C D:ASP104 4.8 40.6 1.0 CA D:ASP94 4.8 34.0 1.0 C D:VAL92 4.8 39.6 1.0 N D:GLY95 4.9 40.9 1.0

S.S.Karade, M.L.Hill, J.L.Kiappes, R.Manne, B.Aakula, N.Zitzmann, K.L.Warfield, A.M.Treston, R.A.Mariuzza. N-Substituted Valiolamine Derivatives As Potent Inhibitors of Endoplasmic Reticulum Alpha-Glucosidases I and II with Antiviral Activity. J.Med.Chem. 2021.
ISSN: ISSN 0022-2623
PubMed: 34870992
DOI: 10.1021/ACS.JMEDCHEM.1C01377