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

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

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

Protein crystallography data

The structure of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltooctaose, PDB code: 3wnn 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) 35.35 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 61.031, 171.256, 173.251, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.4

Other elements in 3wnn:

The structure of D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltooctaose 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 Isomaltooctaose (pdb code 3wnn). 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 Isomaltooctaose, PDB code: 3wnn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3wnn

Go back to Sodium Binding Sites List in 3wnn
Sodium binding site 1 out of 2 in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltooctaose


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

b:44.9
occ:1.00
 O A:GLN666 2.1 48.0 1.0
O A:HOH1197 2.2 50.5 1.0
OD1 A:ASP664 2.3 45.5 1.0
O A:HOH1169 2.3 46.7 1.0
OD1 A:ASN669 2.5 47.3 1.0
C A:GLN666 3.2 49.9 1.0
CG A:ASN669 3.4 46.1 1.0
CG A:ASP664 3.4 50.7 1.0
N A:GLN666 3.6 51.0 1.0
ND2 A:ASN669 3.7 43.5 1.0
CA A:GLN666 3.7 52.7 1.0
O A:ASP664 3.8 54.8 1.0
O A:HOH1116 3.8 39.0 1.0
OH A:TYR388 3.9 48.8 1.0
CB A:GLN666 3.9 54.4 1.0
OD2 A:ASP664 4.0 54.5 1.0
O A:ASN669 4.1 40.0 1.0
C A:ASP664 4.2 47.3 1.0
N A:TRP667 4.4 48.2 1.0
CZ A:TYR388 4.5 50.5 1.0
O A:THR670 4.5 51.6 1.0
CE2 A:TYR388 4.5 47.2 1.0
C A:ASN665 4.6 55.1 1.0
CB A:ASP664 4.7 46.4 1.0
N A:ASP664 4.7 48.2 1.0
O A:HOH1073 4.7 44.8 1.0
CB A:ALA671 4.7 47.9 1.0
N A:ASN665 4.7 49.6 1.0
CA A:ASP664 4.7 46.6 1.0
C A:ASN669 4.7 45.7 1.0
CB A:ASN669 4.8 46.6 1.0
CA A:TRP667 4.8 46.2 1.0
N A:ASN669 4.9 51.5 1.0
C A:TRP667 4.9 47.1 1.0

Sodium binding site 2 out of 2 in 3wnn

Go back to Sodium Binding Sites List in 3wnn
Sodium binding site 2 out of 2 in the D308A Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltooctaose


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

b:49.5
occ:1.00
 O B:HOH1091 2.1 34.6 1.0
O B:GLN666 2.2 46.0 1.0
O B:HOH1166 2.3 53.3 1.0
O B:HOH1165 2.3 57.3 1.0
OD1 B:ASP664 2.3 47.0 1.0
OD1 B:ASN669 2.5 48.7 1.0
C B:GLN666 3.2 46.0 1.0
CG B:ASP664 3.4 53.0 1.0
CG B:ASN669 3.5 56.0 1.0
OD2 B:ASP664 3.7 50.6 1.0
OH B:TYR388 3.8 47.4 1.0
N B:GLN666 3.8 53.7 1.0
ND2 B:ASN669 3.8 55.0 1.0
CA B:GLN666 3.9 52.4 1.0
O B:ASN669 4.0 41.5 1.0
CB B:GLN666 4.0 51.7 1.0
O B:ASP664 4.2 60.4 1.0
N B:TRP667 4.3 46.6 1.0
O B:THR670 4.4 48.4 1.0
CZ B:TYR388 4.4 43.2 1.0
C B:ASP664 4.5 50.3 1.0
CE2 B:TYR388 4.6 47.8 1.0
CA B:TRP667 4.7 42.7 1.0
CB B:ASP664 4.7 48.7 1.0
C B:ASN669 4.7 43.3 1.0
C B:TRP667 4.8 44.8 1.0
CB B:ASN669 4.8 48.9 1.0
N B:ASN669 4.8 42.6 1.0
N B:ASP664 4.8 51.7 1.0
C B:ASN665 4.9 50.3 1.0
CB B:ALA671 4.9 48.8 1.0
CA B:ASP664 4.9 50.2 1.0
O B:TRP667 4.9 42.3 1.0
N B:ASN665 4.9 49.1 1.0
CA B:ASN669 5.0 43.5 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 13:59:00 2024

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