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Gadolinium in PDB 3vx0: Crystal Structure of Alpha-Amylase From Aspergillus Oryzae

Enzymatic activity of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae

All present enzymatic activity of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae:
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae, PDB code: 3vx0 was solved by M.Sugahara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.97 / 1.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.524, 65.619, 130.243, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 19.9

Other elements in 3vx0:

The structure of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Gadolinium Binding Sites:

The binding sites of Gadolinium atom in the Crystal Structure of Alpha-Amylase From Aspergillus Oryzae (pdb code 3vx0). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 6 binding sites of Gadolinium where determined in the Crystal Structure of Alpha-Amylase From Aspergillus Oryzae, PDB code: 3vx0:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6;

Gadolinium binding site 1 out of 6 in 3vx0

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Gadolinium binding site 1 out of 6 in the Crystal Structure of Alpha-Amylase From Aspergillus Oryzae


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1002

b:15.7
occ:0.56
 GD A:GD1003 2.1 35.3 0.4
O A:HOH1678 2.2 36.5 1.0
OD2 A:ASP235 2.3 24.9 1.0
O A:HOH1677 2.4 32.0 1.0
O A:HOH1676 2.4 30.4 1.0
OD2 A:ASP233 2.5 17.8 1.0
OD1 A:ASP233 2.7 16.9 1.0
CG A:ASP233 2.9 17.0 1.0
CG A:ASP235 3.5 22.1 1.0
O A:HOH1144 4.1 26.4 1.0
CB A:ASP235 4.3 17.0 1.0
O A:HOH1212 4.4 23.1 1.0
OD1 A:ASP235 4.4 25.9 1.0
CB A:ASP233 4.4 15.1 1.0
OE1 A:GLU156 4.8 35.8 1.0
O A:HOH1364 4.8 38.2 1.0
N A:ASP235 4.9 13.6 1.0

Gadolinium binding site 2 out of 6 in 3vx0

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Gadolinium binding site 2 out of 6 in the Crystal Structure of Alpha-Amylase From Aspergillus Oryzae


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1003

b:35.3
occ:0.41
 GD A:GD1002 2.1 15.7 0.6
OD2 A:ASP233 2.5 17.8 1.0
O A:HOH1676 2.5 30.4 1.0
O A:HOH1677 2.6 32.0 1.0
OE1 A:GLU156 3.4 35.8 1.0
O A:HOH1209 3.5 41.8 1.0
CG A:ASP233 3.6 17.0 1.0
OE2 A:GLU156 3.6 36.6 1.0
CD A:GLU156 3.9 34.7 1.0
OD1 A:ASP233 4.0 16.9 1.0
O A:HOH1678 4.0 36.5 1.0
OD2 A:ASP235 4.3 24.9 1.0
O A:TYR155 4.7 29.2 1.0
O A:HOH1518 4.8 37.5 1.0
CB A:ASP233 4.8 15.1 1.0

Gadolinium binding site 3 out of 6 in 3vx0

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Gadolinium binding site 3 out of 6 in the Crystal Structure of Alpha-Amylase From Aspergillus Oryzae


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1004

b:23.7
occ:0.56
 O A:HOH1680 2.2 26.9 1.0
O A:HOH1682 2.3 26.3 1.0
O A:HOH1679 2.4 24.6 1.0
OD1 A:ASP282 2.5 22.1 1.0
O A:HOH1681 2.5 28.6 1.0
OG A:SER281 2.8 28.1 1.0
O A:HOH1670 3.0 30.4 1.0
CG A:ASP282 3.4 23.8 1.0
OD2 A:ASP282 3.7 24.2 1.0
CB A:SER281 4.1 23.1 1.0
C A:SER281 4.7 22.6 1.0
O A:SER281 4.8 23.1 1.0
CB A:ASP282 4.8 23.0 1.0
N A:ASP282 4.9 21.9 1.0
CA A:ASP282 5.0 21.9 1.0

Gadolinium binding site 4 out of 6 in 3vx0

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Gadolinium binding site 4 out of 6 in the Crystal Structure of Alpha-Amylase From Aspergillus Oryzae


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1005

b:18.0
occ:0.27
 O A:HOH1684 2.3 33.3 1.0
O A:HOH1683 2.5 34.0 1.0
OD1 A:ASP50 2.6 24.3 1.0
OD2 A:ASP50 2.6 25.8 1.0
O A:HOH1444 2.6 29.9 1.0
O A:HOH1698 2.9 69.7 1.0
CG A:ASP50 3.0 21.6 1.0
O A:HOH1591 3.0 36.0 1.0
O A:HOH1604 3.7 24.8 1.0
O A:HOH1196 3.7 26.2 1.0
NH2 A:ARG110 4.0 18.0 1.0
NH1 A:ARG110 4.4 16.9 1.0
CB A:ASP50 4.5 18.5 1.0
CZ A:ARG110 4.6 16.8 1.0

Gadolinium binding site 5 out of 6 in 3vx0

Go back to Gadolinium Binding Sites List in 3vx0
Gadolinium binding site 5 out of 6 in the Crystal Structure of Alpha-Amylase From Aspergillus Oryzae


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1006

b:16.4
occ:0.55
 O A:HOH1691 2.3 32.3 1.0
O A:HOH1688 2.3 34.8 1.0
O A:HOH1693 2.3 30.1 1.0
O A:HOH1690 2.3 16.7 1.0
O A:HOH1689 2.3 35.4 1.0
OD2 A:ASP47 2.4 22.3 1.0
O A:HOH1687 2.4 38.5 1.0
OD1 A:ASP47 2.5 24.4 1.0
O A:HOH1692 2.5 29.1 1.0
CG A:ASP47 2.7 20.2 1.0
CB A:ASP47 4.2 17.6 1.0
O A:HOH1520 4.4 33.6 1.0
OE1 A:GLN43 4.6 18.0 1.0
O A:HOH1456 4.6 34.0 1.0
O A:HOH1457 4.7 35.0 1.0
O A:GLN43 4.8 12.6 1.0
O A:HOH1639 4.8 38.8 1.0

Gadolinium binding site 6 out of 6 in 3vx0

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Gadolinium binding site 6 out of 6 in the Crystal Structure of Alpha-Amylase From Aspergillus Oryzae


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of Crystal Structure of Alpha-Amylase From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd1007

b:14.6
occ:0.22
 O A:HOH1686 2.1 27.3 1.0
OD1 A:ASP206 2.4 12.8 1.0
O A:HOH1685 2.4 34.7 1.0
OE1 A:GLU230 2.5 14.8 1.0
O A:HOH1124 2.5 14.9 1.0
OE2 A:GLU230 3.0 13.8 1.0
CD A:GLU230 3.1 14.7 1.0
CG A:ASP206 3.3 13.6 1.0
OD2 A:ASP206 3.6 14.7 1.0
CG2 A:THR207 3.8 12.8 1.0
O A:HOH1156 3.9 19.9 1.0
O A:HOH1116 4.1 15.9 1.0
N A:THR207 4.1 10.9 1.0
O A:HOH1348 4.2 24.7 1.0
OD2 A:ASP297 4.3 14.1 1.0
NH2 A:ARG204 4.3 10.8 1.0
O A:HOH1611 4.4 32.1 1.0
CG A:GLU230 4.5 11.6 1.0
CB A:ASP206 4.6 12.0 1.0
CA A:THR207 4.7 11.7 1.0
NH1 A:ARG204 4.8 10.1 1.0
CB A:THR207 4.8 12.5 1.0
CA A:ASP206 4.8 10.1 1.0
O A:HOH1191 4.9 12.3 1.0
C A:ASP206 4.9 11.5 1.0

Reference:

M.Sugahara, M.Sugahara. N/A N/A.
Page generated: Sun Dec 13 18:59:31 2020

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