Calcium in PDB 7kry: Co-Crystal Structure of Alpha Glucosidase with Compound 11

Enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 11

All present enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 11:
3.2.1.207;

Protein crystallography data

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 11, PDB code: 7kry 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) 49.80 / 2.55
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 102.923, 102.923, 240.215, 90, 90, 120
R / Rfree (%) 18.1 / 21.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Co-Crystal Structure of Alpha Glucosidase with Compound 11 (pdb code 7kry). 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 11, PDB code: 7kry:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7kry

Go back to Calcium Binding Sites List in 7kry
Calcium binding site 1 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 11


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

b:58.3
occ:1.00
 O B:TYR55 2.3 54.6 1.0
OD1 B:ASP57 2.3 64.5 1.0
OE2 B:GLU64 2.3 54.1 1.0
OD1 B:ASP53 2.3 55.9 1.0
OD2 B:ASP63 2.4 56.3 1.0
O B:GLN50 2.6 63.3 1.0
CD B:GLU64 3.3 51.4 1.0
C B:TYR55 3.5 51.7 1.0
CG B:ASP57 3.5 59.6 1.0
CG B:ASP53 3.6 59.1 1.0
C B:GLN50 3.6 66.8 1.0
CG B:ASP63 3.7 57.3 1.0
CG B:GLU64 3.8 52.3 1.0
NH1 A:ARG951 4.0 55.7 1.0
N B:ASP57 4.1 58.0 1.0
N B:TYR55 4.2 53.5 1.0
CB B:ASP57 4.2 54.9 1.0
CA B:GLN50 4.3 68.5 1.0
CA B:TYR55 4.3 50.8 1.0
CB B:GLN50 4.3 68.1 1.0
N B:ASP53 4.3 55.1 1.0
OD2 B:ASP53 4.3 57.2 1.0
OE1 B:GLU64 4.4 52.7 1.0
CB B:ASP63 4.4 56.5 1.0
N B:CYS56 4.4 50.5 1.0
O B:ASP63 4.5 53.8 1.0
OD2 B:ASP57 4.5 62.4 1.0
CB B:TYR55 4.5 48.1 1.0
CA B:CYS56 4.6 52.4 1.0
OD1 B:ASP63 4.6 59.3 1.0
CB B:ASP53 4.6 56.1 1.0
C B:CYS56 4.7 57.4 1.0
N B:VAL51 4.7 65.7 1.0
N B:ASN52 4.8 55.8 1.0
CA B:ASP53 4.8 53.6 1.0
CA B:ASP57 4.8 58.0 1.0
N B:ASP54 4.9 51.2 1.0
CA B:VAL51 4.9 61.7 1.0
C B:ASP53 4.9 53.6 1.0
C B:ASP63 4.9 57.1 1.0

Calcium binding site 2 out of 4 in 7kry

Go back to Calcium Binding Sites List in 7kry
Calcium binding site 2 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 11


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

b:43.6
occ:1.00
 O B:VAL96 2.2 42.4 1.0
O B:ARG91 2.3 46.6 1.0
OD2 B:ASP104 2.3 50.6 1.0
OE2 B:GLU105 2.4 42.8 1.0
OD2 B:ASP98 2.5 49.7 1.0
OD1 B:ASP94 2.5 43.9 1.0
C B:VAL96 3.4 44.2 1.0
CD B:GLU105 3.4 43.6 1.0
C B:ARG91 3.4 47.5 1.0
CG B:ASP104 3.5 51.4 1.0
CG B:ASP94 3.5 43.5 1.0
CG B:ASP98 3.6 48.0 1.0
CG B:GLU105 3.8 48.3 1.0
OD2 B:ASP94 3.8 41.4 1.0
N B:ASP98 4.0 46.1 1.0
N B:VAL96 4.0 43.9 1.0
CB B:ASP104 4.0 47.0 1.0
CA B:VAL96 4.1 44.5 1.0
CB B:ASP98 4.1 44.9 1.0
CA B:ARG91 4.2 48.0 1.0
CB B:ARG91 4.2 48.3 1.0
N B:ASP94 4.3 45.8 1.0
N B:CYS97 4.4 45.8 1.0
OE1 B:GLU105 4.4 43.2 1.0
CB B:VAL96 4.4 44.3 1.0
N B:ASN93 4.4 41.3 1.0
N B:VAL92 4.4 45.4 1.0
OD1 B:ASP104 4.5 51.2 1.0
O B:ASP104 4.6 47.3 1.0
CA B:CYS97 4.6 45.5 1.0
CA B:VAL92 4.6 47.4 1.0
C B:CYS97 4.6 45.2 1.0
OD1 B:ASP98 4.7 50.4 1.0
C B:ASP104 4.7 47.3 1.0
CB B:ASP94 4.7 44.4 1.0
CA B:ASP98 4.7 45.0 1.0
N B:GLY95 4.8 41.6 1.0
NH2 A:ARG840 4.8 41.6 1.0
C B:VAL92 4.8 45.0 1.0
CD1 B:ILE87 4.8 49.6 1.0
CA B:ASP94 4.9 38.9 1.0

Calcium binding site 3 out of 4 in 7kry

Go back to Calcium Binding Sites List in 7kry
Calcium binding site 3 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 11


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

b:56.0
occ:1.00
 OD1 D:ASP53 2.3 51.8 1.0
OD2 D:ASP63 2.3 54.6 1.0
O D:TYR55 2.3 49.8 1.0
OD2 D:ASP57 2.4 54.3 1.0
O D:GLN50 2.5 62.7 1.0
OE2 D:GLU64 2.5 57.0 1.0
CD D:GLU64 3.5 54.2 1.0
CG D:ASP63 3.5 58.3 1.0
CG D:ASP53 3.5 54.2 1.0
C D:GLN50 3.5 64.3 1.0
CG D:ASP57 3.5 54.1 1.0
C D:TYR55 3.5 47.6 1.0
CG D:GLU64 3.9 51.8 1.0
N D:ASP57 4.1 57.0 1.0
N D:ASP53 4.2 48.9 1.0
N D:TYR55 4.2 46.0 1.0
CB D:ASP57 4.2 49.7 1.0
NH1 C:ARG951 4.2 49.4 1.0
CA D:GLN50 4.2 61.9 1.0
CB D:ASP63 4.2 57.4 1.0
O D:ASP63 4.3 53.8 1.0
OD2 D:ASP53 4.3 52.4 1.0
CB D:GLN50 4.3 61.0 1.0
CA D:TYR55 4.4 44.8 1.0
OD1 D:ASP63 4.5 55.8 1.0
OD1 D:ASP57 4.5 56.3 1.0
N D:VAL51 4.5 61.5 1.0
CB D:ASP53 4.5 54.4 1.0
N D:CYS56 4.5 48.1 1.0
OE1 D:GLU64 4.5 52.8 1.0
N D:ASN52 4.6 54.8 1.0
CA D:CYS56 4.6 50.7 1.0
CB D:TYR55 4.7 49.8 1.0
CA D:VAL51 4.7 57.1 1.0
CA D:ASP53 4.7 50.2 1.0
C D:CYS56 4.7 54.5 1.0
CD1 D:ILE46 4.8 63.8 1.0
C D:ASP63 4.8 57.0 1.0
CA D:ASP57 4.8 53.0 1.0
N D:ASP54 4.8 50.0 1.0
C D:ASP53 4.9 50.0 1.0
C D:VAL51 4.9 58.5 1.0

Calcium binding site 4 out of 4 in 7kry

Go back to Calcium Binding Sites List in 7kry
Calcium binding site 4 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 11


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

b:46.6
occ:1.00
 O D:ARG91 2.2 43.2 1.0
O D:VAL96 2.3 45.4 1.0
OD1 D:ASP98 2.3 43.6 1.0
OE2 D:GLU105 2.4 41.5 1.0
OD2 D:ASP104 2.4 45.5 1.0
OD1 D:ASP94 2.6 44.1 1.0
CD D:GLU105 3.4 45.3 1.0
C D:ARG91 3.4 44.3 1.0
CG D:ASP98 3.4 46.3 1.0
C D:VAL96 3.4 44.5 1.0
CG D:ASP94 3.5 45.4 1.0
CG D:ASP104 3.6 51.8 1.0
OD2 D:ASP94 3.8 40.8 1.0
CG D:GLU105 3.9 48.1 1.0
N D:ASP98 3.9 46.7 1.0
CB D:ASP98 3.9 48.4 1.0
CB D:ASP104 4.0 49.6 1.0
N D:VAL96 4.1 44.2 1.0
CA D:ARG91 4.2 43.9 1.0
CB D:ARG91 4.2 47.1 1.0
CA D:VAL96 4.2 44.5 1.0
N D:ASP94 4.3 46.8 1.0
O D:ASP104 4.4 47.4 1.0
OE1 D:GLU105 4.4 45.5 1.0
N D:VAL92 4.4 45.2 1.0
N D:ASN93 4.4 45.0 1.0
OD2 D:ASP98 4.4 51.3 1.0
N D:CYS97 4.4 46.5 1.0
CB D:VAL96 4.5 44.4 1.0
CA D:VAL92 4.6 44.4 1.0
CA D:ASP98 4.6 45.4 1.0
C D:ASP104 4.6 46.6 1.0
CA D:CYS97 4.6 44.3 1.0
OD1 D:ASP104 4.7 50.3 1.0
C D:CYS97 4.7 48.2 1.0
CB D:ASP94 4.7 43.5 1.0
NH2 C:ARG840 4.8 43.8 1.0
C D:VAL92 4.8 43.0 1.0
CD1 D:ILE87 4.8 43.8 1.0
N D:GLY95 4.9 41.7 1.0
CA D:ASP94 5.0 42.8 1.0

Reference:

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Alpha Glucosidase with Compound 11 To Be Published.
Page generated: Fri Jul 19 01:23:27 2024

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