Calcium in PDB 7jty: Co-Crystal Structure of Alpha Glucosidase with Compound 1

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 1, PDB code: 7jty 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)	42.17 / 2.21
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	102.561, 102.561, 239.559, 90, 90, 120
R / Rfree (%)	17 / 20.3

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

Calcium binding site 1 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Co-Crystal Structure of Alpha Glucosidase with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1102 b:39.8 occ:1.00 OE2 B:GLU64 2.3 39.9 1.0 O B:TYR55 2.3 39.2 1.0 OD2 B:ASP57 2.3 44.0 1.0 O B:GLN50 2.3 44.6 1.0 OD2 B:ASP63 2.4 48.6 1.0 OD1 B:ASP53 2.4 39.5 1.0 CD B:GLU64 3.4 36.7 1.0 CG B:ASP57 3.4 48.5 1.0 C B:GLN50 3.5 47.6 1.0 C B:TYR55 3.5 40.7 1.0 CG B:ASP63 3.5 47.1 1.0 CG B:ASP53 3.6 47.4 1.0 CG B:GLU64 3.9 40.7 1.0 CB B:ASP57 3.9 40.8 1.0 N B:ASP57 4.0 41.3 1.0 CB B:ASP63 4.1 44.5 1.0 NH1 A:ARG951 4.1 42.4 1.0 CA B:GLN50 4.2 55.5 1.0 CB B:GLN50 4.2 41.7 1.0 N B:TYR55 4.2 38.6 1.0 CA B:TYR55 4.3 34.7 1.0 N B:ASP53 4.3 36.9 1.0 OD2 B:ASP53 4.4 45.6 1.0 O B:ASP63 4.4 41.9 1.0 OE1 B:GLU64 4.4 35.9 1.0 OD1 B:ASP57 4.5 45.6 1.0 N B:VAL51 4.5 50.1 1.0 N B:CYS56 4.5 38.5 1.0 OD1 B:ASP63 4.5 40.5 1.0 CB B:ASP53 4.6 38.2 1.0 CA B:CYS56 4.6 46.7 1.0 CB B:TYR55 4.6 40.4 1.0 C B:CYS56 4.6 43.2 1.0 CA B:ASP57 4.7 42.3 1.0 N B:ASN52 4.7 40.0 1.0 CA B:VAL51 4.7 44.7 1.0 CD1 B:ILE46 4.8 53.2 1.0 C B:ASP63 4.8 37.7 1.0 CA B:ASP53 4.9 41.7 1.0 N B:ASP54 5.0 36.6 1.0 C B:VAL51 5.0 46.1 1.0

Calcium binding site 2 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Co-Crystal Structure of Alpha Glucosidase with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1103 b:35.2 occ:1.00 O B:VAL96 2.1 33.7 1.0 O B:ARG91 2.3 36.2 1.0 OD2 B:ASP98 2.4 36.9 1.0 OE2 B:GLU105 2.4 34.1 1.0 OD1 B:ASP94 2.4 33.2 1.0 OD2 B:ASP104 2.5 40.6 1.0 C B:VAL96 3.3 32.3 1.0 CG B:ASP94 3.3 31.2 1.0 CD B:GLU105 3.3 34.1 1.0 C B:ARG91 3.5 34.9 1.0 CG B:ASP98 3.5 37.9 1.0 CG B:ASP104 3.6 42.9 1.0 OD2 B:ASP94 3.7 36.4 1.0 CG B:GLU105 3.9 35.8 1.0 N B:VAL96 3.9 29.8 1.0 N B:ASP98 4.0 34.3 1.0 CA B:VAL96 4.0 38.7 1.0 CB B:ASP98 4.0 31.8 1.0 N B:ASP94 4.2 38.0 1.0 CB B:ASP104 4.2 36.4 1.0 CB B:ARG91 4.2 35.9 1.0 CA B:ARG91 4.2 32.0 1.0 CB B:VAL96 4.3 33.5 1.0 OE1 B:GLU105 4.3 32.0 1.0 N B:CYS97 4.3 35.8 1.0 N B:ASN93 4.4 33.6 1.0 N B:VAL92 4.5 34.3 1.0 OD1 B:ASP98 4.5 39.8 1.0 O B:ASP104 4.6 38.8 1.0 CB B:ASP94 4.6 33.2 1.0 CA B:CYS97 4.6 33.0 1.0 C B:CYS97 4.6 35.1 1.0 OD1 B:ASP104 4.7 44.4 1.0 NH2 A:ARG840 4.7 30.8 1.0 CA B:ASP98 4.7 35.7 1.0 CA B:VAL92 4.7 35.7 1.0 C B:ASP104 4.8 37.4 1.0 CA B:ASP94 4.8 31.4 1.0 N B:GLY95 4.8 32.3 1.0 C B:VAL92 4.8 28.8 1.0 CG1 B:VAL96 5.0 32.2 1.0 C B:ASP94 5.0 33.6 1.0

Calcium binding site 3 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Co-Crystal Structure of Alpha Glucosidase with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:41.0 occ:1.00 O D:TYR55 2.3 33.6 1.0 OE2 D:GLU64 2.3 46.0 1.0 OD2 D:ASP63 2.3 41.3 1.0 OD1 D:ASP53 2.3 42.5 1.0 O D:GLN50 2.4 45.7 1.0 OD2 D:ASP57 2.5 42.0 1.0 CD D:GLU64 3.3 40.2 1.0 C D:GLN50 3.5 49.3 1.0 CG D:ASP63 3.5 48.4 1.0 C D:TYR55 3.5 34.6 1.0 CG D:ASP53 3.5 41.8 1.0 CG D:ASP57 3.5 39.0 1.0 CG D:GLU64 3.8 34.0 1.0 N D:ASP57 4.0 46.2 1.0 CB D:ASP57 4.0 38.2 1.0 CA D:GLN50 4.1 54.6 1.0 CB D:GLN50 4.2 46.6 1.0 CB D:ASP63 4.2 47.8 1.0 N D:TYR55 4.2 31.6 1.0 OD2 D:ASP53 4.2 44.0 1.0 NH1 C:ARG951 4.3 46.0 1.0 CA D:TYR55 4.3 36.7 1.0 N D:ASP53 4.4 35.0 1.0 OE1 D:GLU64 4.4 34.9 1.0 OD1 D:ASP63 4.5 40.2 1.0 N D:VAL51 4.5 48.7 1.0 O D:ASP63 4.5 46.3 1.0 N D:CYS56 4.5 33.5 1.0 OD1 D:ASP57 4.6 46.1 1.0 CB D:ASP53 4.6 44.0 1.0 CA D:CYS56 4.6 38.6 1.0 C D:CYS56 4.6 42.7 1.0 CB D:TYR55 4.6 38.1 1.0 CA D:ASP57 4.7 43.9 1.0 CA D:VAL51 4.7 39.1 1.0 N D:ASN52 4.7 41.4 1.0 C D:ASP63 4.8 43.4 1.0 CA D:ASP53 4.9 38.5 1.0 CD1 D:ILE46 4.9 55.3 1.0 N D:ASP54 5.0 38.8 1.0 C D:ASP53 5.0 41.4 1.0

Calcium binding site 4 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Co-Crystal Structure of Alpha Glucosidase with Compound 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca602 b:33.8 occ:1.00 O D:VAL96 2.2 34.5 1.0 OD2 D:ASP98 2.3 34.1 1.0 O D:ARG91 2.3 33.5 1.0 OE2 D:GLU105 2.4 28.1 1.0 OD2 D:ASP104 2.4 37.3 1.0 OD1 D:ASP94 2.5 34.8 1.0 CD D:GLU105 3.4 38.2 1.0 CG D:ASP94 3.4 37.0 1.0 C D:VAL96 3.4 36.6 1.0 CG D:ASP98 3.4 39.7 1.0 C D:ARG91 3.5 30.8 1.0 CG D:ASP104 3.5 42.7 1.0 OD2 D:ASP94 3.8 32.1 1.0 CG D:GLU105 3.9 39.3 1.0 CB D:ASP98 3.9 37.5 1.0 N D:ASP98 4.0 36.6 1.0 N D:VAL96 4.0 35.8 1.0 CB D:ASP104 4.1 43.1 1.0 CA D:VAL96 4.1 37.7 1.0 N D:ASP94 4.2 37.8 1.0 CB D:ARG91 4.2 35.5 1.0 CA D:ARG91 4.2 34.8 1.0 CB D:VAL96 4.3 35.0 1.0 O D:ASP104 4.4 40.2 1.0 OE1 D:GLU105 4.4 37.9 1.0 N D:ASN93 4.4 35.1 1.0 N D:CYS97 4.4 35.5 1.0 OD1 D:ASP98 4.5 39.5 1.0 N D:VAL92 4.5 34.3 1.0 OD1 D:ASP104 4.5 45.4 1.0 CA D:ASP98 4.6 35.5 1.0 CB D:ASP94 4.6 30.1 1.0 NH2 C:ARG840 4.6 34.1 1.0 CA D:CYS97 4.7 38.5 1.0 C D:CYS97 4.7 36.3 1.0 CA D:VAL92 4.7 36.8 1.0 C D:ASP104 4.7 37.5 1.0 C D:VAL92 4.8 34.2 1.0 CA D:ASP94 4.8 34.7 1.0 N D:GLY95 4.9 36.1 1.0

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Mouse Alpha Glucosidase (N97D) with Compound 1 To Be Published.