Calcium in PDB 7k9q: Co-Crystal Structure of Alpha Glucosidase with Compound 4

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 4, PDB code: 7k9q 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)	42.49 / 2.30
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	102.876, 102.876, 241.696, 90, 90, 120
R / Rfree (%)	17.2 / 19.7

The binding sites of Calcium atom in the Co-Crystal Structure of Alpha Glucosidase with Compound 4 (pdb code 7k9q). 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 4, PDB code: 7k9q:
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 4


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1902 b:48.6 occ:1.00 OE2 B:GLU64 2.3 51.7 1.0 O B:TYR55 2.3 46.1 1.0 OD2 B:ASP63 2.4 47.6 1.0 O B:GLN50 2.4 55.5 1.0 OD1 B:ASP53 2.4 42.4 1.0 OD2 B:ASP57 2.4 50.7 1.0 CD B:GLU64 3.4 41.3 1.0 CG B:ASP57 3.5 52.0 1.0 C B:GLN50 3.5 57.4 1.0 C B:TYR55 3.5 44.9 1.0 CG B:ASP63 3.6 45.4 1.0 CG B:ASP53 3.6 52.5 1.0 CG B:GLU64 3.9 42.8 1.0 CB B:ASP57 3.9 45.4 1.0 N B:ASP57 4.0 44.3 1.0 NH1 A:ARG951 4.1 47.0 1.0 CB B:GLN50 4.1 52.9 1.0 CA B:GLN50 4.2 63.0 1.0 CB B:ASP63 4.2 51.2 1.0 N B:TYR55 4.3 41.5 1.0 OD2 B:ASP53 4.3 50.0 1.0 CA B:TYR55 4.4 42.8 1.0 OE1 B:GLU64 4.4 46.7 1.0 O B:ASP63 4.4 44.5 1.0 N B:ASP53 4.4 40.6 1.0 N B:CYS56 4.5 43.5 1.0 OD1 B:ASP63 4.5 50.2 1.0 N B:VAL51 4.5 58.9 1.0 OD1 B:ASP57 4.5 50.4 1.0 C B:CYS56 4.6 47.7 1.0 CA B:CYS56 4.6 46.3 1.0 CA B:ASP57 4.6 49.5 1.0 CB B:TYR55 4.7 38.6 1.0 CB B:ASP53 4.7 45.8 1.0 N B:ASN52 4.7 47.4 1.0 CA B:VAL51 4.7 50.9 1.0 C B:ASP63 4.9 46.0 1.0 CA B:ASP53 4.9 44.2 1.0

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1903 b:38.8 occ:1.00 O B:VAL96 2.2 38.1 1.0 O B:ARG91 2.3 38.2 1.0 OD2 B:ASP98 2.3 40.5 1.0 OE2 B:GLU105 2.4 37.3 1.0 OD1 B:ASP94 2.4 35.1 1.0 OD2 B:ASP104 2.5 41.5 1.0 CG B:ASP94 3.3 38.6 1.0 CD B:GLU105 3.4 40.3 1.0 C B:VAL96 3.4 34.3 1.0 CG B:ASP98 3.5 42.5 1.0 C B:ARG91 3.5 39.5 1.0 OD2 B:ASP94 3.6 34.5 1.0 CG B:ASP104 3.6 43.9 1.0 CG B:GLU105 3.9 43.7 1.0 CB B:ASP98 4.0 34.7 1.0 N B:ASP98 4.0 38.9 1.0 N B:VAL96 4.1 34.0 1.0 CB B:ASP104 4.2 41.9 1.0 CB B:ARG91 4.2 35.9 1.0 CA B:VAL96 4.2 36.0 1.0 CA B:ARG91 4.2 40.2 1.0 N B:ASP94 4.3 36.0 1.0 OE1 B:GLU105 4.3 35.7 1.0 N B:ASN93 4.4 36.8 1.0 N B:CYS97 4.4 36.6 1.0 CB B:VAL96 4.4 34.9 1.0 N B:VAL92 4.5 40.6 1.0 OD1 B:ASP98 4.5 37.9 1.0 CB B:ASP94 4.5 37.9 1.0 CA B:CYS97 4.6 40.7 1.0 CA B:VAL92 4.6 42.7 1.0 C B:CYS97 4.7 40.2 1.0 CA B:ASP98 4.7 40.5 1.0 O B:ASP104 4.7 43.7 1.0 OD1 B:ASP104 4.7 49.5 1.0 NH2 A:ARG840 4.7 33.6 1.0 C B:ASP104 4.8 44.7 1.0 C B:VAL92 4.8 40.2 1.0 CA B:ASP94 4.9 34.6 1.0 N B:GLY95 4.9 30.1 1.0 CD1 B:ILE87 5.0 37.0 1.0

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1202 b:42.7 occ:1.00 O D:TYR55 2.3 46.1 1.0 OD1 D:ASP53 2.4 45.1 1.0 OD2 D:ASP63 2.4 43.9 1.0 OD2 D:ASP57 2.4 48.6 1.0 O D:GLN50 2.4 54.8 1.0 OE2 D:GLU64 2.4 49.1 1.0 CG D:ASP57 3.4 46.9 1.0 CD D:GLU64 3.5 45.1 1.0 C D:GLN50 3.5 59.2 1.0 C D:TYR55 3.5 41.1 1.0 CG D:ASP53 3.5 53.1 1.0 CG D:ASP63 3.6 44.2 1.0 CB D:ASP57 3.9 46.0 1.0 CG D:GLU64 3.9 47.7 1.0 N D:ASP57 4.0 50.1 1.0 CA D:GLN50 4.1 61.0 1.0 CB D:GLN50 4.1 50.9 1.0 CB D:ASP63 4.2 52.7 1.0 OD2 D:ASP53 4.2 53.0 1.0 N D:TYR55 4.2 39.7 1.0 NH1 C:ARG951 4.3 44.1 1.0 CA D:TYR55 4.3 35.1 1.0 N D:ASP53 4.4 41.7 1.0 OD1 D:ASP57 4.4 49.6 1.0 O D:ASP63 4.5 42.8 1.0 N D:CYS56 4.5 41.1 1.0 OE1 D:GLU64 4.5 43.9 1.0 N D:VAL51 4.5 54.2 1.0 OD1 D:ASP63 4.5 47.5 1.0 C D:CYS56 4.6 46.9 1.0 CA D:CYS56 4.6 43.9 1.0 CB D:TYR55 4.6 39.1 1.0 CB D:ASP53 4.6 45.4 1.0 CA D:ASP57 4.6 49.2 1.0 CA D:VAL51 4.8 48.3 1.0 N D:ASN52 4.8 44.2 1.0 C D:ASP63 4.9 46.5 1.0 CA D:ASP53 4.9 42.5 1.0 C D:ASP53 5.0 49.6 1.0

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1203 b:40.4 occ:1.00 O D:VAL96 2.2 39.7 1.0 O D:ARG91 2.3 38.8 1.0 OE2 D:GLU105 2.3 36.2 1.0 OD1 D:ASP94 2.4 35.1 1.0 OD2 D:ASP98 2.4 38.9 1.0 OD2 D:ASP104 2.5 40.9 1.0 CD D:GLU105 3.3 36.0 1.0 CG D:ASP94 3.3 37.9 1.0 C D:VAL96 3.4 40.1 1.0 C D:ARG91 3.5 38.5 1.0 CG D:ASP98 3.6 45.2 1.0 CG D:ASP104 3.6 43.4 1.0 OD2 D:ASP94 3.7 33.4 1.0 CG D:GLU105 3.9 39.7 1.0 N D:VAL96 3.9 35.3 1.0 CA D:VAL96 4.1 39.1 1.0 N D:ASP98 4.1 40.3 1.0 CB D:ASP98 4.1 44.0 1.0 CA D:ARG91 4.2 38.6 1.0 CB D:ASP104 4.2 41.5 1.0 N D:ASP94 4.2 36.5 1.0 CB D:ARG91 4.2 35.5 1.0 OE1 D:GLU105 4.2 36.1 1.0 CB D:VAL96 4.3 40.2 1.0 N D:CYS97 4.4 39.9 1.0 N D:ASN93 4.4 34.6 1.0 N D:VAL92 4.5 37.9 1.0 CB D:ASP94 4.6 32.4 1.0 NH2 C:ARG840 4.6 35.2 1.0 OD1 D:ASP98 4.6 43.4 1.0 O D:ASP104 4.6 48.2 1.0 OD1 D:ASP104 4.7 50.0 1.0 CA D:CYS97 4.7 39.1 1.0 CA D:VAL92 4.7 34.4 1.0 C D:CYS97 4.7 41.2 1.0 CA D:ASP98 4.8 43.9 1.0 C D:ASP104 4.8 43.1 1.0 N D:GLY95 4.8 35.4 1.0 CA D:ASP94 4.8 35.6 1.0 C D:VAL92 4.8 37.2 1.0

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Alpha Glucosidase with Compound 4 To Be Published.