Sodium in PDB 7xoi: Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose

Enzymatic activity of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose

All present enzymatic activity of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose:
3.2.1.20;

Protein crystallography data

The structure of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose, PDB code: 7xoi was solved by T.Tonozuka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.14 / 2.30
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 95.325, 106.036, 206.366, 90.58, 90.06, 92.2
R / Rfree (%) 22.7 / 26.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose (pdb code 7xoi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose, PDB code: 7xoi:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7xoi

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Sodium binding site 1 out of 8 in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1001

b:12.6
occ:1.00
 OG B:SER645 2.4 25.2 1.0
O B:GLY675 2.6 29.6 1.0
OE1 B:GLN709 2.8 30.7 1.0
O B:GLY678 2.8 33.2 1.0
O B:PHE676 2.9 35.1 1.0
O B:GLY677 3.2 32.8 1.0
O B:HOH1146 3.4 26.5 1.0
C B:PHE676 3.5 31.3 1.0
C B:GLY675 3.6 29.2 1.0
CD B:GLN709 3.6 31.0 1.0
CB B:SER645 3.7 26.3 1.0
C B:GLY677 3.7 32.0 1.0
C B:GLY678 3.7 34.0 1.0
CB B:ALA706 3.7 32.5 1.0
NE2 B:GLN709 3.9 32.0 1.0
O B:CYS674 4.1 30.5 1.0
CB B:ALA702 4.2 31.9 1.0
N B:GLY677 4.2 31.5 1.0
N B:PHE676 4.2 28.9 1.0
N B:GLY678 4.2 32.5 1.0
CA B:PHE676 4.3 29.4 1.0
N B:VAL680 4.4 32.5 1.0
CA B:GLY677 4.4 31.8 1.0
N B:ASN679 4.5 34.5 1.0
CA B:GLY678 4.5 33.3 1.0
CA B:GLY675 4.5 29.4 1.0
CA B:ALA702 4.6 32.2 1.0
CA B:ASN679 4.6 35.1 1.0
N B:SER645 4.7 28.0 1.0
CA B:SER645 4.7 27.5 1.0
C B:ASN679 4.8 34.2 1.0
N B:GLU703 4.9 34.3 1.0
CB B:VAL680 4.9 31.1 1.0
C B:CYS674 4.9 29.2 1.0
CG B:GLN709 5.0 30.7 1.0

Sodium binding site 2 out of 8 in 7xoi

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Sodium binding site 2 out of 8 in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1001

b:16.9
occ:1.00
 OG D:SER645 2.6 30.2 1.0
O D:GLY675 2.6 31.6 1.0
OE1 D:GLN709 2.7 37.5 1.0
O D:GLY678 2.8 35.0 1.0
O D:PHE676 2.8 38.9 1.0
O D:GLY677 3.2 36.3 1.0
C D:PHE676 3.4 35.7 1.0
C D:GLY675 3.5 32.4 1.0
C D:GLY677 3.6 37.2 1.0
CD D:GLN709 3.7 38.0 1.0
C D:GLY678 3.8 36.1 1.0
O D:HOH1150 3.8 31.7 1.0
CB D:ALA706 3.8 39.5 1.0
CB D:SER645 3.9 30.9 1.0
N D:GLY677 3.9 37.5 1.0
NE2 D:GLN709 4.1 38.4 1.0
N D:PHE676 4.1 32.0 1.0
CB D:ALA702 4.1 34.2 1.0
CA D:PHE676 4.2 33.8 1.0
CA D:GLY677 4.2 37.0 1.0
O D:CYS674 4.2 31.1 1.0
N D:GLY678 4.3 36.9 1.0
N D:VAL680 4.4 36.0 1.0
CA D:GLY675 4.5 32.4 1.0
CA D:GLY678 4.6 36.2 1.0
CA D:ALA702 4.6 33.3 1.0
N D:ASN679 4.6 37.0 1.0
N D:SER645 4.7 31.9 1.0
CA D:ASN679 4.7 37.4 1.0
CA D:SER645 4.8 31.9 1.0
C D:ASN679 4.9 36.5 1.0
C D:CYS674 5.0 31.0 1.0
N D:GLU703 5.0 37.5 1.0
CB D:VAL680 5.0 38.5 1.0

Sodium binding site 3 out of 8 in 7xoi

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Sodium binding site 3 out of 8 in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1001

b:17.7
occ:1.00
 OG F:SER645 2.4 29.0 1.0
O F:GLY678 2.6 34.1 1.0
O F:GLY675 2.7 32.5 1.0
OE1 F:GLN709 2.8 33.2 1.0
O F:PHE676 2.9 33.3 1.0
O F:GLY677 3.1 33.6 1.0
O F:HOH1184 3.5 26.5 1.0
C F:PHE676 3.5 32.2 1.0
C F:GLY675 3.6 31.5 1.0
C F:GLY677 3.6 33.6 1.0
C F:GLY678 3.7 34.3 1.0
CB F:ALA706 3.7 39.4 1.0
CD F:GLN709 3.7 34.6 1.0
CB F:SER645 3.7 28.8 1.0
NE2 F:GLN709 4.0 35.8 1.0
N F:GLY677 4.1 32.9 1.0
O F:CYS674 4.1 31.3 1.0
N F:PHE676 4.2 31.2 1.0
CA F:PHE676 4.2 31.9 1.0
N F:GLY678 4.2 33.0 1.0
CA F:GLY677 4.4 33.8 1.0
CB F:ALA702 4.4 35.9 1.0
N F:VAL680 4.4 33.3 1.0
CA F:GLY678 4.5 33.5 1.0
N F:ASN679 4.6 34.3 1.0
CA F:GLY675 4.6 31.2 1.0
N F:SER645 4.7 29.9 1.0
CA F:ASN679 4.7 35.0 1.0
CA F:SER645 4.7 29.9 1.0
CA F:ALA702 4.8 34.9 1.0
CB F:VAL680 4.8 33.5 1.0
C F:ASN679 4.9 34.3 1.0
C F:CYS674 4.9 30.7 1.0

Sodium binding site 4 out of 8 in 7xoi

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Sodium binding site 4 out of 8 in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1001

b:16.1
occ:1.00
 OG H:SER645 2.5 27.2 1.0
O H:GLY675 2.6 31.3 1.0
O H:GLY678 2.6 35.9 1.0
O H:PHE676 2.9 35.4 1.0
OE1 H:GLN709 2.9 30.6 1.0
O H:GLY677 3.3 35.6 1.0
C H:PHE676 3.5 33.5 1.0
C H:GLY675 3.5 31.8 1.0
CB H:ALA706 3.6 36.2 1.0
C H:GLY678 3.6 35.2 1.0
C H:GLY677 3.7 34.2 1.0
CB H:SER645 3.8 27.8 1.0
CD H:GLN709 3.9 31.9 1.0
CB H:ALA702 4.1 34.7 1.0
N H:PHE676 4.2 31.9 1.0
N H:GLY677 4.2 33.9 1.0
O H:CYS674 4.2 31.2 1.0
CA H:PHE676 4.2 32.8 1.0
N H:GLY678 4.2 33.8 1.0
NE2 H:GLN709 4.3 32.4 1.0
N H:VAL680 4.4 35.1 1.0
N H:ASN679 4.4 36.0 1.0
CA H:GLY677 4.5 34.3 1.0
CA H:GLY678 4.5 35.1 1.0
CA H:ALA702 4.5 34.4 1.0
CA H:GLY675 4.6 31.7 1.0
CA H:ASN679 4.6 37.1 1.0
N H:SER645 4.7 29.3 1.0
CA H:SER645 4.8 28.9 1.0
C H:ASN679 4.8 36.5 1.0
CB H:VAL680 4.9 34.0 1.0
N H:GLU703 4.9 37.0 1.0
CA H:ALA706 4.9 38.2 1.0
C H:CYS674 4.9 32.2 1.0

Sodium binding site 5 out of 8 in 7xoi

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Sodium binding site 5 out of 8 in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Na1001

b:14.0
occ:1.00
 OG J:SER645 2.5 25.1 1.0
O J:PHE676 2.7 32.3 1.0
O J:GLY678 2.7 33.2 1.0
OE1 J:GLN709 2.8 31.8 1.0
O J:GLY675 2.8 28.7 1.0
O J:HOH1152 3.3 21.7 1.0
C J:PHE676 3.4 30.3 1.0
O J:GLY677 3.5 33.0 1.0
CB J:ALA706 3.6 39.4 1.0
C J:GLY675 3.7 28.4 1.0
C J:GLY678 3.7 32.3 1.0
CB J:SER645 3.8 27.1 1.0
CD J:GLN709 3.8 32.8 1.0
C J:GLY677 3.8 31.4 1.0
CB J:ALA702 4.1 34.2 1.0
O J:CYS674 4.1 30.3 1.0
NE2 J:GLN709 4.1 33.1 1.0
N J:GLY677 4.2 31.6 1.0
CA J:PHE676 4.2 28.9 1.0
N J:PHE676 4.3 28.3 1.0
N J:GLY678 4.3 31.3 1.0
CA J:GLY677 4.4 31.2 1.0
N J:VAL680 4.4 32.0 1.0
CA J:ALA702 4.5 33.8 1.0
CA J:GLY678 4.6 31.8 1.0
N J:ASN679 4.6 32.6 1.0
CA J:ASN679 4.6 34.5 1.0
CA J:GLY675 4.7 28.7 1.0
N J:SER645 4.7 28.9 1.0
CA J:SER645 4.8 28.2 1.0
C J:ASN679 4.9 33.8 1.0
N J:GLU703 4.9 37.3 1.0
CB J:VAL680 4.9 32.8 1.0
CA J:ALA706 4.9 40.2 1.0
C J:CYS674 4.9 29.0 1.0

Sodium binding site 6 out of 8 in 7xoi

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Sodium binding site 6 out of 8 in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na1001

b:18.2
occ:1.00
 OG L:SER645 2.5 30.3 1.0
O L:GLY675 2.6 28.8 1.0
O L:GLY678 2.6 36.5 1.0
OE1 L:GLN709 2.6 30.3 1.0
O L:PHE676 3.0 37.6 1.0
O L:GLY677 3.4 36.3 1.0
C L:GLY675 3.5 30.7 1.0
C L:PHE676 3.5 34.7 1.0
O L:HOH1114 3.6 26.5 1.0
CD L:GLN709 3.6 32.5 1.0
CB L:ALA706 3.7 39.8 1.0
C L:GLY678 3.7 37.7 1.0
CB L:SER645 3.7 30.1 1.0
C L:GLY677 3.8 36.4 1.0
NE2 L:GLN709 3.9 33.5 1.0
N L:PHE676 4.1 31.2 1.0
N L:GLY677 4.1 36.0 1.0
O L:CYS674 4.1 31.3 1.0
CA L:PHE676 4.2 33.2 1.0
CB L:ALA702 4.2 32.1 1.0
N L:GLY678 4.3 36.8 1.0
CA L:GLY677 4.4 36.5 1.0
CA L:GLY675 4.5 30.2 1.0
N L:VAL680 4.5 39.4 1.0
CA L:GLY678 4.6 37.8 1.0
N L:ASN679 4.6 40.2 1.0
CA L:ALA702 4.6 31.8 1.0
N L:SER645 4.7 30.6 1.0
CA L:ASN679 4.7 40.2 1.0
CA L:SER645 4.8 30.5 1.0
CB L:VAL680 4.8 38.3 1.0
C L:CYS674 4.9 29.9 1.0
C L:ASN679 4.9 39.4 1.0
CG L:GLN709 5.0 32.9 1.0

Sodium binding site 7 out of 8 in 7xoi

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Sodium binding site 7 out of 8 in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Na1001

b:12.4
occ:1.00
 OG N:SER645 2.4 27.2 1.0
O N:GLY678 2.5 33.6 1.0
O N:GLY675 2.5 30.5 1.0
O N:PHE676 2.6 34.6 1.0
OE1 N:GLN709 2.8 28.8 1.0
O N:GLY677 3.1 36.1 1.0
C N:PHE676 3.4 33.1 1.0
O N:HOH1113 3.5 25.6 1.0
C N:GLY675 3.5 30.8 1.0
C N:GLY678 3.6 34.7 1.0
C N:GLY677 3.6 35.5 1.0
CD N:GLN709 3.7 31.1 1.0
CB N:SER645 3.8 27.7 1.0
CB N:ALA706 3.8 38.5 1.0
NE2 N:GLN709 4.0 32.4 1.0
N N:GLY678 4.2 35.6 1.0
O N:CYS674 4.2 28.7 1.0
N N:PHE676 4.2 30.3 1.0
N N:GLY677 4.2 34.6 1.0
CA N:PHE676 4.2 32.3 1.0
CB N:ALA702 4.2 34.2 1.0
CA N:GLY677 4.4 35.9 1.0
N N:VAL680 4.4 34.2 1.0
CA N:GLY678 4.4 35.1 1.0
CA N:GLY675 4.5 30.0 1.0
N N:ASN679 4.5 34.7 1.0
CA N:ALA702 4.6 34.0 1.0
N N:SER645 4.6 28.6 1.0
CA N:SER645 4.7 28.5 1.0
CA N:ASN679 4.7 35.9 1.0
C N:CYS674 4.9 29.6 1.0
CB N:VAL680 4.9 33.4 1.0
C N:ASN679 4.9 34.7 1.0
N N:GLU703 4.9 35.7 1.0
N N:GLY675 5.0 29.9 1.0

Sodium binding site 8 out of 8 in 7xoi

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Sodium binding site 8 out of 8 in the Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Aspergillus Sojae Alpha-Glucosidase Asojagdl in Complex with Trehalose within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Na1001

b:21.0
occ:1.00
 OG P:SER645 2.4 30.2 1.0
O P:GLY678 2.7 39.6 1.0
O P:GLY675 2.8 33.0 1.0
O P:PHE676 2.9 37.8 1.0
OE1 P:GLN709 2.9 41.3 1.0
O P:GLY677 3.0 40.0 1.0
O P:HOH1134 3.4 29.5 1.0
C P:PHE676 3.6 35.5 1.0
C P:GLY675 3.6 34.6 1.0
C P:GLY678 3.6 40.9 1.0
C P:GLY677 3.6 38.9 1.0
CB P:SER645 3.7 31.1 1.0
CD P:GLN709 3.7 42.4 1.0
CB P:ALA706 3.8 45.1 1.0
NE2 P:GLN709 3.9 43.6 1.0
O P:CYS674 4.0 39.1 1.0
N P:GLY678 4.2 38.6 1.0
N P:GLY677 4.2 36.9 1.0
N P:PHE676 4.2 33.8 1.0
CA P:PHE676 4.3 34.1 1.0
N P:VAL680 4.3 42.1 1.0
N P:ASN679 4.4 42.0 1.0
CB P:ALA702 4.4 37.9 1.0
CA P:GLY678 4.4 40.1 1.0
CA P:GLY677 4.4 38.8 1.0
CA P:GLY675 4.5 35.8 1.0
CA P:ASN679 4.5 42.9 1.0
N P:SER645 4.6 33.1 1.0
CA P:SER645 4.7 32.4 1.0
C P:ASN679 4.7 42.4 1.0
CA P:ALA702 4.7 37.2 1.0
C P:CYS674 4.9 36.2 1.0
CB P:VAL680 4.9 41.0 1.0
CA P:ALA706 5.0 45.8 1.0

Reference:

Y.Ding, A.Oyagi, Y.Miyasaka, T.Kozono, N.Sasaki, Y.Kojima, M.Yoshida, Y.Matsumoto, N.Yasutake, A.Nishikawa, T.Tonozuka. Structural Basis For Proteolytic Processing of Aspergillus Sojae Alpha-Glucosidase L with Strong Transglucosylation Activity. J.Struct.Biol. V. 214 07874 2022.
ISSN: ESSN 1095-8657
PubMed: 35688347
DOI: 10.1016/J.JSB.2022.107874
Page generated: Fri Apr 7 17:11:24 2023

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