Sodium in PDB 1wcq: Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine.

All present enzymatic activity of Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine.:
3.2.1.18;

The structure of Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine., PDB code: 1wcq was solved by S.Newstead, J.N.Watson, A.J.Bennet, G.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	124.03 / 2.1
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	143.258, 143.258, 160.250, 90.00, 90.00, 120.00
R / Rfree (%)	17.5 / 23.8

The binding sites of Sodium atom in the Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine. (pdb code 1wcq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine., PDB code: 1wcq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1648 b:19.9 occ:1.00 O A:ASN533 2.2 35.1 1.0 O A:ASN528 2.3 28.5 1.0 O A:ALA639 2.3 28.5 1.0 OD1 A:ASP531 2.5 31.1 1.0 O A:THR536 2.7 30.4 1.0 OE2 A:GLU640 2.7 38.8 1.0 OG1 A:THR536 2.9 31.5 1.0 C A:ASN533 3.3 36.1 1.0 C A:THR536 3.5 31.3 1.0 C A:ASN528 3.5 25.9 1.0 C A:ALA639 3.5 28.2 1.0 CG A:ASP531 3.6 31.6 1.0 CD A:GLU640 3.7 39.4 1.0 OD2 A:ASP531 3.9 29.2 1.0 N A:ASN533 3.9 35.0 1.0 CA A:ASN533 3.9 36.9 1.0 N A:THR536 4.0 33.6 1.0 CB A:THR536 4.0 31.3 1.0 CA A:THR536 4.0 31.7 1.0 CG A:GLU640 4.1 35.8 1.0 CB A:ASN533 4.1 37.2 1.0 N A:PRO534 4.3 35.1 1.0 CA A:ALA639 4.3 27.7 1.0 CA A:VAL529 4.3 26.2 1.0 N A:PHE537 4.4 29.5 1.0 N A:VAL529 4.4 26.4 1.0 CA A:ASN528 4.4 26.1 1.0 CB A:ASN528 4.5 26.3 1.0 C A:VAL529 4.5 27.3 1.0 N A:GLU640 4.5 29.3 1.0 CA A:PRO534 4.6 34.8 1.0 CA A:GLU640 4.6 29.1 1.0 N A:ASP531 4.6 29.8 1.0 CA A:PHE537 4.7 28.4 1.0 OE1 A:GLU640 4.8 44.0 1.0 O A:VAL529 4.8 28.7 1.0 C A:PRO534 4.8 35.0 1.0 CB A:ALA639 4.8 26.9 1.0 N A:GLY532 4.9 32.9 1.0 CB A:ASP531 4.9 30.5 1.0 CB A:GLU640 4.9 30.6 1.0

Sodium binding site 2 out of 3 in the Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1648 b:17.2 occ:1.00 O B:ASN528 2.4 30.8 1.0 O B:ALA639 2.4 28.6 1.0 O B:ASN533 2.4 34.4 1.0 OE2 B:GLU640 2.4 36.6 1.0 O B:THR536 2.4 30.6 1.0 OD1 B:ASP531 2.5 35.5 1.0 OG1 B:THR536 2.7 30.1 1.0 C B:ASN533 3.4 34.3 1.0 C B:THR536 3.4 30.1 1.0 C B:ASN528 3.5 29.2 1.0 CG B:ASP531 3.6 35.1 1.0 CD B:GLU640 3.6 38.5 1.0 C B:ALA639 3.6 27.7 1.0 CB B:THR536 3.9 30.9 1.0 N B:ASN533 3.9 33.9 1.0 OD2 B:ASP531 4.0 38.9 1.0 CA B:THR536 4.0 30.1 1.0 N B:THR536 4.0 30.8 1.0 CA B:ASN533 4.0 34.2 1.0 CG B:GLU640 4.2 32.8 1.0 CB B:ASN533 4.3 32.9 1.0 CA B:ALA639 4.4 26.2 1.0 N B:PHE537 4.4 28.9 1.0 N B:PRO534 4.4 33.7 1.0 CA B:ASN528 4.4 29.4 1.0 N B:VAL529 4.4 29.1 1.0 CA B:VAL529 4.4 28.1 1.0 CB B:ASN528 4.5 26.8 1.0 N B:GLU640 4.6 27.8 1.0 OE1 B:GLU640 4.6 43.8 1.0 CA B:PRO534 4.6 32.8 1.0 C B:VAL529 4.7 28.9 1.0 CA B:PHE537 4.7 28.7 1.0 CA B:GLU640 4.7 29.0 1.0 N B:ASP531 4.8 32.1 1.0 C B:PRO534 4.8 31.3 1.0 N B:GLY532 4.8 32.3 1.0 CB B:ASP531 4.9 32.1 1.0 CB B:ALA639 4.9 26.9 1.0 CG2 B:THR536 5.0 30.2 1.0 O B:VAL529 5.0 27.8 1.0

Sodium binding site 3 out of 3 in the Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Mutagenesis of the Nucleophilic Tyrosine in A Bacterial Sialidase to Phenylalanine. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1648 b:13.0 occ:1.00 O C:THR536 2.2 23.7 1.0 O C:ASN533 2.2 32.2 1.0 O C:ALA639 2.3 25.8 1.0 O C:ASN528 2.3 29.2 1.0 OE2 C:GLU640 2.3 33.2 1.0 OG1 C:THR536 2.5 27.3 1.0 OD1 C:ASP531 2.6 31.9 1.0 C C:THR536 3.3 26.4 1.0 C C:ASN533 3.3 33.4 1.0 C C:ALA639 3.4 26.7 1.0 CD C:GLU640 3.5 34.7 1.0 C C:ASN528 3.5 29.1 1.0 CG C:ASP531 3.6 31.6 1.0 CB C:THR536 3.7 26.4 1.0 CA C:THR536 3.9 26.7 1.0 OD2 C:ASP531 3.9 32.9 1.0 N C:THR536 3.9 28.5 1.0 CG C:GLU640 4.0 30.2 1.0 N C:ASN533 4.0 34.7 1.0 CA C:ASN533 4.1 33.5 1.0 CA C:ALA639 4.2 25.6 1.0 N C:PRO534 4.2 32.1 1.0 N C:PHE537 4.3 26.3 1.0 CA C:PRO534 4.4 31.8 1.0 CB C:ASN533 4.4 33.0 1.0 N C:VAL529 4.4 29.8 1.0 CA C:ASN528 4.4 28.9 1.0 CA C:VAL529 4.5 30.5 1.0 N C:GLU640 4.5 25.3 1.0 CB C:ASN528 4.5 29.0 1.0 OE1 C:GLU640 4.6 33.7 1.0 CA C:PHE537 4.6 26.1 1.0 CA C:GLU640 4.7 27.1 1.0 C C:PRO534 4.7 31.1 1.0 CB C:ALA639 4.8 26.4 1.0 C C:VAL529 4.8 31.4 1.0 N C:ASP531 4.8 32.5 1.0 CG2 C:THR536 4.9 26.6 1.0 CB C:ASP531 4.9 32.3 1.0 CB C:GLU640 5.0 26.5 1.0

J.N.Watson, S.Newstead, A.A.Narine, G.Taylor, A.J.Bennet. Two Nucleophilic Mutants of the Micromonospora Viridifaciens Sialidase Operate with Retention of Configuration By Two Different Mechanisms. Chembiochem V. 6 1439 2005.
ISSN: ISSN 1439-4227
PubMed: 16206228
DOI: 10.1002/CBIC.200500114