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Calcium in PDB 3wno: D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose

Enzymatic activity of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose

All present enzymatic activity of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose:
2.4.1.248;

Protein crystallography data

The structure of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose, PDB code: 3wno was solved by N.Suzuki, Z.Fujimoto, Y.M.Kim, M.Momma, N.Kishine, R.Suzuki, M.Kobayashi, A.Kimura, K.Funane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.47 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.928, 167.715, 174.861, 90.00, 90.00, 90.00
R / Rfree (%) 17 / 19.5

Other elements in 3wno:

The structure of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose (pdb code 3wno). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose, PDB code: 3wno:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3wno

Go back to Calcium Binding Sites List in 3wno
Calcium binding site 1 out of 2 in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:30.8
occ:1.00
 OE1 A:GLU424 2.1 28.9 1.0
OD1 A:ASP541 2.3 30.6 1.0
O A:THR443 2.4 33.1 1.0
O A:GLY446 2.4 35.1 1.0
OE1 A:GLU426 2.5 28.1 1.0
OE2 A:GLU426 2.7 30.7 1.0
O A:ASP541 2.7 25.7 1.0
CD A:GLU426 2.9 30.3 1.0
CD A:GLU424 3.3 29.8 1.0
CG A:ASP541 3.4 31.7 1.0
C A:THR443 3.5 33.7 1.0
C A:ASP541 3.6 26.8 1.0
C A:GLY446 3.6 33.1 1.0
OG1 A:THR443 3.8 32.6 1.0
CA A:ASP541 3.9 28.1 1.0
OE2 A:GLU424 4.0 33.6 1.0
N A:THR443 4.2 31.8 1.0
OD2 A:ASP541 4.3 32.4 1.0
CB A:ASP541 4.3 29.8 1.0
CB A:GLU424 4.3 28.3 1.0
CG A:GLU424 4.3 29.2 1.0
CA A:THR443 4.3 32.1 1.0
N A:GLY444 4.3 33.3 1.0
CA A:PHE447 4.4 30.9 1.0
N A:PHE447 4.4 30.0 1.0
N A:GLY446 4.4 34.1 1.0
CG A:GLU426 4.4 29.9 1.0
CA A:GLY444 4.5 35.3 1.0
CA A:GLY446 4.6 34.1 1.0
CB A:TYR442 4.6 35.9 1.0
N A:ALA425 4.6 26.3 1.0
CB A:THR443 4.7 32.9 1.0
CA A:GLU424 4.7 26.9 1.0
N A:SER542 4.7 25.2 1.0
CB A:PHE447 4.8 30.7 1.0
C A:GLY444 4.9 35.3 1.0
CB A:SER542 4.9 26.5 1.0
N A:GLU426 5.0 28.2 1.0

Calcium binding site 2 out of 2 in 3wno

Go back to Calcium Binding Sites List in 3wno
Calcium binding site 2 out of 2 in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca809

b:26.3
occ:1.00
 OE1 B:GLU424 2.3 26.1 1.0
OD1 B:ASP541 2.3 23.8 1.0
O B:THR443 2.4 27.0 1.0
O B:GLY446 2.5 25.6 1.0
OE1 B:GLU426 2.6 27.6 1.0
O B:ASP541 2.7 20.3 1.0
OE2 B:GLU426 2.7 30.5 1.0
CD B:GLU426 3.0 28.6 1.0
CD B:GLU424 3.4 25.8 1.0
CG B:ASP541 3.4 23.9 1.0
C B:THR443 3.5 28.1 1.0
C B:ASP541 3.6 21.9 1.0
C B:GLY446 3.6 25.1 1.0
OG1 B:THR443 3.8 27.8 1.0
CA B:ASP541 3.9 21.7 1.0
OE2 B:GLU424 4.1 28.5 1.0
N B:THR443 4.1 27.0 1.0
CB B:GLU424 4.2 24.8 1.0
OD2 B:ASP541 4.3 25.2 1.0
CB B:ASP541 4.3 22.7 1.0
CA B:THR443 4.3 27.8 1.0
CG B:GLU424 4.3 25.4 1.0
CA B:PHE447 4.3 23.4 1.0
N B:GLY444 4.4 28.6 1.0
N B:PHE447 4.4 24.3 1.0
N B:GLY446 4.5 27.8 1.0
CA B:GLY444 4.5 29.2 1.0
N B:ALA425 4.5 23.2 1.0
CG B:GLU426 4.5 28.3 1.0
CB B:TYR442 4.6 27.0 1.0
CA B:GLU424 4.6 24.1 1.0
CA B:GLY446 4.7 26.2 1.0
CB B:PHE447 4.7 22.6 1.0
CB B:THR443 4.7 28.6 1.0
N B:SER542 4.7 21.0 1.0
C B:GLY444 4.9 29.4 1.0
CB B:SER542 4.9 22.0 1.0
N B:SER445 5.0 30.7 1.0
C B:TYR442 5.0 27.2 1.0

Reference:

N.Suzuki, Z.Fujimoto, Y.M.Kim, M.Momma, N.Kishine, R.Suzuki, S.Suzuki, S.Kitamura, M.Kobayashi, A.Kimura, K.Funane. Structural Elucidation of Cyclization Mechanism of Alpha-1,6-Glucan By Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase To Be Published.
Page generated: Tue Jul 8 17:59:11 2025

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