Calcium in PDB 1w0p: Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose

All present enzymatic activity of Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose:
3.2.1.18;

The structure of Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose, PDB code: 1w0p was solved by I.Moustafa, H.Connaris, M.Taylor, V.Zaitsev, J.C.Wilson, M.J.Kiefel, M.Von-Itzstein, G.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50 / 1.6
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	70.310, 74.910, 151.615, 90.00, 90.00, 90.00
R / Rfree (%)	21.45 / n/a

The binding sites of Calcium atom in the Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose (pdb code 1w0p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose, PDB code: 1w0p:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1779 b:6.2 occ:1.00 O A:ALA253 2.3 8.5 1.0 O A:ASN256 2.3 7.3 1.0 OD1 A:ASN256 2.3 7.1 1.0 OD2 A:ASP289 2.3 6.5 1.0 OG1 A:THR313 2.4 6.7 1.0 O A:THR313 2.5 5.7 1.0 OD1 A:ASP289 2.7 5.3 1.0 CG A:ASP289 2.8 5.4 1.0 C A:ASN256 3.2 7.3 1.0 C A:ALA253 3.4 9.9 1.0 C A:THR313 3.4 6.6 1.0 CG A:ASN256 3.5 6.2 1.0 CB A:THR313 3.5 6.5 1.0 CA A:THR313 3.6 6.2 1.0 N A:ALA253 3.6 8.1 1.0 CA A:ASN256 4.0 6.9 1.0 N A:ASN256 4.0 9.4 1.0 CA A:ALA253 4.0 8.8 1.0 N A:THR257 4.1 6.2 1.0 N A:GLY252 4.2 6.2 1.0 C A:GLY252 4.3 7.6 1.0 CB A:ASN256 4.3 7.6 1.0 CB A:ASP289 4.3 4.4 1.0 CA A:THR257 4.4 6.8 1.0 O A:HOH2224 4.4 9.5 1.0 N A:LEU254 4.4 11.3 1.0 CG2 A:THR313 4.5 8.0 1.0 ND2 A:ASN256 4.5 8.3 1.0 CA A:GLY252 4.6 6.4 1.0 CB A:ALA253 4.6 9.1 1.0 N A:ASP314 4.7 7.2 1.0 CA A:LEU254 4.7 12.3 1.0 C A:LEU254 4.8 12.4 1.0 O A:LEU254 5.0 14.2 1.0 O A:GLY252 5.0 9.6 1.0

Calcium binding site 2 out of 4 in the Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1780 b:5.6 occ:1.00 O A:ALA683 2.3 6.2 1.0 OD1 A:ASP682 2.4 6.3 1.0 O A:PRO548 2.4 6.7 1.0 OD1 A:ASP621 2.4 7.9 1.0 OD2 A:ASP621 2.4 9.3 1.0 OD2 A:ASP682 2.5 8.8 1.0 CG A:ASP682 2.7 6.7 1.0 CG A:ASP621 2.8 9.4 1.0 C A:PRO548 3.5 6.7 1.0 C A:ALA683 3.6 4.7 1.0 CA A:GLY549 3.9 7.8 1.0 N A:ALA683 4.1 5.9 1.0 N A:GLY549 4.1 6.3 1.0 O A:HOH2467 4.2 10.1 1.0 CB A:ASP682 4.2 5.6 1.0 CB A:ASP621 4.3 6.7 1.0 CG A:PRO548 4.3 8.0 1.0 O A:ALA620 4.4 6.1 1.0 O A:SER741 4.4 7.5 1.0 O A:HOH2466 4.4 16.8 1.0 N A:SER684 4.5 5.3 1.0 CA A:SER684 4.5 6.7 1.0 CA A:ALA683 4.5 5.3 1.0 NH2 A:ARG294 4.5 13.6 1.0 CB A:PRO548 4.6 6.7 1.0 CA A:PRO548 4.6 7.2 1.0 O A:HOH2151 4.7 12.4 1.0 C A:ASP682 4.7 6.2 1.0 OD1 A:ASP742 4.8 11.0 1.0 C A:ALA620 4.8 7.0 1.0 CA A:ASP682 4.9 5.3 1.0 CB A:SER684 5.0 7.9 1.0

Calcium binding site 3 out of 4 in the Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1781 b:9.8 occ:1.00 N A:TRS1783 2.2 25.8 1.0 O A:PHE578 2.3 7.2 1.0 O1 A:TRS1783 2.4 21.1 1.0 OD2 A:ASP320 2.4 13.1 1.0 O2 A:TRS1783 2.6 28.5 1.0 OD1 A:ASP320 2.7 11.0 1.0 C1 A:TRS1783 2.8 26.7 1.0 C A:TRS1783 2.8 27.3 1.0 CG A:ASP320 2.9 10.1 1.0 C2 A:TRS1783 3.2 27.6 1.0 C A:PHE578 3.4 6.1 1.0 CA A:PHE578 4.0 7.5 1.0 O A:HOH2233 4.2 24.7 1.0 C3 A:TRS1783 4.2 29.0 1.0 O A:HOH2234 4.2 22.6 1.0 OE1 A:GLU616 4.3 12.8 1.0 CB A:PHE578 4.4 7.4 1.0 CB A:ASP320 4.4 10.1 1.0 N A:PHE579 4.5 7.6 1.0 OE2 A:GLU616 4.6 15.7 1.0 O A:HOH2232 4.6 37.4 1.0 CA A:PHE579 4.9 8.3 1.0 CD A:GLU616 4.9 13.9 1.0

Calcium binding site 4 out of 4 in the Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Vibrio Cholerae Sialidase with Alpha-2,6-Sialyllactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1782 b:10.4 occ:1.00 O A:HOH2200 2.3 13.9 1.0 OD1 A:ASP286 2.4 14.2 1.0 CG A:ASP286 3.4 13.0 1.0 OD2 A:ASP286 3.8 15.6 1.0 OE2 A:GLU280 4.3 26.3 1.0 O A:HOH2199 4.3 35.7 1.0 O A:ASN283 4.4 10.4 1.0 OD2 A:ASP259 4.5 10.8 1.0 CG A:GLU280 4.6 23.6 1.0 O A:HOH2173 4.6 15.9 1.0 CG2 A:THR257 4.7 7.4 1.0 CB A:ASP286 4.8 11.8 1.0 CD A:GLU280 5.0 22.9 1.0

I.Moustafa, H.Connaris, M.Taylor, V.Zaitsev, J.C.Wilson, M.J.Kiefel, M.Von Itzstein, G.Taylor. Sialic Acid Recognition By Vibrio Cholerae Neuraminidase. J.Biol.Chem. V. 279 40819 2004.
ISSN: ISSN 0021-9258
PubMed: 15226294
DOI: 10.1074/JBC.M404965200