Sodium in PDB 8iub: Crystal Structure of GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose

The structure of Crystal Structure of GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose, PDB code: 8iub was solved by S.Nakamura, T.Miyazaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.57 / 1.18
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.911, 91.058, 137.354, 90, 90, 90
R / Rfree (%)	16.3 / 19

The binding sites of Sodium atom in the Crystal Structure of GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose (pdb code 8iub). 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 GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose, PDB code: 8iub:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose


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 GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:13.0 occ:1.00 HG1 A:THR119 2.1 30.0 0.0 OE1 A:GLU449 2.3 14.6 1.0 OD2 A:ASP452 2.3 13.4 1.0 OG1 A:THR119 2.3 13.8 1.0 O A:HOH1145 2.4 17.9 1.0 O A:THR119 2.6 14.4 1.0 O A:HOH805 2.8 17.5 1.0 CD A:GLU449 3.1 14.5 1.0 C A:THR119 3.2 13.8 1.0 H A:THR119 3.2 14.3 1.0 OE2 A:GLU449 3.4 17.8 1.0 CG A:ASP452 3.4 11.7 1.0 O A:HOH705 3.6 15.1 1.0 CB A:THR119 3.6 13.9 1.0 HA A:GLU449 3.6 11.5 1.0 HA A:VAL120 3.7 12.4 1.0 CA A:THR119 3.7 14.1 1.0 O A:HOH852 3.8 17.0 1.0 N A:THR119 3.8 14.4 1.0 HB2 A:ASP452 3.8 10.9 1.0 HB A:THR119 4.0 13.9 1.0 CB A:ASP452 4.1 10.8 1.0 HB3 A:ASP452 4.1 11.2 1.0 N A:VAL120 4.1 13.2 1.0 O A:HOH1121 4.1 23.5 1.0 O A:GLY555 4.2 13.2 1.0 HA3 A:GLY555 4.2 15.0 1.0 HA2 A:GLY555 4.3 14.5 1.0 CA A:VAL120 4.4 12.8 1.0 OD1 A:ASP452 4.4 12.0 1.0 CG A:GLU449 4.5 13.2 1.0 CA A:GLU449 4.5 11.3 1.0 HG A:LEU448 4.6 15.1 0.5 HG22 A:THR119 4.6 14.8 1.0 CA A:GLY555 4.6 15.0 1.0 HA A:THR119 4.7 14.6 1.0 CG2 A:THR119 4.7 14.7 1.0 HG2 A:GLU449 4.8 13.0 1.0 H A:VAL120 4.8 13.6 1.0 C A:GLY555 4.8 13.6 1.0 O A:LEU448 4.9 11.4 0.5 O A:HOH1008 4.9 18.6 1.0 CB A:GLU449 4.9 11.8 1.0 HB3 A:GLU449 4.9 12.0 1.0 HB3 A:LEU448 4.9 12.2 0.5 HG21 A:THR119 5.0 14.5 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose


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 GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na603 b:18.1 occ:1.00 O A:HOH986 2.3 16.9 1.0 O A:HOH933 2.3 19.7 1.0 OD1 A:ASP293 2.4 11.3 1.0 OD2 A:ASP293 2.4 12.9 1.0 O A:GLN294 2.4 11.9 1.0 CG A:ASP293 2.7 11.4 1.0 H A:GLN294 3.3 10.1 1.0 HD21 A:ASN334 3.3 12.2 1.0 O A:HOH1191 3.4 22.4 1.0 HG21 A:VAL336 3.6 12.9 1.0 HG23 A:VAL336 3.6 12.4 1.0 C A:GLN294 3.7 11.6 1.0 HD22 A:ASN334 3.8 12.3 1.0 ND2 A:ASN334 3.8 12.9 1.0 HA A:LEU295 3.9 13.7 1.0 N A:GLN294 4.0 10.3 1.0 CG2 A:VAL336 4.0 12.8 1.0 HD21 A:LEU295 4.1 17.4 1.0 O A:HOH815 4.1 20.3 1.0 OE2 A:GLU355 4.1 12.3 1.0 CB A:ASP293 4.2 10.8 1.0 HG22 A:VAL336 4.3 12.5 1.0 HO1 B:GLC1 4.5 14.0 1.0 HD23 A:LEU219 4.5 11.9 1.0 CA A:GLN294 4.5 10.8 1.0 HG3 A:GLN294 4.6 11.4 1.0 HB3 A:ASP293 4.6 10.8 1.0 O A:HOH959 4.6 13.6 1.0 O A:HOH921 4.6 14.8 1.0 OE1 A:GLU355 4.6 11.3 1.0 N A:LEU295 4.6 12.4 1.0 O1 B:GLC1 4.7 14.2 1.0 CA A:LEU295 4.7 13.9 1.0 CD A:GLU355 4.7 10.6 1.0 HB2 A:ASP293 4.7 10.4 1.0 HD21 A:LEU219 4.8 11.6 1.0 HE2 A:TYR217 4.8 10.2 1.0 HA A:ASP293 4.8 9.9 1.0 OH A:TYR217 4.9 11.6 1.0 HB3 A:ASN334 4.9 10.3 1.0 CA A:ASP293 4.9 9.9 1.0 CG A:ASN334 5.0 10.9 1.0 C A:ASP293 5.0 9.9 1.0 HG13 A:VAL336 5.0 12.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose


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 GH66 Endodextranase From Flavobacterium Johnsoniae in Complex with Isomaltotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:16.1 occ:1.00 HB2 A:GLU139 2.6 12.3 1.0 OH A:TYR203 2.7 11.6 1.0 OE1 A:GLU424 2.7 10.0 1.0 O A:GLU139 2.8 11.3 1.0 O A:HOH889 2.8 15.0 1.0 HD11 A:ILE143 2.8 18.1 1.0 HG2 A:GLU424 2.9 10.7 1.0 HE2 A:TYR203 2.9 10.5 1.0 HH A:TYR203 3.2 30.0 0.0 H A:GLU139 3.3 10.4 1.0 CZ A:TYR203 3.4 10.4 1.0 CG A:GLU424 3.4 10.5 1.0 CE2 A:TYR203 3.5 10.4 1.0 CD A:GLU424 3.5 9.7 1.0 HG3 A:GLU424 3.5 10.2 1.0 CD1 A:ILE143 3.5 18.6 1.0 HD13 A:ILE143 3.5 18.4 1.0 CB A:GLU139 3.5 12.4 1.0 HD22 A:LEU137 3.6 11.0 1.0 C A:GLU139 3.7 10.8 1.0 HD12 A:ILE143 3.8 18.1 1.0 HG21 A:VAL151 3.9 12.4 1.0 CA A:GLU139 3.9 11.1 1.0 N A:GLU139 4.0 10.5 1.0 HB3 A:GLU139 4.0 12.8 1.0 HG13 A:VAL151 4.0 11.8 1.0 H A:SER138 4.1 9.3 1.0 HG23 A:ILE143 4.1 16.5 1.0 OE1 A:GLU139 4.4 19.4 1.0 HB3 A:LEU137 4.4 9.7 1.0 HG3 A:GLU139 4.5 13.8 1.0 CG A:GLU139 4.5 14.4 1.0 CD2 A:LEU137 4.6 11.0 1.0 CE1 A:TYR203 4.7 9.7 1.0 OE2 A:GLU424 4.7 9.4 1.0 CD2 A:TYR203 4.7 9.8 1.0 HD21 A:LEU137 4.8 10.8 1.0 CG1 A:ILE143 4.8 18.1 1.0 CG2 A:VAL151 4.8 12.5 1.0 CB A:GLU424 4.8 10.3 1.0 HA A:PHE140 4.9 10.2 1.0 O A:HOH1212 4.9 21.0 1.0 N A:PHE140 4.9 10.3 1.0 HA A:GLU139 4.9 11.3 1.0 HG12 A:ILE143 4.9 18.2 1.0 CD A:GLU139 5.0 17.2 1.0 CG1 A:VAL151 5.0 12.1 1.0 HB3 A:GLU424 5.0 10.6 1.0 N A:SER138 5.0 9.1 1.0

S.Nakamura, R.Kurata, T.Tonozuka, K.Funane, E.Y.Park, T.Miyazaki. Bacteroidota Polysaccharide Utilization System For Branched Dextran Exopolysaccharides From Lactic Acid Bacteria. J.Biol.Chem. 04885 2023.
ISSN: ESSN 1083-351X
PubMed: 37269952
DOI: 10.1016/J.JBC.2023.104885