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

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

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

Protein crystallography data

The structure of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltooctaose, PDB code: 3wnn was solved by N.Suzuki, Z.Fujimoto, Y.M.Kim, M.Momma, N.Kishine, R.Suzuki, S.Suzuki, S.Kitamura, 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) 35.35 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.031, 171.256, 173.251, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.4

Other elements in 3wnn:

The structure of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltooctaose 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 Isomaltooctaose (pdb code 3wnn). 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 Isomaltooctaose, PDB code: 3wnn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3wnn

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


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 Isomaltooctaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:49.6
occ:1.00
 OD1 A:ASP541 2.1 48.0 1.0
O A:THR443 2.3 45.0 1.0
O A:GLY446 2.3 52.0 1.0
OE1 A:GLU424 2.3 43.8 1.0
OE1 A:GLU426 2.5 39.2 1.0
O A:ASP541 2.6 47.4 1.0
OE2 A:GLU426 2.7 50.4 1.0
CD A:GLU426 3.0 51.8 1.0
CG A:ASP541 3.2 50.0 1.0
CD A:GLU424 3.4 51.0 1.0
C A:THR443 3.4 54.8 1.0
C A:GLY446 3.5 51.8 1.0
C A:ASP541 3.6 47.4 1.0
OG1 A:THR443 3.6 50.0 1.0
OD2 A:ASP541 3.9 45.5 1.0
CA A:ASP541 3.9 47.4 1.0
OE2 A:GLU424 4.0 43.1 1.0
N A:THR443 4.2 60.8 1.0
CB A:ASP541 4.2 44.2 1.0
CA A:PHE447 4.2 50.9 1.0
CA A:THR443 4.3 55.3 1.0
N A:PHE447 4.3 51.1 1.0
N A:GLY446 4.4 52.8 1.0
N A:GLY444 4.4 53.4 1.0
CB A:GLU424 4.4 46.8 1.0
CG A:GLU424 4.4 50.4 1.0
CB A:PHE447 4.5 52.7 1.0
CA A:GLY446 4.5 51.2 1.0
CG A:GLU426 4.5 52.4 1.0
CA A:GLY444 4.6 56.6 1.0
CB A:THR443 4.6 49.2 1.0
N A:ALA425 4.6 47.5 1.0
N A:SER542 4.7 42.5 1.0
CA A:GLU424 4.8 46.4 1.0
CB A:SER542 4.8 46.0 1.0
CB A:TYR442 4.9 62.5 1.0
C A:GLY444 5.0 60.5 1.0

Calcium binding site 2 out of 2 in 3wnn

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


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 Isomaltooctaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:44.2
occ:1.00
 OD1 B:ASP541 2.2 39.9 1.0
O B:GLY446 2.3 46.4 1.0
OE1 B:GLU424 2.4 41.8 1.0
O B:THR443 2.5 55.2 1.0
O B:ASP541 2.6 39.7 1.0
OE1 B:GLU426 2.6 47.9 1.0
OE2 B:GLU426 2.6 48.2 1.0
CD B:GLU426 2.9 46.7 1.0
CD B:GLU424 3.4 47.6 1.0
CG B:ASP541 3.4 37.3 1.0
C B:GLY446 3.5 47.9 1.0
C B:ASP541 3.6 35.4 1.0
C B:THR443 3.6 56.2 1.0
CA B:ASP541 4.0 35.6 1.0
OG1 B:THR443 4.0 41.6 1.0
OE2 B:GLU424 4.1 55.0 1.0
OD2 B:ASP541 4.2 36.2 1.0
CB B:GLU424 4.2 42.8 1.0
N B:THR443 4.3 48.6 1.0
CB B:ASP541 4.3 35.0 1.0
CG B:GLU424 4.3 44.2 1.0
CA B:PHE447 4.3 48.0 1.0
N B:GLY446 4.4 49.8 1.0
N B:ALA425 4.4 42.8 1.0
N B:PHE447 4.4 47.5 1.0
CG B:GLU426 4.4 46.5 1.0
CA B:THR443 4.4 52.1 1.0
N B:GLY444 4.5 61.4 1.0
CA B:GLY446 4.5 47.1 1.0
CA B:GLY444 4.6 61.4 1.0
CA B:GLU424 4.6 42.7 1.0
CB B:TYR442 4.7 52.5 1.0
N B:SER542 4.7 35.7 1.0
CB B:PHE447 4.8 52.2 1.0
C B:GLY444 4.8 61.9 1.0
CB B:SER542 4.9 40.7 1.0
CB B:THR443 4.9 48.4 1.0
C B:GLU424 5.0 45.2 1.0
N B:GLU426 5.0 44.1 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 17:59:07 2025

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