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Calcium in PDB 7kad: Co-Crystal Structure of Alpha Glucosidase with Compound 6

Enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 6

All present enzymatic activity of Co-Crystal Structure of Alpha Glucosidase with Compound 6:
3.2.1.207;

Protein crystallography data

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 6, PDB code: 7kad 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) 42.28 / 2.51
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 102.689, 102.689, 240.275, 90, 90, 120
R / Rfree (%) 17.2 / 20.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Co-Crystal Structure of Alpha Glucosidase with Compound 6 (pdb code 7kad). 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 6, PDB code: 7kad:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7kad

Go back to Calcium Binding Sites List in 7kad
Calcium binding site 1 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 6


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

b:46.4
occ:1.00
 O B:VAL96 2.2 40.6 1.0
O B:ARG91 2.3 43.0 1.0
OD2 B:ASP98 2.3 49.1 1.0
OE2 B:GLU105 2.3 42.4 1.0
OD2 B:ASP104 2.4 54.0 1.0
OD1 B:ASP94 2.5 42.5 1.0
CD B:GLU105 3.3 38.1 1.0
CG B:ASP94 3.4 42.2 1.0
C B:VAL96 3.4 43.8 1.0
C B:ARG91 3.4 47.9 1.0
CG B:ASP98 3.5 47.8 1.0
CG B:ASP104 3.6 55.2 1.0
OD2 B:ASP94 3.7 34.6 1.0
CG B:GLU105 3.9 51.5 1.0
N B:VAL96 4.0 35.9 1.0
N B:ASP98 4.1 44.2 1.0
CB B:ASP98 4.1 39.0 1.0
CA B:VAL96 4.1 48.2 1.0
CB B:ASP104 4.2 43.9 1.0
CB B:ARG91 4.2 48.6 1.0
CA B:ARG91 4.2 40.8 1.0
N B:ASP94 4.3 42.5 1.0
CB B:VAL96 4.3 44.9 1.0
OE1 B:GLU105 4.3 34.1 1.0
N B:ASN93 4.4 38.1 1.0
N B:VAL92 4.4 45.4 1.0
OD1 B:ASP98 4.5 50.6 1.0
N B:CYS97 4.5 46.1 1.0
O B:ASP104 4.5 44.1 1.0
OD1 B:ASP104 4.6 53.7 1.0
CB B:ASP94 4.6 39.8 1.0
CA B:VAL92 4.6 43.5 1.0
CA B:CYS97 4.7 47.1 1.0
C B:CYS97 4.7 47.5 1.0
C B:ASP104 4.7 43.1 1.0
NH2 A:ARG840 4.7 40.6 1.0
CA B:ASP98 4.8 39.1 1.0
C B:VAL92 4.8 48.6 1.0
CA B:ASP94 4.9 38.0 1.0
N B:GLY95 4.9 40.1 1.0
CG1 B:VAL96 5.0 38.1 1.0
CD1 B:ILE87 5.0 43.9 1.0

Calcium binding site 2 out of 4 in 7kad

Go back to Calcium Binding Sites List in 7kad
Calcium binding site 2 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 6


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

b:53.3
occ:1.00
 O B:TYR55 2.3 53.9 1.0
OE2 B:GLU64 2.3 51.2 1.0
OD2 B:ASP63 2.4 59.4 1.0
O B:GLN50 2.4 59.3 1.0
OD1 B:ASP53 2.4 49.6 1.0
OD2 B:ASP57 2.4 58.0 1.0
CD B:GLU64 3.4 44.8 1.0
C B:TYR55 3.5 42.8 1.0
CG B:ASP57 3.5 53.6 1.0
C B:GLN50 3.5 62.6 1.0
CG B:ASP63 3.6 60.7 1.0
CG B:ASP53 3.6 50.7 1.0
CG B:GLU64 3.8 46.7 1.0
N B:ASP57 4.0 51.0 1.0
CB B:ASP57 4.0 53.3 1.0
NH1 A:ARG951 4.0 43.5 1.0
N B:TYR55 4.2 52.1 1.0
CA B:GLN50 4.2 66.0 1.0
CB B:GLN50 4.3 55.5 1.0
OD2 B:ASP53 4.3 49.4 1.0
CA B:TYR55 4.3 41.1 1.0
CB B:ASP63 4.3 56.4 1.0
O B:ASP63 4.3 49.1 1.0
N B:ASP53 4.4 36.1 1.0
N B:CYS56 4.4 50.0 1.0
OE1 B:GLU64 4.4 49.8 1.0
OD1 B:ASP57 4.5 59.6 1.0
OD1 B:ASP63 4.5 63.1 1.0
N B:VAL51 4.5 61.9 1.0
CB B:TYR55 4.6 49.6 1.0
CA B:CYS56 4.6 49.2 1.0
C B:CYS56 4.6 58.0 1.0
CB B:ASP53 4.7 44.3 1.0
CA B:ASP57 4.7 50.2 1.0
N B:ASN52 4.7 40.3 1.0
CA B:VAL51 4.7 52.9 1.0
C B:ASP63 4.8 52.4 1.0
CD1 B:ILE46 4.9 61.1 1.0
CA B:ASP53 4.9 44.9 1.0
C B:ASP53 5.0 52.2 1.0

Calcium binding site 3 out of 4 in 7kad

Go back to Calcium Binding Sites List in 7kad
Calcium binding site 3 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 6


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

b:56.4
occ:1.00
 O D:TYR55 2.3 51.1 1.0
OD2 D:ASP63 2.3 54.6 1.0
OD1 D:ASP53 2.3 46.5 1.0
OD2 D:ASP57 2.4 51.5 1.0
O D:GLN50 2.4 59.0 1.0
OE2 D:GLU64 2.4 60.1 1.0
CG D:ASP57 3.4 47.3 1.0
CD D:GLU64 3.4 45.1 1.0
C D:TYR55 3.5 44.7 1.0
CG D:ASP63 3.5 63.8 1.0
CG D:ASP53 3.5 59.5 1.0
C D:GLN50 3.5 67.2 1.0
CG D:GLU64 3.8 40.6 1.0
N D:ASP57 3.9 51.6 1.0
CB D:ASP57 3.9 37.6 1.0
CB D:ASP63 4.1 52.0 1.0
OD2 D:ASP53 4.2 56.8 1.0
NH1 C:ARG951 4.2 49.3 1.0
N D:TYR55 4.2 41.8 1.0
CA D:GLN50 4.3 58.5 1.0
CB D:GLN50 4.3 55.6 1.0
CA D:TYR55 4.3 42.0 1.0
O D:ASP63 4.3 47.3 1.0
OD1 D:ASP57 4.4 50.5 1.0
N D:CYS56 4.4 41.8 1.0
N D:ASP53 4.4 40.6 1.0
OD1 D:ASP63 4.5 54.0 1.0
C D:CYS56 4.5 49.5 1.0
OE1 D:GLU64 4.5 43.1 1.0
CA D:CYS56 4.5 47.4 1.0
N D:VAL51 4.5 71.7 1.0
CA D:ASP57 4.6 50.3 1.0
CB D:TYR55 4.6 54.5 1.0
CB D:ASP53 4.6 48.0 1.0
CD1 D:ILE46 4.7 68.0 1.0
CA D:VAL51 4.7 56.4 1.0
N D:ASN52 4.8 46.0 1.0
C D:ASP63 4.8 58.1 1.0
CA D:ASP53 4.9 48.5 1.0

Calcium binding site 4 out of 4 in 7kad

Go back to Calcium Binding Sites List in 7kad
Calcium binding site 4 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 6


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

b:44.1
occ:1.00
 O D:VAL96 2.3 41.9 1.0
OD2 D:ASP98 2.3 39.5 1.0
O D:ARG91 2.3 44.9 1.0
OE2 D:GLU105 2.3 36.3 1.0
OD2 D:ASP104 2.4 42.3 1.0
OD1 D:ASP94 2.5 43.6 1.0
CD D:GLU105 3.3 41.8 1.0
CG D:ASP94 3.4 48.3 1.0
C D:VAL96 3.4 48.0 1.0
CG D:ASP98 3.5 46.2 1.0
C D:ARG91 3.5 42.6 1.0
CG D:ASP104 3.6 54.7 1.0
OD2 D:ASP94 3.7 41.3 1.0
CG D:GLU105 3.9 47.6 1.0
N D:VAL96 4.0 35.6 1.0
CB D:ASP98 4.0 49.2 1.0
N D:ASP98 4.1 40.2 1.0
CA D:VAL96 4.2 46.2 1.0
CB D:ASP104 4.2 51.5 1.0
N D:ASP94 4.2 47.4 1.0
CA D:ARG91 4.3 40.4 1.0
CB D:ARG91 4.3 46.4 1.0
OE1 D:GLU105 4.4 44.9 1.0
N D:ASN93 4.4 36.6 1.0
CB D:VAL96 4.4 45.3 1.0
O D:ASP104 4.4 44.1 1.0
N D:VAL92 4.5 41.2 1.0
N D:CYS97 4.5 51.6 1.0
OD1 D:ASP98 4.5 54.4 1.0
OD1 D:ASP104 4.6 45.8 1.0
CB D:ASP94 4.6 41.8 1.0
CA D:VAL92 4.6 45.4 1.0
NH2 C:ARG840 4.6 41.1 1.0
CA D:CYS97 4.7 42.7 1.0
CA D:ASP98 4.7 47.1 1.0
C D:CYS97 4.7 46.6 1.0
C D:ASP104 4.7 43.6 1.0
C D:VAL92 4.8 43.7 1.0
N D:GLY95 4.8 37.3 1.0
CA D:ASP94 4.9 41.2 1.0

Reference:

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Alpha Glucosidase with Compound 6 To Be Published.
Page generated: Fri Jul 19 01:13:37 2024

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