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Calcium in PDB 3wnp: D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose

Enzymatic activity of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose

All present enzymatic activity of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose:
2.4.1.248;

Protein crystallography data

The structure of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose, PDB code: 3wnp was solved by R.Suzuki, N.Suzuki, Z.Fujimoto, M.Momma, K.Kimura, S.Kitamura, A.Kimura, K.Funane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.85 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.987, 172.813, 172.305, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.3

Other elements in 3wnp:

The structure of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose (pdb code 3wnp). 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, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose, PDB code: 3wnp:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 3wnp

Go back to Calcium Binding Sites List in 3wnp
Calcium binding site 1 out of 2 in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca801

b:67.7
occ:1.00
 O A:GLY446 2.3 67.2 1.0
OD1 A:ASP541 2.4 75.0 1.0
OE1 A:GLU424 2.5 66.3 1.0
O A:ASP541 2.6 56.4 1.0
OE1 A:GLU426 2.6 66.5 1.0
O A:THR443 2.6 59.9 1.0
OE2 A:GLU426 2.9 66.5 1.0
CD A:GLU426 3.1 66.9 1.0
CG A:ASP541 3.3 69.2 1.0
C A:ASP541 3.5 56.6 1.0
C A:GLY446 3.5 66.1 1.0
CD A:GLU424 3.7 69.5 1.0
C A:THR443 3.7 77.3 1.0
CA A:ASP541 3.8 59.9 1.0
OG1 A:THR443 3.9 77.5 1.0
OD2 A:ASP541 4.1 68.8 1.0
N A:THR443 4.1 75.9 1.0
CB A:ASP541 4.2 62.2 1.0
CA A:PHE447 4.3 65.8 1.0
N A:PHE447 4.4 61.9 1.0
N A:GLY446 4.4 73.9 1.0
CA A:THR443 4.4 78.3 1.0
OE2 A:GLU424 4.4 65.0 1.0
N A:ALA425 4.4 58.2 1.0
CA A:GLY446 4.5 67.7 1.0
CB A:GLU424 4.6 62.6 1.0
CG A:GLU426 4.6 66.7 1.0
CG A:GLU424 4.6 67.3 1.0
CB A:PHE447 4.6 67.3 1.0
N A:GLY444 4.7 71.5 1.0
N A:SER542 4.7 54.4 1.0
CA A:GLU424 4.8 57.8 1.0
CB A:THR443 4.8 81.2 1.0
CB A:SER542 4.9 58.7 1.0
CB A:TYR442 4.9 74.2 1.0
N A:GLU426 5.0 64.2 1.0
CD1 A:TYR442 5.0 72.8 1.0

Calcium binding site 2 out of 2 in 3wnp

Go back to Calcium Binding Sites List in 3wnp
Calcium binding site 2 out of 2 in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca801

b:67.3
occ:1.00
 OD1 B:ASP541 2.3 74.4 1.0
O B:GLY446 2.3 59.2 1.0
OE1 B:GLU424 2.5 66.7 1.0
O B:ASP541 2.5 56.1 1.0
OE1 B:GLU426 2.6 64.8 1.0
O B:THR443 2.7 73.1 1.0
OE2 B:GLU426 2.8 66.7 1.0
CD B:GLU426 3.1 69.2 1.0
CG B:ASP541 3.3 69.3 1.0
C B:GLY446 3.5 67.2 1.0
C B:ASP541 3.5 56.7 1.0
OG1 B:THR443 3.6 83.8 1.0
CD B:GLU424 3.7 72.3 1.0
C B:THR443 3.7 80.9 1.0
CA B:ASP541 3.9 63.1 1.0
OD2 B:ASP541 4.0 73.0 1.0
N B:THR443 4.2 78.8 1.0
CB B:ASP541 4.2 58.8 1.0
CA B:PHE447 4.3 68.4 1.0
N B:PHE447 4.3 62.3 1.0
CA B:THR443 4.3 84.7 1.0
N B:ALA425 4.4 56.3 1.0
N B:GLY446 4.4 72.8 1.0
OE2 B:GLU424 4.4 64.7 1.0
CB B:GLU424 4.4 64.5 1.0
CA B:GLY446 4.5 68.7 1.0
CG B:GLU424 4.6 68.1 1.0
CG B:GLU426 4.6 71.6 1.0
CB B:PHE447 4.6 74.2 1.0
CB B:THR443 4.6 86.9 1.0
CA B:GLU424 4.6 60.8 1.0
N B:SER542 4.7 50.8 1.0
N B:GLY444 4.7 77.3 1.0
CB B:SER542 4.8 60.0 1.0
CB B:TYR442 4.9 79.5 1.0
N B:GLU426 5.0 66.0 1.0
CA B:GLY444 5.0 69.1 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 17:59:31 2025

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