Sodium in PDB 2bzd: Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase.

All present enzymatic activity of Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase.:
3.2.1.18;

The structure of Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase., PDB code: 2bzd was solved by S.L.Newstead, G.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	122.17 / 2.0
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	141.457, 141.457, 158.880, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 26.7

The binding sites of Sodium atom in the Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase. (pdb code 2bzd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase., PDB code: 2bzd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1648 b:20.3 occ:1.00 O A:ASN533 2.2 27.5 1.0 O A:ALA639 2.3 18.9 1.0 O A:ASN528 2.4 16.3 1.0 O A:THR536 2.5 19.0 1.0 OG1 A:THR536 2.7 19.0 1.0 OD1 A:ASP531 2.8 20.7 1.0 OE2 A:GLU640 3.2 32.8 1.0 C A:ASN533 3.2 27.1 1.0 C A:THR536 3.4 19.3 1.0 C A:ALA639 3.6 19.4 1.0 C A:ASN528 3.6 15.5 1.0 N A:ASN533 3.8 25.5 1.0 CG A:ASP531 3.8 21.0 1.0 CA A:ASN533 3.9 26.5 1.0 CB A:THR536 3.9 19.8 1.0 CD A:GLU640 4.0 30.5 1.0 CA A:THR536 4.1 20.0 1.0 CG A:GLU640 4.1 25.6 1.0 CB A:ASN533 4.1 26.8 1.0 N A:THR536 4.1 22.2 1.0 N A:PRO534 4.2 27.0 1.0 OD2 A:ASP531 4.2 21.0 1.0 N A:PHE537 4.3 18.3 1.0 CA A:ALA639 4.4 19.1 1.0 CA A:ASN528 4.4 14.6 1.0 N A:VAL529 4.5 16.0 1.0 CA A:PRO534 4.5 26.7 1.0 CA A:VAL529 4.5 16.1 1.0 CB A:ASN528 4.5 14.7 1.0 N A:GLU640 4.6 19.8 1.0 CA A:PHE537 4.6 18.4 1.0 C A:VAL529 4.7 16.0 1.0 C A:PRO534 4.8 25.8 1.0 CA A:GLU640 4.8 19.9 1.0 N A:ASP531 4.8 18.8 1.0 N A:SER535 4.9 25.5 1.0 N A:GLY532 4.9 21.9 1.0 CG2 A:THR536 4.9 18.7 1.0 CB A:ALA639 4.9 18.3 1.0 O A:VAL529 4.9 16.3 1.0 C A:GLY532 4.9 24.9 1.0 CB A:GLU640 5.0 20.2 1.0

Sodium binding site 2 out of 3 in the Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1648 b:8.4 occ:1.00 O B:ALA639 2.3 16.2 1.0 O B:ASN528 2.3 16.1 1.0 OE1 B:GLU640 2.3 21.6 0.5 O B:ASN533 2.4 21.3 1.0 O B:THR536 2.5 18.2 1.0 OD1 B:ASP531 2.7 12.1 1.0 OG1 B:THR536 2.7 17.8 1.0 C B:THR536 3.3 19.1 1.0 C B:ALA639 3.4 15.7 1.0 C B:ASN528 3.5 15.7 1.0 C B:ASN533 3.5 20.6 1.0 CD B:GLU640 3.6 18.8 0.5 CG B:ASP531 3.6 16.2 1.0 CB B:THR536 3.9 18.5 1.0 OD2 B:ASP531 4.0 17.0 1.0 CA B:THR536 4.0 18.8 1.0 N B:THR536 4.0 18.3 1.0 N B:ASN533 4.1 19.7 1.0 CA B:ASN533 4.2 21.1 1.0 CA B:ALA639 4.2 15.9 1.0 CG B:GLU640 4.2 17.7 0.5 N B:PHE537 4.3 18.2 1.0 CA B:VAL529 4.3 14.7 1.0 CB B:ASN533 4.3 20.1 1.0 CG B:GLU640 4.3 15.2 0.5 CA B:ASN528 4.3 15.4 1.0 N B:VAL529 4.3 15.3 1.0 N B:GLU640 4.4 16.2 1.0 CB B:ASN528 4.5 15.8 1.0 N B:PRO534 4.5 21.4 1.0 OE2 B:GLU640 4.5 15.8 0.5 C B:VAL529 4.6 14.7 1.0 CA B:PRO534 4.7 20.7 1.0 CA B:PHE537 4.7 17.3 1.0 CA B:GLU640 4.7 16.4 1.0 CB B:ALA639 4.8 14.9 1.0 N B:ASP531 4.9 16.0 1.0 C B:PRO534 4.9 20.0 1.0 O B:VAL529 4.9 15.3 1.0 CB B:ASP531 4.9 16.9 1.0 N B:GLY532 4.9 16.9 1.0 CG2 B:THR536 5.0 19.4 1.0

Sodium binding site 3 out of 3 in the Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1648 b:16.9 occ:1.00 O C:ASN533 2.3 29.6 1.0 O C:THR536 2.4 20.6 1.0 O C:ASN528 2.4 21.2 1.0 OG1 C:THR536 2.6 20.0 1.0 O C:ALA639 2.6 17.7 1.0 OD1 C:ASP531 2.7 28.6 1.0 OE2 C:GLU640 2.9 33.1 1.0 C C:THR536 3.3 20.8 1.0 C C:ASN528 3.4 20.4 1.0 C C:ASN533 3.5 29.4 1.0 CG C:ASP531 3.6 26.8 1.0 C C:ALA639 3.7 16.0 1.0 OD2 C:ASP531 3.8 19.1 1.0 CB C:THR536 3.8 21.5 1.0 CA C:THR536 3.9 21.1 1.0 CD C:GLU640 4.0 27.6 1.0 N C:THR536 4.0 21.6 1.0 N C:PHE537 4.2 20.8 1.0 N C:ASN533 4.2 28.8 1.0 CA C:ASN533 4.2 29.6 1.0 CB C:ASN533 4.2 29.6 1.0 CA C:ALA639 4.3 15.8 1.0 CA C:ASN528 4.3 19.1 1.0 N C:VAL529 4.3 19.2 1.0 CA C:VAL529 4.4 18.5 1.0 CB C:ASN528 4.4 19.3 1.0 CA C:PHE537 4.5 20.8 1.0 N C:PRO534 4.5 28.9 1.0 CA C:PRO534 4.6 27.7 1.0 CG C:GLU640 4.7 22.4 1.0 C C:PRO534 4.7 26.1 1.0 CB C:ALA639 4.8 15.9 1.0 OE1 C:GLU640 4.8 27.6 1.0 N C:GLU640 4.8 15.2 1.0 C C:VAL529 4.9 19.1 1.0 N C:SER535 4.9 24.1 1.0 CB C:ASP531 4.9 26.6 1.0 N C:ASP531 5.0 25.5 1.0 CG C:ASN533 5.0 30.8 1.0

S.L.Newstead, J.N.Watson, A.J.Bennet, G.Taylor. Galactose Recognition By the Carbohydrate-Binding Module of A Bacterial Sialidase. Acta Crystallogr.,Sect.D V. 61 1483 2005.
ISSN: ISSN 0907-4449
PubMed: 16239725
DOI: 10.1107/S0907444905026132