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Strontium in PDB 8orp: Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose

Enzymatic activity of Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose

All present enzymatic activity of Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose:
3.2.1.1;

Protein crystallography data

The structure of Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose, PDB code: 8orp was solved by N.Aghajari, R.Haser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.57 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.08, 72.54, 98.21, 90, 98.41, 90
R / Rfree (%) 17.4 / 21.2

Other elements in 8orp:

The structure of Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Strontium Binding Sites:

The binding sites of Strontium atom in the Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose (pdb code 8orp). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 4 binding sites of Strontium where determined in the Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose, PDB code: 8orp:
Jump to Strontium binding site number: 1; 2; 3; 4;

Strontium binding site 1 out of 4 in 8orp

Go back to Strontium Binding Sites List in 8orp
Strontium binding site 1 out of 4 in the Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr520

b:19.3
occ:1.00
 O A:ARG147 2.5 17.7 1.0
O A:HOH639 2.5 15.3 1.0
O A:HIS190 2.5 17.3 1.0
OD1 A:ASP156 2.6 17.5 1.0
OD2 A:ASP156 2.6 17.5 1.0
O A:HOH663 2.6 18.2 1.0
O A:HOH698 2.6 17.3 1.0
OD1 A:ASN98 2.7 13.6 1.0
CG A:ASP156 2.9 18.3 1.0
C A:ARG147 3.5 20.9 1.0
CG A:ASN98 3.6 19.1 1.0
C A:HIS190 3.7 17.7 1.0
ND2 A:ASN98 4.0 12.5 1.0
CA A:ARG147 4.1 20.0 1.0
CB A:HIS190 4.2 15.9 1.0
O A:ASN98 4.3 18.3 1.0
O A:LEU157 4.4 18.3 1.0
CB A:ASP156 4.4 14.3 1.0
CG A:MET191 4.4 14.3 1.0
ND2 A:ASN132 4.5 22.0 1.0
N A:ASN148 4.5 18.1 1.0
CA A:HIS190 4.5 17.4 1.0
O A:CYS149 4.6 19.2 1.0
N A:MET191 4.6 15.3 1.0
O A:HOH864 4.6 22.2 1.0
CA A:MET191 4.6 22.4 1.0
OE1 A:GLN159 4.7 17.0 1.0
O A:VAL146 4.8 20.4 1.0
CA A:ASN148 4.8 21.3 1.0
O A:HOH649 4.9 14.8 1.0
CB A:ARG147 4.9 20.9 1.0
CB A:ASN98 4.9 13.0 1.0
NE2 A:GLN159 4.9 17.6 1.0

Strontium binding site 2 out of 4 in 8orp

Go back to Strontium Binding Sites List in 8orp
Strontium binding site 2 out of 4 in the Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Sr521

b:23.9
occ:1.00
 OE1 A:GLN263 2.5 15.5 1.0
O A:HOH655 2.6 21.4 1.0
O A:HOH733 2.6 14.5 1.0
O A:HOH650 2.7 16.9 1.0
O A:HOH944 2.7 20.4 1.0
O A:HOH966 2.7 20.1 1.0
O A:HOH1034 2.9 26.9 1.0
CD A:GLN263 3.7 18.3 1.0
O A:HOH940 4.3 37.2 1.0
NE2 A:GLN263 4.4 15.7 1.0
OD1 A:ASP391 4.6 17.6 1.0
CB A:GLN263 4.7 12.7 1.0
CG A:GLN263 4.8 14.2 1.0
OD2 A:ASP391 4.8 17.3 1.0
O2 A:EDO514 4.9 20.8 1.0

Strontium binding site 3 out of 4 in 8orp

Go back to Strontium Binding Sites List in 8orp
Strontium binding site 3 out of 4 in the Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 3 of Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr522

b:18.4
occ:1.00
 O B:HOH656 2.4 10.8 1.0
O B:ARG147 2.5 17.8 1.0
O B:HIS190 2.5 16.4 1.0
OD1 B:ASP156 2.5 15.3 1.0
OD2 B:ASP156 2.6 19.0 1.0
O B:HOH676 2.6 16.5 1.0
OD1 B:ASN98 2.6 10.0 1.0
O B:HOH657 2.8 14.7 1.0
CG B:ASP156 2.9 19.1 1.0
C B:ARG147 3.5 17.9 1.0
CG B:ASN98 3.6 14.8 1.0
C B:HIS190 3.7 16.1 1.0
ND2 B:ASN98 4.0 9.9 1.0
CA B:ARG147 4.1 19.8 1.0
CB B:HIS190 4.2 15.3 1.0
O B:ASN98 4.3 15.0 1.0
CB B:ASP156 4.4 13.7 1.0
CG B:MET191 4.4 14.5 1.0
O B:LEU157 4.4 16.9 1.0
ND2 B:ASN132 4.5 18.9 1.0
N B:ASN148 4.5 18.0 1.0
CA B:HIS190 4.5 15.5 1.0
O B:HOH780 4.5 22.6 1.0
O B:CYS149 4.6 18.2 1.0
N B:MET191 4.6 14.3 1.0
CA B:MET191 4.7 18.4 1.0
OE1 B:GLN159 4.7 18.9 1.0
O B:VAL146 4.7 20.1 1.0
CA B:ASN148 4.8 21.1 1.0
CB B:ARG147 4.9 20.6 1.0
CB B:ASN98 4.9 13.4 1.0
NE2 B:GLN159 4.9 11.4 1.0
O B:HOH737 5.0 17.2 1.0
C B:ASN148 5.0 20.9 1.0

Strontium binding site 4 out of 4 in 8orp

Go back to Strontium Binding Sites List in 8orp
Strontium binding site 4 out of 4 in the Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 4 of Crystal Structure of Drosophila Melanogaster Alpha-Amylase in Complex with the Inhibitor Acarbose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Sr523

b:23.2
occ:1.00
 OE1 B:GLN263 2.5 16.6 1.0
O B:HOH836 2.5 18.1 1.0
O B:HOH963 2.6 19.7 1.0
O B:HOH654 2.7 13.3 1.0
O B:HOH813 2.7 16.2 1.0
O B:HOH987 2.7 17.3 1.0
O B:HOH1034 3.0 26.8 1.0
CD B:GLN263 3.6 18.6 1.0
NE2 B:GLN263 4.2 14.3 1.0
O B:HOH903 4.4 29.9 1.0
OD1 B:ASP391 4.6 17.2 1.0
CG B:GLN263 4.7 14.9 1.0
CB B:GLN263 4.7 16.2 1.0
OD2 B:ASP391 4.9 19.9 1.0

Reference:

M.Rhimi, J.L.Da Lage, R.Haser, G.Feller, N.Aghajari. Structural and Functional Characterization of Drosophila Melanogaster Alpha-Amylase. Molecules V. 28 2023.
ISSN: ESSN 1420-3049
PubMed: 37513201
DOI: 10.3390/MOLECULES28145327
Page generated: Thu Dec 28 12:01:15 2023

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