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Calcium in PDB 7kb6: Co-Crystal Structure of Alpha Glucosidase with Compound 7

Enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 7

All present enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 7:
3.2.1.207;

Protein crystallography data

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 7, PDB code: 7kb6 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) 44.56 / 2.20
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 102.909, 102.909, 239.827, 90, 90, 120
R / Rfree (%) 16.7 / 19.4

Calcium Binding Sites:

The binding sites of Calcium atom in the Co-Crystal Structure of Alpha Glucosidase with Compound 7 (pdb code 7kb6). 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 7, PDB code: 7kb6:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7kb6

Go back to Calcium Binding Sites List in 7kb6
Calcium binding site 1 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:39.5
occ:1.00
 O B:TYR55 2.3 45.5 1.0
OE2 B:GLU64 2.3 42.2 1.0
OD1 B:ASP53 2.3 44.9 1.0
O B:GLN50 2.4 45.2 1.0
OD2 B:ASP57 2.4 47.6 1.0
OD2 B:ASP63 2.4 41.5 1.0
CD B:GLU64 3.4 36.1 1.0
CG B:ASP57 3.5 46.4 1.0
C B:GLN50 3.5 49.0 1.0
C B:TYR55 3.5 38.4 1.0
CG B:ASP53 3.5 51.4 1.0
CG B:ASP63 3.6 49.4 1.0
CG B:GLU64 3.9 41.1 1.0
CB B:ASP57 4.0 42.5 1.0
N B:ASP57 4.1 41.9 1.0
NH1 A:ARG951 4.2 35.5 1.0
N B:TYR55 4.2 40.9 1.0
CA B:GLN50 4.2 61.7 1.0
CB B:ASP63 4.2 41.6 1.0
OD2 B:ASP53 4.3 48.5 1.0
CB B:GLN50 4.3 46.0 1.0
N B:ASP53 4.3 33.1 1.0
CA B:TYR55 4.3 40.1 1.0
O B:ASP63 4.4 35.5 1.0
OE1 B:GLU64 4.4 33.3 1.0
N B:CYS56 4.5 37.9 1.0
N B:VAL51 4.5 47.1 1.0
OD1 B:ASP57 4.5 51.8 1.0
OD1 B:ASP63 4.6 45.6 1.0
CB B:TYR55 4.6 35.8 1.0
CB B:ASP53 4.6 32.8 1.0
N B:ASN52 4.6 38.0 1.0
CA B:CYS56 4.6 46.8 1.0
C B:CYS56 4.6 50.7 1.0
CA B:VAL51 4.7 44.2 1.0
CA B:ASP57 4.7 49.6 1.0
CA B:ASP53 4.8 42.3 1.0
C B:ASP63 4.8 42.1 1.0
C B:VAL51 4.9 55.5 1.0
C B:ASP53 5.0 39.1 1.0
N B:ASP54 5.0 37.0 1.0

Calcium binding site 2 out of 4 in 7kb6

Go back to Calcium Binding Sites List in 7kb6
Calcium binding site 2 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:34.0
occ:1.00
 O B:VAL96 2.2 31.2 1.0
O B:ARG91 2.3 33.4 1.0
OE2 B:GLU105 2.3 35.7 1.0
OD2 B:ASP98 2.5 31.9 1.0
OD2 B:ASP104 2.5 42.4 1.0
OD1 B:ASP94 2.5 31.0 1.0
CD B:GLU105 3.3 25.2 1.0
CG B:ASP94 3.3 30.6 1.0
C B:VAL96 3.4 26.1 1.0
C B:ARG91 3.5 37.1 1.0
CG B:ASP98 3.6 33.9 1.0
CG B:ASP104 3.6 51.4 1.0
OD2 B:ASP94 3.7 33.9 1.0
CG B:GLU105 3.9 38.3 1.0
N B:VAL96 4.0 33.7 1.0
CB B:ASP98 4.1 31.9 1.0
N B:ASP98 4.1 29.9 1.0
CA B:VAL96 4.1 39.9 1.0
CB B:ASP104 4.2 37.3 1.0
N B:ASP94 4.2 38.3 1.0
CB B:ARG91 4.2 34.2 1.0
CA B:ARG91 4.2 26.8 1.0
OE1 B:GLU105 4.3 28.4 1.0
N B:ASN93 4.4 28.1 1.0
CB B:VAL96 4.4 28.0 1.0
N B:CYS97 4.5 35.8 1.0
N B:VAL92 4.5 40.4 1.0
CB B:ASP94 4.6 38.8 1.0
O B:ASP104 4.6 38.5 1.0
OD1 B:ASP104 4.6 47.7 1.0
OD1 B:ASP98 4.7 37.9 1.0
CA B:VAL92 4.7 35.3 1.0
CA B:CYS97 4.7 36.8 1.0
CA B:ASP98 4.7 36.7 1.0
C B:CYS97 4.7 29.1 1.0
C B:ASP104 4.8 32.6 1.0
N B:GLY95 4.8 31.2 1.0
NH2 A:ARG840 4.8 29.8 1.0
C B:VAL92 4.8 28.9 1.0
CA B:ASP94 4.8 33.4 1.0

Calcium binding site 3 out of 4 in 7kb6

Go back to Calcium Binding Sites List in 7kb6
Calcium binding site 3 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca601

b:42.2
occ:1.00
 O D:TYR55 2.3 32.4 1.0
OD1 D:ASP53 2.3 41.2 1.0
O D:GLN50 2.4 51.2 1.0
OE2 D:GLU64 2.4 50.7 1.0
OD2 D:ASP63 2.5 47.0 1.0
OD2 D:ASP57 2.5 38.5 1.0
CG D:ASP53 3.5 48.4 1.0
CD D:GLU64 3.5 38.5 1.0
CG D:ASP57 3.5 42.3 1.0
C D:TYR55 3.5 32.0 1.0
C D:GLN50 3.5 51.1 1.0
CG D:ASP63 3.6 45.8 1.0
CG D:GLU64 3.9 32.4 1.0
CB D:ASP57 3.9 37.6 1.0
N D:ASP57 4.0 45.6 1.0
OD2 D:ASP53 4.1 42.7 1.0
CB D:GLN50 4.1 38.5 1.0
CA D:GLN50 4.1 58.9 1.0
N D:TYR55 4.2 31.3 1.0
NH1 C:ARG951 4.2 39.6 1.0
CB D:ASP63 4.3 45.5 1.0
CA D:TYR55 4.3 34.0 1.0
N D:ASP53 4.4 33.7 1.0
O D:ASP63 4.4 45.8 1.0
N D:CYS56 4.5 35.9 1.0
OD1 D:ASP57 4.5 44.6 1.0
N D:VAL51 4.5 52.6 1.0
OE1 D:GLU64 4.5 38.1 1.0
CB D:TYR55 4.6 41.0 1.0
CB D:ASP53 4.6 38.7 1.0
C D:CYS56 4.6 46.4 1.0
OD1 D:ASP63 4.6 47.0 1.0
CA D:ASP57 4.6 43.9 1.0
CA D:CYS56 4.6 37.9 1.0
N D:ASN52 4.8 44.6 1.0
CA D:VAL51 4.8 35.3 1.0
CA D:ASP53 4.9 32.5 1.0
CD1 D:ILE46 4.9 50.3 1.0
C D:ASP63 4.9 42.8 1.0
C D:ASP53 5.0 38.3 1.0

Calcium binding site 4 out of 4 in 7kb6

Go back to Calcium Binding Sites List in 7kb6
Calcium binding site 4 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 7


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 7 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca602

b:32.4
occ:1.00
 O D:VAL96 2.3 31.8 1.0
OD2 D:ASP98 2.3 33.2 1.0
O D:ARG91 2.3 36.5 1.0
OE2 D:GLU105 2.4 31.2 1.0
OD2 D:ASP104 2.4 41.0 1.0
OD1 D:ASP94 2.5 37.2 1.0
CG D:ASP94 3.3 39.0 1.0
CD D:GLU105 3.4 37.9 1.0
CG D:ASP98 3.4 37.6 1.0
C D:VAL96 3.5 36.7 1.0
C D:ARG91 3.5 28.8 1.0
CG D:ASP104 3.6 42.5 1.0
OD2 D:ASP94 3.7 31.9 1.0
CG D:GLU105 3.9 34.5 1.0
CB D:ASP98 3.9 33.0 1.0
N D:ASP98 4.0 28.7 1.0
N D:VAL96 4.1 31.1 1.0
CB D:ASP104 4.1 38.8 1.0
CA D:VAL96 4.2 32.1 1.0
CB D:ARG91 4.2 35.1 1.0
CA D:ARG91 4.2 35.0 1.0
N D:ASP94 4.3 36.3 1.0
OE1 D:GLU105 4.4 38.0 1.0
CB D:VAL96 4.4 33.7 1.0
N D:ASN93 4.4 25.9 1.0
N D:VAL92 4.5 36.1 1.0
OD1 D:ASP98 4.5 39.8 1.0
N D:CYS97 4.5 34.6 1.0
O D:ASP104 4.5 42.5 1.0
CB D:ASP94 4.6 33.0 1.0
OD1 D:ASP104 4.6 46.2 1.0
CA D:ASP98 4.6 31.7 1.0
CA D:VAL92 4.6 31.7 1.0
NH2 C:ARG840 4.7 32.0 1.0
C D:CYS97 4.7 30.2 1.0
CA D:CYS97 4.7 36.8 1.0
C D:ASP104 4.7 33.6 1.0
C D:VAL92 4.8 31.1 1.0
CA D:ASP94 4.9 28.1 1.0
N D:GLY95 4.9 30.6 1.0

Reference:

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Alpha Glucosidase with Compound 7 To Be Published.
Page generated: Fri Jul 19 01:13:50 2024

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