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Cadmium in PDB 3wnk: Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase

Enzymatic activity of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase

All present enzymatic activity of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase:
2.4.1.248;

Protein crystallography data

The structure of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase, PDB code: 3wnk 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) 44.34 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 106.437, 106.437, 160.625, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 19.2

Other elements in 3wnk:

The structure of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase (pdb code 3wnk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 10 binding sites of Cadmium where determined in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase, PDB code: 3wnk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 10 in 3wnk

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Cadmium binding site 1 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd801

b:31.8
occ:1.00
 O A:HOH1038 2.0 21.2 1.0
O A:GLN666 2.2 24.6 1.0
OD1 A:ASN669 2.3 31.3 1.0
O A:HOH1087 2.3 28.2 1.0
O A:HOH1086 2.4 25.9 1.0
OD1 A:ASP664 2.4 32.3 1.0
CG A:ASP664 3.2 33.1 1.0
CG A:ASN669 3.3 30.8 1.0
OD2 A:ASP664 3.3 32.2 1.0
C A:GLN666 3.3 28.4 1.0
ND2 A:ASN669 3.7 29.9 1.0
N A:GLN666 3.9 29.6 1.0
CA A:GLN666 3.9 31.1 1.0
CB A:GLN666 3.9 32.2 1.0
O A:ASN669 4.0 27.4 1.0
OH A:TYR388 4.1 28.6 1.0
O A:ASP664 4.2 32.8 1.0
O A:THR670 4.3 33.9 1.0
O A:HOH1023 4.3 31.1 1.0
N A:TRP667 4.4 28.1 1.0
C A:ASP664 4.5 31.8 1.0
CB A:ASP664 4.6 33.0 1.0
C A:ASN669 4.6 26.6 1.0
CB A:ASN669 4.6 27.9 1.0
N A:ASN669 4.6 25.8 1.0
CB A:ALA671 4.6 33.7 1.0
O A:HOH1010 4.7 30.0 1.0
CZ A:TYR388 4.8 27.7 1.0
CA A:TRP667 4.8 29.0 1.0
N A:ASP664 4.8 33.3 1.0
CA A:ASN669 4.8 26.4 1.0
CA A:ASP664 4.9 32.4 1.0
C A:TRP667 4.9 27.7 1.0
CE2 A:TYR388 4.9 27.8 1.0
C A:ASN665 4.9 31.3 1.0
CG A:GLN666 5.0 35.3 1.0
C A:THR670 5.0 32.7 1.0

Cadmium binding site 2 out of 10 in 3wnk

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Cadmium binding site 2 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd802

b:30.8
occ:1.00
 O A:HOH1127 1.9 26.2 1.0
O A:HOH1286 2.1 30.1 1.0
OD2 A:ASP221 2.2 33.1 1.0
OD2 A:ASP225 2.3 24.6 1.0
OXT A:ACT815 2.6 41.4 1.0
O A:ACT815 2.6 39.3 1.0
CG A:ASP225 3.0 24.4 1.0
C A:ACT815 3.0 39.9 1.0
OD1 A:ASP225 3.0 22.9 1.0
CG A:ASP221 3.0 32.6 1.0
OD1 A:ASP221 3.1 36.6 1.0
CB A:ASP221 4.4 31.0 1.0
O A:HOH1255 4.4 41.0 1.0
CB A:ASP225 4.5 24.4 1.0
O A:ASP221 4.5 30.8 1.0
CH3 A:ACT815 4.5 40.3 1.0
O A:HOH1175 4.7 39.5 1.0
C A:ASP221 4.8 28.2 1.0

Cadmium binding site 3 out of 10 in 3wnk

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Cadmium binding site 3 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd803

b:59.0
occ:1.00
 O A:HOH1380 2.3 58.7 1.0
OE1 A:GLU380 2.4 26.4 1.0
O A:HOH1357 2.5 39.5 1.0
OE2 A:GLU380 2.6 25.3 1.0
O A:HOH1356 2.8 39.5 1.0
CD A:GLU380 2.8 26.3 1.0
O A:HOH1523 3.7 54.3 1.0
ND2 A:ASN354 4.1 29.0 1.0
CG A:GLU380 4.3 26.2 1.0
O A:HOH1073 4.4 28.1 1.0
OD2 A:ASP308 4.4 30.6 1.0
NE1 A:TRP382 4.5 30.8 1.0
OD1 A:ASP308 4.5 28.9 1.0
CB A:GLU580 4.5 25.9 1.0
O A:GLN309 4.6 31.4 1.0
O A:HOH1251 4.6 40.3 1.0
OH A:TYR412 4.8 20.7 1.0
CZ2 A:TRP382 4.8 28.3 1.0
CG2 A:VAL356 4.8 33.0 1.0
CB A:GLU380 4.9 26.3 1.0
CG A:ASP308 4.9 29.5 1.0
CG1 A:VAL356 5.0 31.0 1.0

Cadmium binding site 4 out of 10 in 3wnk

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Cadmium binding site 4 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd804

b:60.2
occ:1.00
 O A:THR443 2.4 34.3 1.0
OE1 A:GLU424 2.4 33.8 1.0
OD1 A:ASP541 2.4 35.3 1.0
O A:GLY446 2.5 37.0 1.0
OE1 A:GLU426 2.6 36.7 1.0
OE2 A:GLU426 2.7 37.5 1.0
O A:ASP541 2.9 31.1 1.0
CD A:GLU426 3.0 38.4 1.0
CD A:GLU424 3.3 33.5 1.0
C A:THR443 3.5 35.6 1.0
CG A:ASP541 3.5 35.0 1.0
C A:GLY446 3.6 36.0 1.0
OG1 A:THR443 3.8 34.4 1.0
C A:ASP541 3.8 32.5 1.0
OE2 A:GLU424 4.0 33.8 1.0
N A:THR443 4.1 36.5 1.0
CB A:GLU424 4.1 35.9 1.0
CA A:ASP541 4.2 32.9 1.0
CG A:GLU424 4.2 34.7 1.0
OD2 A:ASP541 4.3 39.4 1.0
CA A:THR443 4.3 36.1 1.0
CA A:PHE447 4.3 34.1 1.0
N A:GLY446 4.3 38.8 1.0
N A:GLY444 4.4 37.4 1.0
N A:PHE447 4.4 35.1 1.0
CB A:ASP541 4.5 33.5 1.0
CA A:GLY444 4.5 40.6 1.0
CG A:GLU426 4.5 37.6 1.0
CA A:GLY446 4.6 37.6 1.0
CB A:TYR442 4.6 38.2 1.0
N A:ALA425 4.6 37.7 1.0
CA A:GLU424 4.6 36.6 1.0
CB A:THR443 4.7 36.8 1.0
CB A:PHE447 4.7 33.9 1.0
N A:SER445 4.8 40.6 1.0
C A:GLY444 4.8 41.5 1.0
N A:SER542 4.9 33.1 1.0
C A:TYR442 5.0 35.7 1.0
CB A:SER542 5.0 33.6 1.0

Cadmium binding site 5 out of 10 in 3wnk

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Cadmium binding site 5 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd805

b:57.3
occ:1.00
 O A:HOH1121 2.3 38.9 1.0
O A:ALA671 2.3 33.8 1.0
OD1 A:ASP549 2.4 35.5 1.0
ND1 A:HIS551 2.5 31.1 1.0
O A:HOH1192 2.6 42.4 1.0
CG A:ASP549 3.2 32.2 1.0
CE1 A:HIS551 3.2 31.7 1.0
C A:ALA671 3.5 34.5 1.0
CG A:HIS551 3.6 29.9 1.0
OD2 A:ASP549 3.7 31.4 1.0
CB A:HIS551 4.0 29.6 1.0
CA A:SER672 4.2 34.1 1.0
CB A:ASP549 4.3 31.2 1.0
N A:SER672 4.3 33.4 1.0
N A:ALA671 4.4 34.4 1.0
O A:HOH1327 4.4 38.6 1.0
O A:HOH1395 4.4 52.3 1.0
NE2 A:HIS551 4.4 31.7 1.0
CA A:ALA671 4.6 33.8 1.0
C A:SER672 4.6 31.5 1.0
CD2 A:HIS551 4.6 31.0 1.0
O A:HOH1130 4.8 41.1 1.0
N A:GLN673 4.8 32.8 1.0
N A:HIS551 4.8 30.7 1.0

Cadmium binding site 6 out of 10 in 3wnk

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Cadmium binding site 6 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd806

b:76.1
occ:1.00
 OE1 A:GLU162 2.7 38.8 1.0
OE2 A:GLU162 2.9 44.5 1.0
O A:HOH1261 3.0 45.5 1.0
O A:GLY157 3.1 41.2 1.0
CD A:GLU162 3.1 40.2 1.0
C A:GLY157 3.9 38.4 1.0
CA A:GLU158 4.2 33.4 1.0
N A:GLU158 4.4 34.9 1.0
CG A:GLU162 4.6 37.6 1.0
N A:THR159 4.6 32.1 1.0
CA A:GLY157 4.9 37.2 1.0
C A:GLU158 5.0 31.6 1.0

Cadmium binding site 7 out of 10 in 3wnk

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Cadmium binding site 7 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd807

b:89.4
occ:1.00
 O A:ASN371 2.2 45.8 1.0
OD2 A:ASP335 2.7 39.5 1.0
OD1 A:ASP335 2.8 37.8 1.0
CG A:ASP335 3.0 36.8 1.0
O A:HOH1318 3.0 46.1 1.0
C A:ASN371 3.4 38.8 1.0
O A:HOH1290 4.0 50.5 1.0
N A:ASP373 4.1 33.5 1.0
CA A:ASN371 4.2 38.0 1.0
O A:HOH1453 4.2 53.0 1.0
N A:ALA372 4.3 35.6 1.0
CA A:ALA372 4.4 34.5 1.0
C A:ALA372 4.4 32.5 1.0
CB A:ASP335 4.4 36.1 1.0
CB A:ASN371 4.6 38.4 1.0
CB A:ASP373 4.7 35.8 1.0
CA A:ASP373 4.8 35.1 1.0

Cadmium binding site 8 out of 10 in 3wnk

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Cadmium binding site 8 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd808

b:63.8
occ:1.00
 OE1 A:GLU153 2.5 38.7 0.7
O A:HOH1429 2.6 53.8 1.0
OE2 A:GLU153 2.8 37.6 0.7
O A:HOH1359 2.9 46.6 1.0
CD A:GLU153 3.0 36.9 0.7
O A:HOH1173 3.0 32.7 1.0
OE2 A:GLU153 3.3 30.6 0.3
NH2 A:ARG585 3.9 54.0 1.0
CD A:GLU153 4.0 32.1 0.3
OE1 A:GLU153 4.1 33.7 0.3
OE1 A:GLU155 4.2 67.3 1.0
CG A:GLU153 4.4 33.4 0.7
O A:HOH1428 4.5 45.2 1.0
CZ A:ARG585 4.7 49.6 1.0
NH1 A:ARG585 4.9 48.5 1.0
O A:HOH1211 5.0 34.7 1.0

Cadmium binding site 9 out of 10 in 3wnk

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Cadmium binding site 9 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd809

b:46.0
occ:1.00
 O A:HOH1353 2.2 27.7 1.0
OH A:TYR415 2.4 31.9 1.0
OE2 A:GLU580 2.5 26.1 1.0
O A:HOH1354 2.6 38.4 1.0
CD A:GLU580 3.4 25.0 1.0
OE1 A:GLU580 3.5 25.3 1.0
CZ A:TYR415 3.7 30.4 1.0
NE2 A:HIS579 3.8 25.5 1.0
CE1 A:HIS579 4.3 26.0 1.0
CE2 A:TYR415 4.3 28.7 1.0
CD2 A:HIS579 4.7 25.6 1.0
CE1 A:TYR415 4.7 29.4 1.0
CG A:GLU580 4.8 24.6 1.0

Cadmium binding site 10 out of 10 in 3wnk

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Cadmium binding site 10 out of 10 in the Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd810

b:0.4
occ:1.00
 NE2 A:HIS260 2.9 67.4 1.0
CE1 A:HIS260 3.4 68.3 1.0
CD2 A:HIS260 4.1 67.8 1.0
OH A:TYR319 4.4 57.2 1.0
ND1 A:HIS260 4.7 66.8 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: Thu Jul 10 13:09:38 2025

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