Atomistry » Sodium » PDB 7xft-7ypy » 7xoi
Atomistry »
  Sodium »
    PDB 7xft-7ypy »
      7xoi »

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

Go back to Sodium Binding Sites List in 7xoi
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

Go back to Sodium Binding Sites List in 7xoi
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

Go back to Sodium Binding Sites List in 7xoi
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

Go back to Sodium Binding Sites List in 7xoi
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

Go back to Sodium Binding Sites List in 7xoi
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

Go back to Sodium Binding Sites List in 7xoi
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

Go back to Sodium Binding Sites List in 7xoi
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

Go back to Sodium Binding Sites List in 7xoi
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: Wed Oct 9 09:49:34 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy