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

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

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

Protein crystallography data

The structure of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoheptaose, PDB code: 3wnm 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) 30.35 / 2.25
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 171.576, 171.576, 61.299, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 20.5

Other elements in 3wnm:

The structure of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoheptaose 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 Isomaltoheptaose (pdb code 3wnm). 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 Isomaltoheptaose, PDB code: 3wnm:

Sodium binding site 1 out of 1 in 3wnm

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


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

b:42.5
occ:1.00
 OD1 A:ASP664 2.2 42.7 1.0
O A:HOH1128 2.3 39.1 1.0
O A:HOH1115 2.3 38.0 1.0
O A:GLN666 2.5 39.4 1.0
OD1 A:ASN669 2.5 43.0 1.0
CG A:ASP664 3.2 43.8 1.0
CG A:ASN669 3.4 37.3 1.0
OD2 A:ASP664 3.5 47.9 1.0
C A:GLN666 3.6 35.2 1.0
ND2 A:ASN669 3.7 40.2 1.0
O A:HOH1125 3.9 42.6 1.0
O A:ASN669 4.0 34.6 1.0
N A:GLN666 4.0 37.8 1.0
O A:THR670 4.0 40.6 1.0
OH A:TYR388 4.1 35.1 1.0
CA A:GLN666 4.1 37.7 1.0
CB A:GLN666 4.1 38.0 1.0
O A:ASP664 4.2 40.6 1.0
C A:ASP664 4.4 41.4 1.0
CB A:ASP664 4.5 41.2 1.0
CB A:ALA671 4.5 37.3 1.0
N A:ASP664 4.6 38.6 1.0
C A:ASN669 4.6 33.7 1.0
N A:TRP667 4.7 34.6 1.0
CB A:ASN669 4.7 34.9 1.0
CA A:ASP664 4.7 39.3 1.0
C A:THR670 4.8 36.5 1.0
CZ A:TYR388 4.8 35.8 1.0
CE2 A:TYR388 4.8 34.9 1.0
N A:ASN669 4.8 32.6 1.0
CA A:ASN669 5.0 34.1 1.0
N A:ASN665 5.0 41.8 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: Mon Oct 7 13:58:53 2024

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