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Sodium 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:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Cycloisomaltooctaose, PDB code: 3wno:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3wno

Go back to Sodium Binding Sites List in 3wno
Sodium 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 Sodium with other atoms in the Na 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:Na802

b:24.2
occ:1.00
 O A:HOH1391 2.3 25.1 1.0
O A:HOH1202 2.3 24.4 1.0
O A:HOH1403 2.3 31.3 1.0
O A:GLN666 2.3 22.7 1.0
OD1 A:ASP664 2.4 23.6 1.0
OD1 A:ASN669 2.4 26.0 1.0
CG A:ASP664 3.4 25.4 1.0
C A:GLN666 3.4 22.4 1.0
CG A:ASN669 3.5 26.7 1.0
OD2 A:ASP664 3.8 25.9 1.0
OH A:TYR388 3.9 20.2 1.0
N A:GLN666 4.0 22.9 1.0
ND2 A:ASN669 4.0 27.7 1.0
CA A:GLN666 4.0 22.9 1.0
CB A:GLN666 4.1 23.1 1.0
O A:ASN669 4.1 21.7 1.0
O A:HOH1219 4.2 26.5 1.0
O A:ASP664 4.2 23.3 1.0
O A:THR670 4.3 22.1 1.0
C A:ASP664 4.5 23.5 1.0
N A:TRP667 4.6 21.8 1.0
CB A:ALA671 4.6 23.7 1.0
C A:ASN669 4.6 23.0 1.0
CZ A:TYR388 4.6 20.5 1.0
O A:HOH1110 4.7 21.1 1.0
N A:ASN669 4.7 21.9 1.0
N A:ASP664 4.7 24.7 1.0
CB A:ASP664 4.7 24.9 1.0
CE2 A:TYR388 4.7 20.9 1.0
CB A:ASN669 4.8 24.4 1.0
CA A:ASP664 4.8 24.4 1.0
CA A:TRP667 4.9 20.5 1.0
C A:TRP667 4.9 20.4 1.0
CA A:ASN669 4.9 22.8 1.0
C A:THR670 5.0 23.0 1.0

Sodium binding site 2 out of 2 in 3wno

Go back to Sodium Binding Sites List in 3wno
Sodium 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 Sodium with other atoms in the Na 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:Na810

b:28.1
occ:1.00
 O B:HOH1327 2.1 33.9 1.0
O B:HOH1319 2.3 27.6 1.0
O B:GLN666 2.3 25.3 1.0
O B:HOH1346 2.3 33.1 1.0
OD1 B:ASP664 2.4 29.5 1.0
OD1 B:ASN669 2.4 30.6 1.0
CG B:ASP664 3.4 30.6 1.0
C B:GLN666 3.5 23.4 1.0
CG B:ASN669 3.5 28.0 1.0
OD2 B:ASP664 3.7 32.7 1.0
ND2 B:ASN669 3.9 29.5 1.0
N B:GLN666 4.0 24.0 1.0
OH B:TYR388 4.0 21.3 1.0
CA B:GLN666 4.0 24.3 1.0
O B:ASN669 4.0 25.0 1.0
CB B:GLN666 4.1 24.8 1.0
O B:ASP664 4.1 28.6 1.0
O B:HOH1142 4.1 29.0 1.0
O B:THR670 4.2 25.4 1.0
CB B:ALA671 4.5 26.8 1.0
C B:ASP664 4.5 28.0 1.0
N B:TRP667 4.6 22.7 1.0
O B:HOH1089 4.6 20.7 1.0
C B:ASN669 4.6 25.2 1.0
CB B:ASP664 4.7 29.8 1.0
CZ B:TYR388 4.7 20.6 1.0
CE2 B:TYR388 4.7 21.1 1.0
N B:ASN669 4.8 23.8 1.0
N B:ASP664 4.8 28.9 1.0
CB B:ASN669 4.8 26.4 1.0
CA B:TRP667 4.8 21.9 1.0
CA B:ASP664 4.9 29.1 1.0
C B:TRP667 4.9 21.7 1.0
C B:THR670 4.9 26.2 1.0
CA B:ASN669 4.9 25.0 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 Dec 15 06:30:11 2020

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