Calcium in PDB 7k9t: Co-Crystal Structure of Alpha Glucosidase with Compound 5

Protein crystallography data

The structure of Co-Crystal Structure of Alpha Glucosidase with Compound 5, PDB code: 7k9t 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) 42.35 / 2.10
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 102.87, 102.87, 240.653, 90, 90, 120
R / Rfree (%) 17.1 / 19.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Co-Crystal Structure of Alpha Glucosidase with Compound 5 (pdb code 7k9t). 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 5, PDB code: 7k9t:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 7k9t

Go back to Calcium Binding Sites List in 7k9t
Calcium binding site 1 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 5


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

b:39.6
occ:1.00
 OD1 B:ASP53 2.3 41.0 1.0
O B:TYR55 2.3 41.8 1.0
OE2 B:GLU64 2.3 38.1 1.0
OD2 B:ASP57 2.4 43.3 1.0
OD2 B:ASP63 2.4 43.6 1.0
O B:GLN50 2.4 45.9 1.0
CD B:GLU64 3.4 34.0 1.0
CG B:ASP57 3.4 42.6 1.0
C B:GLN50 3.5 54.9 1.0
CG B:ASP53 3.5 44.9 1.0
C B:TYR55 3.5 37.5 1.0
CG B:ASP63 3.5 43.9 1.0
CG B:GLU64 3.8 32.5 1.0
CB B:ASP57 3.9 38.7 1.0
N B:ASP57 4.0 48.2 1.0
OD2 B:ASP53 4.2 44.3 1.0
CB B:ASP63 4.2 45.4 1.0
CA B:GLN50 4.2 61.8 1.0
N B:TYR55 4.2 34.3 1.0
CB B:GLN50 4.2 47.2 1.0
NH1 A:ARG951 4.3 41.8 1.0
N B:ASP53 4.3 35.3 1.0
CA B:TYR55 4.3 32.4 1.0
O B:ASP63 4.4 45.2 1.0
OE1 B:GLU64 4.4 37.0 1.0
OD1 B:ASP57 4.5 45.2 1.0
N B:CYS56 4.5 36.3 1.0
N B:VAL51 4.5 51.6 1.0
OD1 B:ASP63 4.5 46.6 1.0
CB B:ASP53 4.6 39.0 1.0
CA B:CYS56 4.6 46.0 1.0
CB B:TYR55 4.6 36.7 1.0
C B:CYS56 4.6 43.2 1.0
N B:ASN52 4.6 38.9 1.0
CA B:ASP57 4.7 42.9 1.0
CA B:VAL51 4.7 44.5 1.0
C B:ASP63 4.8 44.3 1.0
CD1 B:ILE46 4.8 62.2 1.0
CA B:ASP53 4.8 42.7 1.0
C B:ASP53 5.0 42.9 1.0
C B:VAL51 5.0 47.0 1.0
N B:ASP54 5.0 36.3 1.0

Calcium binding site 2 out of 4 in 7k9t

Go back to Calcium Binding Sites List in 7k9t
Calcium binding site 2 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 5


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

b:34.6
occ:1.00
 O B:VAL96 2.2 27.9 1.0
O B:ARG91 2.3 31.5 1.0
OD2 B:ASP98 2.4 35.6 1.0
OD2 B:ASP104 2.4 41.2 1.0
OE2 B:GLU105 2.4 32.9 1.0
OD1 B:ASP94 2.5 35.5 1.0
CG B:ASP94 3.4 32.0 1.0
CD B:GLU105 3.4 31.4 1.0
C B:VAL96 3.4 31.4 1.0
C B:ARG91 3.5 35.2 1.0
CG B:ASP98 3.5 34.5 1.0
CG B:ASP104 3.5 44.8 1.0
OD2 B:ASP94 3.8 34.2 1.0
CG B:GLU105 3.9 36.2 1.0
CB B:ASP98 4.0 34.5 1.0
N B:ASP98 4.0 33.4 1.0
N B:VAL96 4.1 33.9 1.0
CB B:ASP104 4.1 36.3 1.0
CB B:ARG91 4.2 36.1 1.0
CA B:ARG91 4.2 33.9 1.0
CA B:VAL96 4.2 35.7 1.0
N B:ASP94 4.2 34.4 1.0
OE1 B:GLU105 4.4 30.7 1.0
CB B:VAL96 4.4 29.1 1.0
N B:CYS97 4.4 34.9 1.0
N B:ASN93 4.5 29.3 1.0
N B:VAL92 4.5 35.0 1.0
OD1 B:ASP104 4.5 42.4 1.0
OD1 B:ASP98 4.5 43.6 1.0
CB B:ASP94 4.6 31.5 1.0
CA B:ASP98 4.6 35.1 1.0
O B:ASP104 4.6 34.2 1.0
CA B:CYS97 4.6 34.9 1.0
C B:CYS97 4.6 32.1 1.0
NH2 A:ARG840 4.7 28.8 1.0
CA B:VAL92 4.7 32.8 1.0
C B:ASP104 4.8 30.5 1.0
CA B:ASP94 4.8 32.6 1.0
C B:VAL92 4.9 30.1 1.0
N B:GLY95 4.9 30.4 1.0
CD1 B:ILE87 5.0 36.8 1.0

Calcium binding site 3 out of 4 in 7k9t

Go back to Calcium Binding Sites List in 7k9t
Calcium binding site 3 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2002

b:40.2
occ:1.00
 OD1 D:ASP53 2.3 39.7 1.0
O D:TYR55 2.3 32.3 1.0
OD2 D:ASP63 2.4 44.8 1.0
O D:GLN50 2.4 45.1 1.0
OE2 D:GLU64 2.4 50.1 1.0
OD2 D:ASP57 2.4 34.5 1.0
CD D:GLU64 3.4 39.6 1.0
CG D:ASP57 3.5 38.9 1.0
CG D:ASP53 3.5 53.2 1.0
C D:TYR55 3.5 32.3 1.0
C D:GLN50 3.5 57.8 1.0
CG D:ASP63 3.6 42.7 1.0
CG D:GLU64 3.9 35.8 1.0
CB D:ASP57 4.0 38.1 1.0
N D:ASP57 4.1 46.4 1.0
OD2 D:ASP53 4.2 45.8 1.0
N D:TYR55 4.2 26.9 1.0
CA D:GLN50 4.2 57.8 1.0
CB D:GLN50 4.2 42.9 1.0
NH1 C:ARG951 4.2 37.2 1.0
CB D:ASP63 4.3 50.3 1.0
CA D:TYR55 4.3 31.6 1.0
N D:ASP53 4.3 39.4 1.0
N D:CYS56 4.5 32.0 1.0
OE1 D:GLU64 4.5 33.9 1.0
OD1 D:ASP57 4.5 40.9 1.0
O D:ASP63 4.5 40.8 1.0
OD1 D:ASP63 4.5 49.0 1.0
N D:VAL51 4.5 55.3 1.0
CB D:ASP53 4.6 32.8 1.0
CB D:TYR55 4.6 32.7 1.0
CA D:CYS56 4.6 35.2 1.0
C D:CYS56 4.6 41.6 1.0
CA D:ASP57 4.7 43.7 1.0
N D:ASN52 4.7 43.0 1.0
CA D:VAL51 4.8 41.1 1.0
CD1 D:ILE46 4.8 57.9 1.0
CA D:ASP53 4.8 39.8 1.0
C D:ASP63 4.9 39.1 1.0
C D:ASP53 5.0 46.4 1.0
N D:ASP54 5.0 42.0 1.0

Calcium binding site 4 out of 4 in 7k9t

Go back to Calcium Binding Sites List in 7k9t
Calcium binding site 4 out of 4 in the Co-Crystal Structure of Alpha Glucosidase with Compound 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca2003

b:33.9
occ:1.00
 O D:VAL96 2.2 29.6 1.0
O D:ARG91 2.3 32.4 1.0
OD2 D:ASP98 2.3 31.7 1.0
OE2 D:GLU105 2.3 30.8 1.0
OD2 D:ASP104 2.3 40.7 1.0
OD1 D:ASP94 2.4 31.5 1.0
CG D:ASP94 3.3 38.4 1.0
CD D:GLU105 3.3 29.5 1.0
C D:VAL96 3.4 36.5 1.0
CG D:ASP98 3.4 40.8 1.0
CG D:ASP104 3.5 42.0 1.0
C D:ARG91 3.5 32.5 1.0
OD2 D:ASP94 3.7 29.6 1.0
CG D:GLU105 3.9 34.8 1.0
CB D:ASP98 4.0 37.8 1.0
N D:ASP98 4.0 38.1 1.0
CB D:ASP104 4.1 37.6 1.0
N D:VAL96 4.1 28.5 1.0
CA D:ARG91 4.2 32.1 1.0
N D:ASP94 4.2 35.4 1.0
CA D:VAL96 4.2 33.9 1.0
CB D:ARG91 4.2 35.0 1.0
OE1 D:GLU105 4.3 33.3 1.0
N D:ASN93 4.4 29.5 1.0
N D:CYS97 4.5 37.0 1.0
OD1 D:ASP104 4.5 41.1 1.0
N D:VAL92 4.5 32.1 1.0
CB D:VAL96 4.5 34.3 1.0
OD1 D:ASP98 4.5 39.0 1.0
O D:ASP104 4.5 39.4 1.0
CB D:ASP94 4.5 29.6 1.0
NH2 C:ARG840 4.6 34.3 1.0
CA D:ASP98 4.6 30.1 1.0
CA D:CYS97 4.6 31.6 1.0
C D:CYS97 4.6 35.5 1.0
CA D:VAL92 4.7 26.4 1.0
C D:ASP104 4.7 34.3 1.0
CA D:ASP94 4.8 28.1 1.0
C D:VAL92 4.8 28.4 1.0
N D:GLY95 4.9 29.6 1.0

Reference:

S.S.Karade, R.A.Mariuzza. Co-Crystal Structure of Alpha Glucosidase with Compound 5 To Be Published.
Page generated: Fri Jul 19 01:12:50 2024

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