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Calcium in PDB 7kb8: Co-Crystal Structure of Alpha Glucosidase with Compound 8

Enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 8

All present enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 8:
3.2.1.207;

Protein crystallography data

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 8, PDB code: 7kb8 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) 40.02 / 2.39
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 102.782, 102.782, 240.124, 90, 90, 120
R / Rfree (%) 17.4 / 21

Calcium Binding Sites:

The binding sites of Calcium atom in the Co-Crystal Structure of Alpha Glucosidase with Compound 8 (pdb code 7kb8). 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 8, PDB code: 7kb8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7kb8

Go back to Calcium Binding Sites List in 7kb8
Calcium binding site 1 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 8


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 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca606

b:45.5
occ:1.00
 O B:VAL96 2.2 42.3 1.0
O B:ARG91 2.2 44.1 1.0
OE2 B:GLU105 2.3 39.2 1.0
OD2 B:ASP104 2.4 51.2 1.0
OD2 B:ASP98 2.4 45.3 1.0
OD1 B:ASP94 2.6 39.8 1.0
CD B:GLU105 3.3 38.8 1.0
CG B:ASP94 3.4 41.4 1.0
C B:VAL96 3.4 38.7 1.0
C B:ARG91 3.4 44.3 1.0
CG B:ASP98 3.5 48.3 1.0
CG B:ASP104 3.5 54.2 1.0
OD2 B:ASP94 3.6 37.8 1.0
CG B:GLU105 3.9 48.0 1.0
CB B:ASP98 4.0 42.9 1.0
N B:ASP98 4.0 44.2 1.0
N B:VAL96 4.0 36.8 1.0
CB B:ASP104 4.1 42.9 1.0
CA B:VAL96 4.1 45.2 1.0
CB B:ARG91 4.1 40.0 1.0
CA B:ARG91 4.2 41.2 1.0
N B:ASP94 4.3 42.8 1.0
OE1 B:GLU105 4.3 33.6 1.0
CB B:VAL96 4.4 42.1 1.0
N B:CYS97 4.4 43.7 1.0
N B:ASN93 4.5 37.9 1.0
N B:VAL92 4.5 41.2 1.0
O B:ASP104 4.6 41.3 1.0
OD1 B:ASP104 4.6 51.1 1.0
OD1 B:ASP98 4.6 44.1 1.0
CB B:ASP94 4.6 39.8 1.0
CA B:CYS97 4.6 48.7 1.0
CA B:VAL92 4.6 36.3 1.0
C B:CYS97 4.6 45.7 1.0
CA B:ASP98 4.7 40.0 1.0
NH2 A:ARG840 4.7 37.5 1.0
C B:ASP104 4.7 39.9 1.0
N B:GLY95 4.9 37.2 1.0
C B:VAL92 4.9 38.7 1.0
CD1 B:ILE87 4.9 45.9 1.0
CA B:ASP94 4.9 38.8 1.0
CG1 B:VAL96 5.0 40.9 1.0

Calcium binding site 2 out of 4 in 7kb8

Go back to Calcium Binding Sites List in 7kb8
Calcium binding site 2 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 8


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 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca607

b:51.2
occ:1.00
 O B:TYR55 2.3 55.7 1.0
OE2 B:GLU64 2.3 55.1 1.0
OD2 B:ASP63 2.3 53.4 1.0
OD1 B:ASP53 2.3 53.2 1.0
OD2 B:ASP57 2.3 55.5 1.0
O B:GLN50 2.4 55.0 1.0
CD B:GLU64 3.3 50.1 1.0
CG B:ASP57 3.4 51.7 1.0
C B:TYR55 3.4 45.6 1.0
CG B:ASP63 3.6 60.4 1.0
C B:GLN50 3.6 63.7 1.0
CG B:ASP53 3.6 55.7 1.0
CG B:GLU64 3.9 45.7 1.0
N B:ASP57 4.0 52.4 1.0
CB B:ASP57 4.0 51.1 1.0
NH1 A:ARG951 4.1 47.9 1.0
N B:TYR55 4.1 50.5 1.0
CA B:GLN50 4.2 72.4 1.0
CA B:TYR55 4.2 46.7 1.0
CB B:GLN50 4.2 58.8 1.0
OD2 B:ASP53 4.3 55.1 1.0
N B:ASP53 4.3 49.3 1.0
CB B:ASP63 4.3 52.0 1.0
OE1 B:GLU64 4.4 46.7 1.0
OD1 B:ASP57 4.4 58.9 1.0
N B:CYS56 4.4 46.8 1.0
OD1 B:ASP63 4.5 53.9 1.0
O B:ASP63 4.5 49.0 1.0
CB B:TYR55 4.5 47.0 1.0
CA B:CYS56 4.6 55.0 1.0
C B:CYS56 4.6 57.7 1.0
N B:VAL51 4.6 62.2 1.0
CB B:ASP53 4.6 46.0 1.0
CA B:ASP57 4.7 54.4 1.0
N B:ASN52 4.7 52.6 1.0
CA B:VAL51 4.8 54.2 1.0
CA B:ASP53 4.8 52.5 1.0
CD1 B:ILE46 4.9 69.0 1.0
C B:ASP63 4.9 50.3 1.0
N B:ASP54 5.0 50.2 1.0
C B:ASP53 5.0 52.4 1.0

Calcium binding site 3 out of 4 in 7kb8

Go back to Calcium Binding Sites List in 7kb8
Calcium binding site 3 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 8


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 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca604

b:51.5
occ:1.00
 OD2 D:ASP63 2.2 54.3 1.0
OD1 D:ASP53 2.3 51.4 1.0
O D:TYR55 2.3 44.9 1.0
OD2 D:ASP57 2.4 46.4 1.0
O D:GLN50 2.4 64.8 1.0
OE2 D:GLU64 2.4 62.5 1.0
CG D:ASP57 3.4 50.5 1.0
CG D:ASP63 3.5 58.8 1.0
C D:GLN50 3.5 69.6 1.0
CD D:GLU64 3.5 51.6 1.0
C D:TYR55 3.5 47.3 1.0
CG D:ASP53 3.5 55.1 1.0
N D:ASP57 3.9 54.4 1.0
CB D:ASP57 3.9 48.1 1.0
CG D:GLU64 3.9 42.4 1.0
NH1 C:ARG951 4.1 46.2 1.0
CA D:GLN50 4.1 66.7 1.0
CB D:GLN50 4.2 61.1 1.0
OD2 D:ASP53 4.2 54.2 1.0
N D:TYR55 4.2 44.3 1.0
CB D:ASP63 4.3 50.7 1.0
OD1 D:ASP63 4.3 54.4 1.0
CA D:TYR55 4.4 41.2 1.0
N D:ASP53 4.4 46.0 1.0
OD1 D:ASP57 4.4 59.7 1.0
N D:CYS56 4.5 51.5 1.0
O D:ASP63 4.5 48.6 1.0
N D:VAL51 4.5 62.6 1.0
C D:CYS56 4.5 54.9 1.0
CA D:ASP57 4.5 52.4 1.0
CA D:CYS56 4.6 52.7 1.0
CB D:ASP53 4.6 45.0 1.0
OE1 D:GLU64 4.6 47.3 1.0
CB D:TYR55 4.6 46.2 1.0
CA D:VAL51 4.8 52.9 1.0
N D:ASN52 4.8 50.0 1.0
CD1 D:ILE46 4.8 68.0 1.0
CA D:ASP53 4.8 46.0 1.0
C D:ASP63 4.9 53.2 1.0
C D:ASP53 4.9 46.8 1.0
N D:ASP54 5.0 46.7 1.0

Calcium binding site 4 out of 4 in 7kb8

Go back to Calcium Binding Sites List in 7kb8
Calcium binding site 4 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 8


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 8 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca605

b:45.7
occ:1.00
 O D:VAL96 2.2 43.6 1.0
OE2 D:GLU105 2.2 40.1 1.0
O D:ARG91 2.3 45.2 1.0
OD2 D:ASP98 2.3 47.2 1.0
OD2 D:ASP104 2.5 42.8 1.0
OD1 D:ASP94 2.5 46.1 1.0
CG D:ASP94 3.3 43.9 1.0
CD D:GLU105 3.3 48.0 1.0
C D:VAL96 3.4 43.3 1.0
CG D:ASP98 3.4 47.6 1.0
C D:ARG91 3.5 39.3 1.0
OD2 D:ASP94 3.5 40.9 1.0
CG D:ASP104 3.6 51.8 1.0
CG D:GLU105 3.9 47.6 1.0
CB D:ASP98 4.0 50.3 1.0
N D:VAL96 4.0 41.1 1.0
N D:ASP98 4.0 38.4 1.0
CA D:VAL96 4.1 44.4 1.0
CB D:ASP104 4.2 50.3 1.0
CB D:ARG91 4.2 44.0 1.0
CA D:ARG91 4.2 45.1 1.0
N D:ASP94 4.3 46.6 1.0
OE1 D:GLU105 4.3 41.6 1.0
CB D:VAL96 4.3 49.5 1.0
N D:CYS97 4.4 42.5 1.0
O D:ASP104 4.4 46.4 1.0
N D:VAL92 4.5 41.8 1.0
OD1 D:ASP98 4.5 55.2 1.0
N D:ASN93 4.5 42.7 1.0
CB D:ASP94 4.5 45.3 1.0
NH2 C:ARG840 4.6 45.3 1.0
CA D:CYS97 4.6 41.7 1.0
OD1 D:ASP104 4.7 47.4 1.0
C D:CYS97 4.7 43.8 1.0
CA D:VAL92 4.7 41.3 1.0
CA D:ASP98 4.7 43.0 1.0
C D:ASP104 4.7 46.1 1.0
N D:GLY95 4.8 38.5 1.0
CA D:ASP94 4.8 40.7 1.0
C D:VAL92 4.9 45.4 1.0
CG1 D:VAL96 5.0 46.2 1.0

Reference:

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Alpha Glucosidase with Compound 8 To Be Published.
Page generated: Wed Jul 9 22:52:36 2025

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