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Sodium in PDB 3wnl: D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltohexaose

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

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

Protein crystallography data

The structure of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltohexaose, PDB code: 3wnl 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) 47.78 / 2.60
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 172.107, 172.107, 60.926, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.7

Other elements in 3wnl:

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

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltohexaose (pdb code 3wnl). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltohexaose, PDB code: 3wnl:

Sodium binding site 1 out of 1 in 3wnl

Go back to Sodium Binding Sites List in 3wnl
Sodium binding site 1 out of 1 in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltohexaose


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 Isomaltohexaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:83.2
occ:1.00
 OD1 A:ASP664 2.3 69.7 1.0
O A:GLN666 2.5 66.9 1.0
OD1 A:ASN669 2.7 71.3 1.0
CG A:ASP664 3.4 69.4 1.0
C A:GLN666 3.6 61.7 1.0
OH A:TYR388 3.7 80.7 1.0
CG A:ASN669 3.7 70.0 1.0
OD2 A:ASP664 3.8 60.3 1.0
O A:ASN669 4.0 66.2 1.0
O A:HOH1028 4.1 61.9 1.0
O A:THR670 4.1 71.4 1.0
ND2 A:ASN669 4.1 68.9 1.0
CB A:ALA671 4.2 71.4 1.0
N A:GLN666 4.3 72.6 1.0
CA A:GLN666 4.3 66.6 1.0
N A:ASP664 4.4 64.3 1.0
O A:ASP664 4.4 61.8 1.0
CZ A:TYR388 4.5 72.8 1.0
CB A:GLN666 4.5 68.3 1.0
CE2 A:TYR388 4.5 77.0 1.0
C A:ASP664 4.6 66.6 1.0
CB A:ASP664 4.7 65.0 1.0
C A:ASN669 4.7 56.4 1.0
N A:TRP667 4.7 61.1 1.0
CA A:ASP664 4.8 60.5 1.0
C A:THR670 4.8 65.5 1.0
CA A:ALA671 4.9 65.2 1.0
CB A:ASN663 4.9 68.8 1.0
CA A:TRP667 5.0 57.5 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: Mon Oct 7 13:58:50 2024

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