Calcium in PDB 7kbr: Co-Crystal Structure of Alpha Glucosidase with Compound 10

Enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 10

All present enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 10:
3.2.1.207;

Protein crystallography data

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 10, PDB code: 7kbr 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) 42.33 / 2.09
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 102.815, 102.815, 240.552, 90, 90, 120
R / Rfree (%) 16.3 / 18.6

Calcium Binding Sites:

The binding sites of Calcium atom in the Co-Crystal Structure of Alpha Glucosidase with Compound 10 (pdb code 7kbr). 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 10, PDB code: 7kbr:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7kbr

Go back to Calcium Binding Sites List in 7kbr
Calcium binding site 1 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 10


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 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca204

b:27.2
occ:1.00
 O B:VAL96 2.2 22.1 1.0
O B:ARG91 2.3 27.2 1.0
OD2 B:ASP98 2.3 26.6 1.0
OD2 B:ASP104 2.4 32.8 1.0
OE2 B:GLU105 2.4 27.4 1.0
OD1 B:ASP94 2.5 24.8 1.0
CD B:GLU105 3.3 28.8 1.0
C B:VAL96 3.4 25.2 1.0
CG B:ASP94 3.4 29.4 1.0
CG B:ASP98 3.5 30.2 1.0
C B:ARG91 3.5 29.0 1.0
CG B:ASP104 3.5 35.9 1.0
OD2 B:ASP94 3.8 30.0 1.0
CG B:GLU105 3.8 28.7 1.0
N B:ASP98 3.9 28.3 1.0
CB B:ASP98 3.9 25.3 1.0
N B:VAL96 4.0 27.6 1.0
CB B:ASP104 4.1 29.9 1.0
CA B:VAL96 4.1 23.6 1.0
CB B:ARG91 4.2 26.2 1.0
CA B:ARG91 4.2 27.6 1.0
N B:ASP94 4.2 25.4 1.0
CB B:VAL96 4.4 27.4 1.0
OE1 B:GLU105 4.4 26.7 1.0
N B:CYS97 4.4 24.8 1.0
N B:ASN93 4.5 26.0 1.0
N B:VAL92 4.5 33.4 1.0
OD1 B:ASP104 4.5 33.8 1.0
OD1 B:ASP98 4.5 32.1 1.0
CA B:ASP98 4.6 24.6 1.0
CB B:ASP94 4.6 23.0 1.0
NH2 A:ARG840 4.6 19.1 1.0
CA B:CYS97 4.6 24.2 1.0
C B:CYS97 4.6 26.0 1.0
O B:ASP104 4.7 29.6 1.0
CA B:VAL92 4.7 28.7 1.0
C B:ASP104 4.8 28.6 1.0
CA B:ASP94 4.8 23.5 1.0
N B:GLY95 4.9 26.4 1.0
C B:VAL92 4.9 29.0 1.0
CD1 B:ILE87 5.0 34.6 1.0

Calcium binding site 2 out of 4 in 7kbr

Go back to Calcium Binding Sites List in 7kbr
Calcium binding site 2 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 10


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 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca205

b:35.1
occ:1.00
 OE2 B:GLU64 2.3 30.8 1.0
OD1 B:ASP53 2.3 33.9 1.0
O B:TYR55 2.3 33.5 1.0
OD2 B:ASP63 2.3 35.8 1.0
OD2 B:ASP57 2.3 42.0 1.0
O B:GLN50 2.4 47.0 1.0
CD B:GLU64 3.4 31.7 1.0
CG B:ASP57 3.4 36.7 1.0
C B:GLN50 3.5 44.6 1.0
CG B:ASP53 3.5 40.5 1.0
CG B:ASP63 3.5 39.7 1.0
C B:TYR55 3.5 34.0 1.0
CG B:GLU64 3.9 28.0 1.0
CB B:ASP57 3.9 38.4 1.0
N B:ASP57 4.0 35.4 1.0
CA B:GLN50 4.1 50.4 1.0
CB B:GLN50 4.1 36.5 1.0
NH1 A:ARG951 4.2 37.5 1.0
OD2 B:ASP53 4.2 38.9 1.0
CB B:ASP63 4.2 36.2 1.0
N B:TYR55 4.2 30.1 1.0
CA B:TYR55 4.3 27.4 1.0
N B:ASP53 4.3 32.1 1.0
O B:ASP63 4.4 35.9 1.0
OE1 B:GLU64 4.4 29.9 1.0
OD1 B:ASP57 4.4 36.7 1.0
OD1 B:ASP63 4.5 40.1 1.0
N B:CYS56 4.5 32.4 1.0
N B:VAL51 4.5 44.4 1.0
CA B:CYS56 4.6 38.2 1.0
CB B:ASP53 4.6 28.8 1.0
CB B:TYR55 4.6 29.2 1.0
C B:CYS56 4.6 41.0 1.0
CA B:ASP57 4.6 43.7 1.0
N B:ASN52 4.7 36.3 1.0
CA B:VAL51 4.8 38.1 1.0
CD1 B:ILE46 4.9 51.9 1.0
CA B:ASP53 4.9 36.7 1.0
C B:ASP63 4.9 42.9 1.0

Calcium binding site 3 out of 4 in 7kbr

Go back to Calcium Binding Sites List in 7kbr
Calcium binding site 3 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 10


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 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca203

b:28.2
occ:1.00
 O D:VAL96 2.2 25.3 1.0
O D:ARG91 2.4 28.4 1.0
OD2 D:ASP104 2.4 32.2 1.0
OD1 D:ASP94 2.4 24.0 1.0
OE2 D:GLU105 2.4 27.5 1.0
OD2 D:ASP98 2.4 25.1 1.0
CG D:ASP94 3.3 33.0 1.0
CD D:GLU105 3.3 25.9 1.0
C D:VAL96 3.4 31.4 1.0
C D:ARG91 3.5 29.1 1.0
CG D:ASP104 3.5 35.4 1.0
CG D:ASP98 3.5 35.2 1.0
OD2 D:ASP94 3.7 26.0 1.0
CG D:GLU105 3.8 30.5 1.0
N D:ASP98 4.0 31.0 1.0
CB D:ASP98 4.0 26.2 1.0
N D:VAL96 4.0 29.2 1.0
CB D:ASP104 4.1 31.4 1.0
CA D:VAL96 4.1 28.0 1.0
N D:ASP94 4.2 26.0 1.0
CA D:ARG91 4.2 28.5 1.0
CB D:ARG91 4.2 28.9 1.0
OE1 D:GLU105 4.3 30.0 1.0
CB D:VAL96 4.4 26.0 1.0
N D:CYS97 4.4 28.1 1.0
N D:ASN93 4.5 22.1 1.0
CB D:ASP94 4.5 21.1 1.0
N D:VAL92 4.5 26.6 1.0
OD1 D:ASP104 4.5 32.9 1.0
OD1 D:ASP98 4.6 31.8 1.0
O D:ASP104 4.6 31.0 1.0
NH2 C:ARG840 4.6 25.7 1.0
CA D:ASP98 4.7 25.5 1.0
CA D:CYS97 4.7 24.4 1.0
C D:CYS97 4.7 34.0 1.0
CA D:VAL92 4.7 23.2 1.0
CA D:ASP94 4.8 21.0 1.0
C D:ASP104 4.8 27.7 1.0
N D:GLY95 4.8 24.6 1.0
C D:VAL92 4.9 25.3 1.0

Calcium binding site 4 out of 4 in 7kbr

Go back to Calcium Binding Sites List in 7kbr
Calcium binding site 4 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 10


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 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca204

b:34.4
occ:1.00
 O D:TYR55 2.3 29.2 1.0
OD1 D:ASP53 2.3 29.5 1.0
OD2 D:ASP63 2.3 32.9 1.0
O D:GLN50 2.4 41.5 1.0
OD2 D:ASP57 2.4 34.7 1.0
OE2 D:GLU64 2.4 39.7 1.0
CD D:GLU64 3.4 35.1 1.0
CG D:ASP57 3.5 37.2 1.0
C D:TYR55 3.5 30.6 1.0
C D:GLN50 3.5 43.0 1.0
CG D:ASP53 3.5 39.9 1.0
CG D:ASP63 3.5 39.4 1.0
CG D:GLU64 3.8 30.6 1.0
N D:ASP57 3.9 36.6 1.0
CB D:ASP57 3.9 32.7 1.0
CA D:GLN50 4.2 45.4 1.0
N D:TYR55 4.2 21.6 1.0
CB D:GLN50 4.2 33.5 1.0
OD2 D:ASP53 4.2 35.2 1.0
CB D:ASP63 4.2 37.0 1.0
NH1 C:ARG951 4.3 36.9 1.0
N D:ASP53 4.3 30.1 1.0
CA D:TYR55 4.3 26.5 1.0
OD1 D:ASP57 4.5 37.5 1.0
N D:CYS56 4.5 29.8 1.0
O D:ASP63 4.5 34.2 1.0
OD1 D:ASP63 4.5 39.3 1.0
OE1 D:GLU64 4.5 31.2 1.0
CA D:CYS56 4.6 29.5 1.0
N D:VAL51 4.6 39.9 1.0
C D:CYS56 4.6 34.0 1.0
CA D:ASP57 4.6 40.2 1.0
CB D:ASP53 4.6 30.3 1.0
CB D:TYR55 4.6 28.6 1.0
N D:ASN52 4.7 35.9 1.0
CA D:VAL51 4.8 35.2 1.0
CD1 D:ILE46 4.8 49.7 1.0
CA D:ASP53 4.8 30.0 1.0
C D:ASP63 4.9 37.5 1.0
C D:ASP53 5.0 37.4 1.0
N D:ASP54 5.0 35.4 1.0

Reference:

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Alpha Glucosidase with Compound 10 To Be Published.
Page generated: Fri Jul 19 01:15:30 2024

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