Calcium in PDB 7k9o: Co-Crystal Structure of Alpha Glucosidase with Compound 3

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 3, PDB code: 7k9o 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)	39.94 / 2.30
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	102.716, 102.716, 239.625, 90, 90, 120
R / Rfree (%)	21 / 23.8

The binding sites of Calcium atom in the Co-Crystal Structure of Alpha Glucosidase with Compound 3 (pdb code 7k9o). 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 3, PDB code: 7k9o:
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 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca601 b:51.4 occ:1.00 OE2 B:GLU64 2.3 51.6 1.0 O B:TYR55 2.3 50.1 1.0 OD2 B:ASP57 2.4 52.8 1.0 OD1 B:ASP53 2.4 49.0 1.0 O B:GLN50 2.4 56.8 1.0 OD2 B:ASP63 2.5 53.1 1.0 CD B:GLU64 3.4 47.7 1.0 CG B:ASP57 3.5 56.6 1.0 C B:GLN50 3.5 59.0 1.0 C B:TYR55 3.5 45.4 1.0 CG B:ASP53 3.6 53.2 1.0 CG B:ASP63 3.7 54.2 1.0 CG B:GLU64 4.0 49.0 1.0 CB B:ASP57 4.0 54.2 1.0 NH1 A:ARG951 4.1 48.2 1.0 N B:ASP57 4.1 48.5 1.0 CA B:GLN50 4.1 63.1 1.0 CB B:GLN50 4.2 59.2 1.0 N B:TYR55 4.2 46.8 1.0 OD2 B:ASP53 4.3 51.9 1.0 CA B:TYR55 4.3 46.4 1.0 CB B:ASP63 4.4 52.8 1.0 N B:ASP53 4.4 42.5 1.0 OE1 B:GLU64 4.4 46.1 1.0 OD1 B:ASP57 4.5 53.0 1.0 N B:VAL51 4.5 57.4 1.0 N B:CYS56 4.5 46.8 1.0 O B:ASP63 4.5 49.7 1.0 CB B:ASP53 4.5 50.0 1.0 CB B:TYR55 4.6 45.1 1.0 CA B:CYS56 4.6 52.6 1.0 OD1 B:ASP63 4.7 54.7 1.0 C B:CYS56 4.7 51.0 1.0 CA B:VAL51 4.7 55.1 1.0 CA B:ASP57 4.7 53.4 1.0 N B:ASN52 4.8 48.4 1.0 CD1 B:ILE46 4.8 66.1 1.0 CA B:ASP53 4.9 47.0 1.0 C B:ASP63 5.0 49.8 1.0

Calcium binding site 2 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca602 b:42.4 occ:1.00 O B:ARG91 2.2 43.5 1.0 O B:VAL96 2.3 42.0 1.0 OD1 B:ASP98 2.4 45.8 1.0 OD2 B:ASP104 2.4 50.9 1.0 OE2 B:GLU105 2.5 40.2 1.0 OD1 B:ASP94 2.6 42.4 1.0 CG B:ASP94 3.3 36.5 1.0 C B:ARG91 3.4 43.9 1.0 C B:VAL96 3.4 43.6 1.0 CD B:GLU105 3.4 42.2 1.0 CG B:ASP98 3.5 45.8 1.0 CG B:ASP104 3.6 49.3 1.0 OD2 B:ASP94 3.6 37.1 1.0 CG B:GLU105 4.0 43.3 1.0 CB B:ASP98 4.0 47.6 1.0 N B:ASP98 4.0 44.6 1.0 N B:VAL96 4.1 39.0 1.0 CB B:ARG91 4.1 41.3 1.0 CB B:ASP104 4.1 45.4 1.0 CA B:ARG91 4.1 41.3 1.0 CA B:VAL96 4.2 41.9 1.0 N B:ASP94 4.2 40.2 1.0 CB B:VAL96 4.4 42.3 1.0 N B:ASN93 4.4 36.9 1.0 OE1 B:GLU105 4.4 41.8 1.0 N B:VAL92 4.4 45.1 1.0 N B:CYS97 4.5 42.2 1.0 O B:ASP104 4.5 45.8 1.0 OD2 B:ASP98 4.5 48.0 1.0 CB B:ASP94 4.6 39.7 1.0 OD1 B:ASP104 4.6 51.7 1.0 CA B:VAL92 4.6 43.4 1.0 CA B:ASP98 4.7 46.2 1.0 CA B:CYS97 4.7 39.6 1.0 C B:CYS97 4.7 41.9 1.0 C B:ASP104 4.8 45.5 1.0 C B:VAL92 4.8 39.1 1.0 CA B:ASP94 4.9 40.2 1.0 NH2 A:ARG840 4.9 40.1 1.0 N B:GLY95 4.9 36.2 1.0

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


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca601 b:49.5 occ:1.00 OE2 D:GLU64 2.4 52.5 1.0 O D:TYR55 2.4 46.5 1.0 OD1 D:ASP53 2.4 51.2 1.0 O D:GLN50 2.4 58.6 1.0 OD2 D:ASP63 2.5 52.0 1.0 OD2 D:ASP57 2.5 51.5 1.0 CD D:GLU64 3.4 50.5 1.0 C D:GLN50 3.5 57.1 1.0 CG D:ASP53 3.5 53.9 1.0 CG D:ASP63 3.6 55.3 1.0 C D:TYR55 3.6 48.0 1.0 CG D:ASP57 3.6 49.4 1.0 CG D:GLU64 3.9 45.7 1.0 N D:ASP57 4.0 49.6 1.0 CB D:ASP57 4.1 49.4 1.0 CA D:GLN50 4.2 59.0 1.0 CB D:ASP63 4.2 52.9 1.0 CB D:GLN50 4.2 56.6 1.0 OD2 D:ASP53 4.2 51.4 1.0 N D:TYR55 4.3 44.7 1.0 N D:ASP53 4.3 44.1 1.0 O D:ASP63 4.4 50.0 1.0 NH1 C:ARG951 4.4 51.9 1.0 CA D:TYR55 4.4 41.0 1.0 N D:VAL51 4.4 58.3 1.0 OE1 D:GLU64 4.5 46.9 1.0 CB D:ASP53 4.5 51.6 1.0 N D:CYS56 4.5 49.6 1.0 OD1 D:ASP63 4.6 57.0 1.0 CA D:CYS56 4.6 49.0 1.0 OD1 D:ASP57 4.6 54.0 1.0 CA D:VAL51 4.6 51.5 1.0 C D:CYS56 4.6 51.1 1.0 N D:ASN52 4.7 53.3 1.0 CA D:ASP57 4.7 52.5 1.0 CD1 D:ILE46 4.8 63.1 1.0 CB D:TYR55 4.8 49.3 1.0 C D:ASP63 4.8 51.1 1.0 CA D:ASP53 4.8 47.8 1.0 N D:ASP54 5.0 47.1 1.0 C D:VAL51 5.0 52.7 1.0 C D:ASP53 5.0 46.6 1.0

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


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca602 b:45.3 occ:1.00 O D:VAL96 2.2 45.3 1.0 OE2 D:GLU105 2.3 39.1 1.0 OD2 D:ASP104 2.3 43.5 1.0 O D:ARG91 2.3 41.5 1.0 OD2 D:ASP98 2.4 43.9 1.0 OD1 D:ASP94 2.4 44.3 1.0 CG D:ASP94 3.2 41.4 1.0 CD D:GLU105 3.3 43.0 1.0 C D:VAL96 3.4 42.6 1.0 CG D:ASP98 3.4 42.7 1.0 CG D:ASP104 3.5 47.4 1.0 C D:ARG91 3.5 42.0 1.0 OD2 D:ASP94 3.6 38.4 1.0 CG D:GLU105 3.9 43.2 1.0 CB D:ASP98 3.9 46.9 1.0 N D:ASP98 4.0 42.6 1.0 N D:VAL96 4.0 36.8 1.0 CB D:ASP104 4.1 46.6 1.0 CA D:VAL96 4.1 43.5 1.0 N D:ASP94 4.2 43.9 1.0 CB D:ARG91 4.2 38.9 1.0 CA D:ARG91 4.2 43.3 1.0 OE1 D:GLU105 4.3 40.4 1.0 CB D:VAL96 4.3 41.3 1.0 N D:CYS97 4.4 43.4 1.0 N D:ASN93 4.4 38.9 1.0 O D:ASP104 4.5 43.0 1.0 OD1 D:ASP98 4.5 45.1 1.0 CB D:ASP94 4.5 39.1 1.0 OD1 D:ASP104 4.5 47.6 1.0 N D:VAL92 4.5 44.0 1.0 CA D:ASP98 4.6 46.8 1.0 CA D:CYS97 4.6 40.8 1.0 NH2 C:ARG840 4.7 40.4 1.0 C D:CYS97 4.7 45.9 1.0 C D:ASP104 4.7 42.3 1.0 CA D:VAL92 4.7 41.6 1.0 CA D:ASP94 4.8 39.8 1.0 N D:GLY95 4.8 36.8 1.0 C D:VAL92 4.8 39.6 1.0

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Alpha Glucosidase with Compound 3 To Be Published.