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Calcium in PDB 7kbj: Co-Crystal Structure of Alpha Glucosidase with Compound 9

Enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 9

All present enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 9:
3.2.1.207;

Protein crystallography data

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 9, PDB code: 7kbj 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) 42.09 / 2.21
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 102.652, 102.652, 238.908, 90, 90, 120
R / Rfree (%) 16.7 / 20

Calcium Binding Sites:

The binding sites of Calcium atom in the Co-Crystal Structure of Alpha Glucosidase with Compound 9 (pdb code 7kbj). 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 9, PDB code: 7kbj:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7kbj

Go back to Calcium Binding Sites List in 7kbj
Calcium binding site 1 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 9


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 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1804

b:41.8
occ:1.00
 OE2 B:GLU64 2.3 43.7 1.0
O B:TYR55 2.3 43.1 1.0
OD2 B:ASP57 2.4 46.2 1.0
OD1 B:ASP53 2.4 37.8 1.0
O B:GLN50 2.4 50.0 1.0
OD2 B:ASP63 2.4 44.9 1.0
CD B:GLU64 3.4 39.8 1.0
CG B:ASP57 3.4 45.9 1.0
C B:GLN50 3.5 43.0 1.0
C B:TYR55 3.5 36.2 1.0
CG B:ASP53 3.6 39.2 1.0
CG B:ASP63 3.6 52.6 1.0
CG B:GLU64 3.9 36.8 1.0
CB B:ASP57 3.9 42.5 1.0
N B:ASP57 4.0 41.9 1.0
CA B:GLN50 4.2 59.3 1.0
CB B:ASP63 4.2 48.0 1.0
N B:TYR55 4.2 35.6 1.0
NH1 A:ARG951 4.3 40.1 1.0
CB B:GLN50 4.3 44.0 1.0
O B:ASP63 4.3 41.9 1.0
N B:ASP53 4.3 29.1 1.0
OD2 B:ASP53 4.3 48.0 1.0
CA B:TYR55 4.3 30.5 1.0
OE1 B:GLU64 4.4 34.8 1.0
N B:CYS56 4.5 40.9 1.0
OD1 B:ASP57 4.5 48.4 1.0
N B:VAL51 4.5 44.5 1.0
CA B:CYS56 4.6 49.1 1.0
OD1 B:ASP63 4.6 50.5 1.0
C B:CYS56 4.6 43.3 1.0
CB B:ASP53 4.6 33.9 1.0
CA B:ASP57 4.6 46.8 1.0
CB B:TYR55 4.6 31.9 1.0
CA B:VAL51 4.7 45.7 1.0
N B:ASN52 4.7 38.1 1.0
C B:ASP63 4.8 39.5 1.0
CA B:ASP53 4.8 33.0 1.0
CD1 B:ILE46 4.9 52.2 1.0
C B:VAL51 5.0 48.6 1.0
C B:ASP53 5.0 41.2 1.0
N B:ASP54 5.0 32.2 1.0

Calcium binding site 2 out of 4 in 7kbj

Go back to Calcium Binding Sites List in 7kbj
Calcium binding site 2 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 9


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 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1805

b:33.5
occ:1.00
 O B:VAL96 2.2 30.5 1.0
O B:ARG91 2.3 30.2 1.0
OE2 B:GLU105 2.4 31.8 1.0
OD2 B:ASP98 2.4 37.0 1.0
OD2 B:ASP104 2.5 34.5 1.0
OD1 B:ASP94 2.5 33.8 1.0
CD B:GLU105 3.4 31.3 1.0
C B:VAL96 3.4 33.0 1.0
CG B:ASP94 3.4 32.9 1.0
C B:ARG91 3.4 30.6 1.0
CG B:ASP98 3.5 36.2 1.0
CG B:ASP104 3.6 42.0 1.0
OD2 B:ASP94 3.8 30.1 1.0
CG B:GLU105 3.9 36.9 1.0
N B:VAL96 4.0 28.1 1.0
CB B:ASP98 4.1 31.6 1.0
N B:ASP98 4.1 32.1 1.0
CB B:ASP104 4.1 35.3 1.0
CA B:VAL96 4.1 33.2 1.0
CA B:ARG91 4.2 35.2 1.0
N B:ASP94 4.2 36.8 1.0
CB B:ARG91 4.2 35.4 1.0
OE1 B:GLU105 4.3 29.3 1.0
N B:ASN93 4.4 29.8 1.0
CB B:VAL96 4.4 35.9 1.0
N B:VAL92 4.4 34.6 1.0
N B:CYS97 4.5 33.9 1.0
O B:ASP104 4.5 37.0 1.0
OD1 B:ASP98 4.6 38.7 1.0
CA B:VAL92 4.6 35.7 1.0
OD1 B:ASP104 4.6 45.5 1.0
CB B:ASP94 4.6 32.9 1.0
CA B:CYS97 4.7 36.9 1.0
NH2 A:ARG840 4.7 30.5 1.0
C B:ASP104 4.7 34.8 1.0
C B:CYS97 4.7 38.7 1.0
CA B:ASP98 4.7 34.9 1.0
C B:VAL92 4.8 33.7 1.0
N B:GLY95 4.8 32.9 1.0
CA B:ASP94 4.8 34.7 1.0
CD1 B:ILE87 5.0 34.2 1.0

Calcium binding site 3 out of 4 in 7kbj

Go back to Calcium Binding Sites List in 7kbj
Calcium binding site 3 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 9


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 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1404

b:40.9
occ:1.00
 OD1 D:ASP53 2.2 40.8 1.0
OE2 D:GLU64 2.3 43.1 1.0
O D:TYR55 2.3 36.7 1.0
O D:GLN50 2.4 50.0 1.0
OD2 D:ASP63 2.4 45.3 1.0
OD2 D:ASP57 2.5 39.3 1.0
CD D:GLU64 3.4 38.2 1.0
CG D:ASP53 3.5 49.4 1.0
C D:GLN50 3.5 52.9 1.0
C D:TYR55 3.6 35.6 1.0
CG D:ASP57 3.6 37.5 1.0
CG D:ASP63 3.6 46.8 1.0
CG D:GLU64 3.9 31.6 1.0
CB D:ASP57 4.0 37.3 1.0
N D:ASP57 4.1 41.7 1.0
CA D:GLN50 4.2 52.6 1.0
N D:TYR55 4.2 32.3 1.0
OD2 D:ASP53 4.2 42.1 1.0
CB D:ASP63 4.3 39.5 1.0
CB D:GLN50 4.3 52.0 1.0
N D:ASP53 4.3 34.4 1.0
NH1 C:ARG951 4.3 39.4 1.0
CA D:TYR55 4.3 33.5 1.0
O D:ASP63 4.3 43.1 1.0
OE1 D:GLU64 4.4 38.3 1.0
CB D:ASP53 4.5 38.7 1.0
N D:VAL51 4.5 56.2 1.0
N D:CYS56 4.6 38.7 1.0
OD1 D:ASP63 4.6 49.0 1.0
CB D:TYR55 4.6 40.8 1.0
OD1 D:ASP57 4.7 47.1 1.0
C D:CYS56 4.7 47.4 1.0
CA D:CYS56 4.7 38.1 1.0
CA D:VAL51 4.7 47.3 1.0
N D:ASN52 4.7 36.0 1.0
CA D:ASP57 4.7 48.6 1.0
CA D:ASP53 4.8 33.3 1.0
C D:ASP63 4.8 44.4 1.0
CD1 D:ILE46 4.9 58.1 1.0
C D:ASP53 4.9 37.0 1.0
N D:ASP54 4.9 38.6 1.0
C D:VAL51 4.9 46.5 1.0

Calcium binding site 4 out of 4 in 7kbj

Go back to Calcium Binding Sites List in 7kbj
Calcium binding site 4 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 9


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 9 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1405

b:31.4
occ:1.00
 OD2 D:ASP98 2.3 32.2 1.0
O D:VAL96 2.3 32.1 1.0
O D:ARG91 2.3 32.5 1.0
OE2 D:GLU105 2.4 29.1 1.0
OD2 D:ASP104 2.4 34.8 1.0
OD1 D:ASP94 2.5 35.7 1.0
CG D:ASP94 3.3 32.2 1.0
CD D:GLU105 3.4 35.4 1.0
CG D:ASP98 3.4 38.4 1.0
C D:VAL96 3.4 28.5 1.0
C D:ARG91 3.5 34.9 1.0
CG D:ASP104 3.5 43.2 1.0
OD2 D:ASP94 3.7 28.8 1.0
CB D:ASP98 3.9 33.8 1.0
CG D:GLU105 3.9 36.5 1.0
N D:ASP98 4.0 31.6 1.0
N D:VAL96 4.0 27.6 1.0
CB D:ASP104 4.0 32.8 1.0
CA D:VAL96 4.1 32.0 1.0
CA D:ARG91 4.2 34.5 1.0
CB D:ARG91 4.2 31.6 1.0
N D:ASP94 4.2 30.7 1.0
CB D:VAL96 4.3 29.2 1.0
OE1 D:GLU105 4.4 31.8 1.0
N D:ASN93 4.4 26.4 1.0
O D:ASP104 4.4 36.0 1.0
OD1 D:ASP98 4.5 36.4 1.0
N D:VAL92 4.5 40.3 1.0
N D:CYS97 4.5 32.0 1.0
OD1 D:ASP104 4.6 42.3 1.0
CB D:ASP94 4.6 29.5 1.0
CA D:ASP98 4.6 31.4 1.0
NH2 C:ARG840 4.6 30.3 1.0
CA D:VAL92 4.7 34.8 1.0
C D:CYS97 4.7 33.6 1.0
CA D:CYS97 4.7 34.3 1.0
C D:ASP104 4.7 35.3 1.0
C D:VAL92 4.8 31.8 1.0
CA D:ASP94 4.8 29.9 1.0
N D:GLY95 4.8 30.7 1.0

Reference:

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Alpha Glucosidase with Compound 9 To Be Published.
Page generated: Wed Jul 9 22:53:44 2025

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