Sodium in PDB 9fz3: Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe

The structure of Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe, PDB code: 9fz3 was solved by I.B.Pickles, O.Moroz, G.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	66.24 / 2.02
Space group	P 2 3
Cell size a, b, c (Å), α, β, γ (°)	132.486, 132.486, 132.486, 90, 90, 90
R / Rfree (%)	20.1 / 24.2

The binding sites of Sodium atom in the Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe (pdb code 9fz3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe, PDB code: 9fz3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:45.4 occ:1.00 O A:SER358 2.2 37.7 1.0 OD1 A:ASP346 2.3 39.9 1.0 O A:VAL345 2.3 34.8 1.0 OD1 A:ASN310 2.4 49.4 1.0 CG A:ASP346 2.9 38.0 1.0 CG A:ASN310 3.4 57.2 1.0 C A:SER358 3.5 42.2 1.0 OD2 A:ASP346 3.5 35.5 1.0 C A:VAL345 3.5 33.6 1.0 CG2 A:VAL360 3.7 42.6 1.0 CA A:ASP346 3.8 40.6 1.0 CB A:ASP346 3.9 40.6 1.0 OG1 A:THR350 3.9 41.0 1.0 ND2 A:ASN310 4.0 50.9 1.0 CB A:THR350 4.0 36.5 1.0 OG A:SER358 4.0 40.3 1.0 N A:VAL360 4.1 39.4 1.0 N A:ASP346 4.1 36.8 1.0 O A:ASN310 4.2 50.0 1.0 CA A:TRP359 4.2 37.3 1.0 CG2 A:THR350 4.3 41.9 1.0 N A:TRP359 4.3 35.5 1.0 C A:TRP359 4.4 35.1 1.0 CB A:SER358 4.4 40.9 1.0 CA A:SER358 4.5 42.3 1.0 CB A:VAL360 4.6 39.6 1.0 CB A:ASN310 4.6 53.0 1.0 CA A:VAL345 4.7 35.2 1.0 C A:ASN310 4.8 43.0 1.0 CB A:TYR314 4.8 47.9 1.0 CA A:ASN310 4.9 45.6 1.0 CA A:VAL360 4.9 39.7 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Na605 b:43.4 occ:1.00 O A:ASP215 2.2 43.0 1.0 O A:HOH844 2.3 40.7 1.0 OD1 A:ASN125 2.3 50.0 1.0 OD1 A:ASP215 2.3 46.3 1.0 O A:HIS256 2.4 50.4 1.0 OD1 A:ASN221 2.5 54.9 1.0 C A:ASP215 3.2 46.1 1.0 CG A:ASN221 3.3 49.5 1.0 ND2 A:ASN221 3.4 53.5 1.0 C A:HIS256 3.4 41.5 1.0 CG A:ASN125 3.5 48.2 1.0 CG A:ASP215 3.5 49.5 1.0 CA A:ASP215 3.8 49.4 1.0 CB A:HIS256 3.8 45.7 1.0 ND2 A:ASN125 4.0 52.0 1.0 O A:ASN125 4.1 43.1 1.0 CB A:ASP215 4.2 49.2 1.0 CA A:HIS256 4.2 47.5 1.0 O A:HOH721 4.3 44.7 1.0 N A:TYR216 4.3 41.4 1.0 N A:ILE257 4.3 43.1 1.0 OD2 A:ASP215 4.4 50.6 1.0 ND2 A:ASN204 4.5 50.3 1.0 CA A:ILE257 4.6 44.8 1.0 CB A:ASN125 4.6 43.3 1.0 CA A:TYR216 4.7 46.1 1.0 CB A:ASN221 4.8 43.9 1.0 O A:ILE222 4.8 48.5 1.0 C A:ASN125 4.8 45.9 1.0 CA A:ASN125 4.8 45.7 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of K38 Amylase From Bacillus Sp. Strain Ksm-K38 Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:54.2 occ:1.00 O A:GLY321 2.2 45.5 1.0 O A:HOH859 2.2 59.0 1.0 O A:TYR323 2.4 45.8 1.0 OD1 A:ASP425 2.4 47.1 1.0 O A:TRP424 2.6 47.3 1.0 OD1 A:ASN448 2.7 48.8 1.0 C A:GLY321 3.4 45.3 1.0 ND2 A:ASN448 3.4 44.0 1.0 C A:TRP424 3.4 53.0 1.0 CG A:ASN448 3.4 44.2 1.0 C A:TYR323 3.5 54.9 1.0 CG A:ASP425 3.6 40.3 1.0 CA A:ASP425 3.7 46.8 1.0 N A:ASP425 3.9 51.6 1.0 C A:SER322 4.1 53.6 1.0 CA A:GLY321 4.2 52.5 1.0 N A:TYR323 4.2 48.4 1.0 CB A:ASP425 4.2 47.4 1.0 N A:ASP324 4.3 50.2 1.0 CA A:ASP324 4.3 46.2 1.0 O A:SER322 4.4 50.1 1.0 N A:SER322 4.4 50.7 1.0 N A:MET325 4.4 37.9 1.0 CA A:TYR323 4.4 52.6 1.0 CD1 A:TRP424 4.5 59.5 1.0 CG A:MET325 4.5 53.2 1.0 CA A:SER322 4.5 53.6 1.0 CA A:TRP424 4.5 50.2 1.0 OD2 A:ASP425 4.5 51.4 1.0 CB A:TRP424 4.6 47.1 1.0 C A:ASP324 4.9 39.1 1.0 CB A:ASN448 4.9 43.4 1.0 C A:ASP425 4.9 43.5 1.0 CG A:TRP424 5.0 55.0 1.0

I.B.Pickles, Y.Chen, O.Moroz, H.A.Brown, C.De Boer, Z.Armstrong, N.G.S.Mcgregor, M.Artola, J.D.C.Codee, N.M.Koropatkin, H.S.Overkleeft, G.J.Davies. Precision Activity-Based Alpha-Amylase Probes For Dissection and Annotation of Linear and Branched-Chain Starch-Degrading Enzymes. Angew.Chem.Int.Ed.Engl. 15219 2024.
ISSN: ESSN 1521-3773
PubMed: 39601378
DOI: 10.1002/ANIE.202415219