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Sodium in PDB 3wnp: D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose

Enzymatic activity of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose

All present enzymatic activity of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose:
2.4.1.248;

Protein crystallography data

The structure of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose, PDB code: 3wnp was solved by R.Suzuki, N.Suzuki, Z.Fujimoto, M.Momma, K.Kimura, S.Kitamura, A.Kimura, K.Funane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.85 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.987, 172.813, 172.305, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.3

Other elements in 3wnp:

The structure of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose (pdb code 3wnp). 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, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose, PDB code: 3wnp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3wnp

Go back to Sodium Binding Sites List in 3wnp
Sodium binding site 1 out of 2 in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:93.2
occ:1.00
 OD1 A:ASP664 2.5 65.2 1.0
O A:GLN666 2.7 68.4 1.0
OD1 A:ASN669 2.8 71.6 1.0
OH A:TYR388 3.2 74.6 1.0
CG A:ASP664 3.7 63.1 1.0
CG A:ASN669 3.8 72.9 1.0
C A:GLN666 3.9 67.8 1.0
O A:ASN669 4.0 75.6 1.0
CZ A:TYR388 4.0 74.8 1.0
O A:THR670 4.1 64.2 1.0
CE2 A:TYR388 4.1 75.0 1.0
ND2 A:ASN669 4.1 75.3 1.0
O A:ASP664 4.2 67.0 1.0
CB A:ALA671 4.2 70.8 1.0
N A:GLN666 4.3 71.4 1.0
OD2 A:ASP664 4.4 66.1 1.0
C A:ASP664 4.4 71.0 1.0
N A:ASP664 4.5 66.9 1.0
CA A:GLN666 4.6 68.1 1.0
C A:ASN669 4.8 65.0 1.0
CA A:ASP664 4.8 65.0 1.0
OD1 A:ASN663 4.8 61.4 1.0
CB A:ASP664 4.8 60.9 1.0
CB A:GLN666 4.8 66.5 1.0
C A:THR670 4.9 67.1 1.0
N A:TRP667 4.9 67.7 1.0
CA A:ALA671 4.9 73.0 1.0
N A:ASN665 5.0 73.1 1.0
CB A:ASN663 5.0 76.5 1.0

Sodium binding site 2 out of 2 in 3wnp

Go back to Sodium Binding Sites List in 3wnp
Sodium binding site 2 out of 2 in the D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D308A, F268V, D469Y, A513V, and Y515S Quintuple Mutant of Bacillus Circulans T-3040 Cycloisomaltooligosaccharide Glucanotransferase Complexed with Isomaltoundecaose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:81.1
occ:1.00
 O B:GLN666 2.6 66.7 1.0
OD1 B:ASP664 2.7 70.1 1.0
OD1 B:ASN669 2.8 70.4 1.0
OH B:TYR388 3.1 68.8 1.0
C B:GLN666 3.8 73.1 1.0
CG B:ASP664 3.8 64.0 1.0
CG B:ASN669 3.9 67.2 1.0
O B:ASN669 4.0 68.2 1.0
CZ B:TYR388 4.0 67.6 1.0
O B:ASP664 4.1 71.0 1.0
N B:GLN666 4.1 76.1 1.0
CE2 B:TYR388 4.2 72.0 1.0
ND2 B:ASN669 4.3 68.8 1.0
C B:ASP664 4.3 71.8 1.0
N B:ASP664 4.4 68.6 1.0
O B:THR670 4.4 70.6 1.0
CA B:GLN666 4.4 74.3 1.0
CB B:ALA671 4.4 65.5 1.0
OD2 B:ASP664 4.5 63.5 1.0
CB B:GLN666 4.7 74.1 1.0
OD1 B:ASN663 4.7 64.8 1.0
CA B:ASP664 4.7 68.7 1.0
C B:ASN669 4.8 64.9 1.0
CB B:ASP664 4.9 66.0 1.0
CB B:ASN663 4.9 73.4 1.0
N B:ASN665 4.9 77.5 1.0
N B:TRP667 4.9 70.7 1.0
CA B:ALA671 5.0 69.5 1.0
C B:ASN665 5.0 78.1 1.0
CG B:ASN663 5.0 69.2 1.0
C B:THR670 5.0 69.7 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 13:59:30 2024

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