Sodium in PDB 6gn6: Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus

All present enzymatic activity of Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus:
3.2.1.51;

The structure of Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus, PDB code: 6gn6 was solved by T.Kovalova, T.Koval, P.Lipovova, J.Dohnalek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.93 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	107.772, 148.758, 194.895, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 21.7

The binding sites of Sodium atom in the Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus (pdb code 6gn6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus, PDB code: 6gn6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:69.9 occ:1.00 O7 C:P6G502 3.1 67.9 1.0 O4 C:P6G502 3.3 57.8 1.0 O13 C:P6G502 3.6 81.3 1.0 O10 C:P6G502 3.6 77.2 1.0 O1 C:P6G502 3.6 58.4 1.0 C6 C:P6G502 3.6 61.7 1.0 O19 C:P6G502 3.7 63.7 1.0 C2 C:P6G502 3.8 56.5 1.0 O16 C:P6G502 3.8 65.7 1.0 C11 C:P6G502 3.8 80.9 1.0 C18 C:P6G502 3.9 68.5 1.0 C5 C:P6G502 3.9 56.2 1.0 C3 C:P6G502 3.9 52.4 1.0 C14 C:P6G502 4.0 65.5 1.0 C9 C:P6G502 4.0 75.2 1.0 C8 C:P6G502 4.0 71.9 1.0 C12 C:P6G502 4.1 81.8 1.0 C15 C:P6G502 4.3 60.5 1.0 C17 C:P6G502 4.3 66.8 1.0

Sodium binding site 2 out of 2 in the Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus within 5.0Å range: probe atom residue distance (Å) B Occ F:Na506 b:63.6 occ:1.00 OH7 F:1PE505 3.0 65.0 1.0 OH5 F:1PE505 3.1 65.9 1.0 C22 F:1PE505 3.2 75.6 1.0 OH6 F:1PE505 3.4 80.9 1.0 C15 F:1PE505 3.6 67.5 1.0 OH2 F:1PE505 3.6 56.1 1.0 C26 F:1PE505 3.6 76.7 1.0 C24 F:1PE505 3.7 79.7 1.0 C14 F:1PE505 3.8 76.3 1.0 C16 F:1PE505 3.8 69.7 1.0 C13 F:1PE505 3.8 77.8 1.0 C25 F:1PE505 3.9 66.0 1.0 C12 F:1PE505 4.0 62.8 1.0 OH4 F:1PE505 4.1 82.8 1.0 OH3 F:1PE505 4.4 83.6 1.0 C23 F:1PE505 4.5 73.2 1.0

T.Kovalova, T.Koval, E.Benesova, P.Vodickova, V.Spiwok, P.Lipovova, J.Dohnalek. Active Site Complementation and Hexameric Arrangement in the Gh Family 29; A Structure-Function Study of Alpha-L-Fucosidase Isoenzyme 1 From Paenibacillus Thiaminolyticus. Glycobiology V. 29 59 2019.
ISSN: ESSN 1460-2423
PubMed: 30544181
DOI: 10.1093/GLYCOB/CWY078