Calcium in PDB 1w0o: Vibrio Cholerae Sialidase

All present enzymatic activity of Vibrio Cholerae Sialidase:
3.2.1.18;

The structure of Vibrio Cholerae Sialidase, PDB code: 1w0o 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)	100 / 1.9
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 (%)	17.94 / 21.78

The binding sites of Calcium atom in the Vibrio Cholerae Sialidase (pdb code 1w0o). 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, PDB code: 1w0o:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Vibrio Cholerae Sialidase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1779 b:8.0 occ:1.00 OD2 A:ASP289 2.3 7.1 1.0 O A:ALA253 2.3 9.0 1.0 O A:ASN256 2.3 9.1 1.0 OD1 A:ASN256 2.3 9.8 1.0 OG1 A:THR313 2.4 8.3 1.0 O A:THR313 2.5 7.0 1.0 OD1 A:ASP289 2.6 9.1 1.0 CG A:ASP289 2.8 7.7 1.0 C A:ASN256 3.2 10.0 1.0 C A:ALA253 3.4 10.2 1.0 C A:THR313 3.4 9.3 1.0 CB A:THR313 3.5 8.8 1.0 CG A:ASN256 3.5 9.4 1.0 CA A:THR313 3.6 8.0 1.0 N A:ALA253 3.6 8.7 1.0 CA A:ALA253 4.0 8.8 1.0 CA A:ASN256 4.0 9.0 1.0 N A:ASN256 4.1 9.4 1.0 N A:THR257 4.2 8.2 1.0 N A:GLY252 4.2 9.1 1.0 CB A:ASP289 4.2 6.6 1.0 C A:GLY252 4.3 9.0 1.0 CB A:ASN256 4.3 7.7 1.0 O A:HOH2453 4.4 12.7 1.0 CA A:THR257 4.4 8.8 1.0 N A:LEU254 4.4 9.8 1.0 CG2 A:THR313 4.5 8.9 1.0 ND2 A:ASN256 4.5 6.4 1.0 CA A:GLY252 4.6 9.7 1.0 CB A:ALA253 4.6 10.2 1.0 N A:ASP314 4.7 8.1 1.0 CA A:LEU254 4.7 11.0 1.0 C A:LEU254 4.8 10.9 1.0 N A:ASN258 4.9 7.5 1.0 N A:THR313 5.0 8.0 1.0

Calcium binding site 2 out of 4 in the Vibrio Cholerae Sialidase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1780 b:6.8 occ:1.00 O A:ALA683 2.3 5.8 1.0 OD1 A:ASP682 2.4 8.8 1.0 O A:PRO548 2.4 6.3 1.0 OD2 A:ASP621 2.4 10.0 1.0 OD2 A:ASP682 2.4 9.2 1.0 OD1 A:ASP621 2.5 7.5 1.0 CG A:ASP682 2.7 8.7 1.0 CG A:ASP621 2.8 8.6 1.0 C A:PRO548 3.4 6.4 1.0 C A:ALA683 3.6 6.6 1.0 CA A:GLY549 3.9 7.5 1.0 N A:ALA683 4.0 8.1 1.0 N A:GLY549 4.1 5.9 1.0 O A:HOH2769 4.2 11.8 1.0 CB A:ASP682 4.2 8.5 1.0 CB A:ASP621 4.3 7.5 1.0 O A:ALA620 4.3 8.2 1.0 CG A:PRO548 4.3 8.1 1.0 O A:HOH2770 4.4 12.8 1.0 N A:SER684 4.5 6.8 1.0 CA A:SER684 4.5 8.0 1.0 CA A:ALA683 4.5 8.2 1.0 O A:SER741 4.5 7.3 1.0 CA A:PRO548 4.6 7.2 1.0 CB A:PRO548 4.6 6.1 1.0 OD1 A:ASP742 4.7 5.8 1.0 C A:ASP682 4.7 8.5 1.0 O A:HOH2327 4.7 10.4 1.0 C A:ALA620 4.8 8.3 1.0 NH2 A:ARG294 4.8 8.7 1.0 CA A:ASP682 4.9 7.7 1.0 CB A:SER684 4.9 7.1 1.0

Calcium binding site 3 out of 4 in the Vibrio Cholerae Sialidase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1781 b:10.4 occ:1.00 O A:HOH2466 2.3 11.5 1.0 O A:PHE578 2.3 8.0 1.0 OD2 A:ASP320 2.4 10.3 1.0 OD1 A:ASP320 2.7 10.5 1.0 CG A:ASP320 2.9 10.9 1.0 C A:PHE578 3.4 8.8 1.0 CA A:PHE578 3.9 9.2 1.0 O A:HOH2460 4.2 19.6 1.0 OE1 A:GLU616 4.3 8.6 1.0 CB A:PHE578 4.3 11.0 1.0 O A:HOH2465 4.4 20.0 1.0 CB A:ASP320 4.4 8.2 1.0 OE2 A:GLU616 4.5 10.7 1.0 N A:PHE579 4.6 7.6 1.0 CD A:GLU616 4.8 11.2 1.0 O A:HOH2464 4.8 40.4 1.0 CA A:PHE579 4.9 7.9 1.0

Calcium binding site 4 out of 4 in the Vibrio Cholerae Sialidase


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1782 b:14.3 occ:1.00 O A:HOH2426 2.3 11.3 1.0 OD1 A:ASP286 2.3 11.9 1.0 O A:HOH2367 2.4 9.9 1.0 O A:HOH2433 2.5 13.5 1.0 O A:HOH2434 2.7 20.5 1.0 CG A:ASP286 3.4 14.1 1.0 OD2 A:ASP286 3.7 17.0 1.0 O A:ASN283 4.3 8.9 1.0 O A:HOH2412 4.4 44.6 1.0 OD2 A:ASP259 4.5 12.2 1.0 O A:HOH2176 4.5 44.3 1.0 CG2 A:THR257 4.5 11.1 1.0 O A:HOH2404 4.5 11.5 1.0 O A:HOH2366 4.6 12.4 1.0 CB A:ASP286 4.7 11.6 1.0 OE2 A:GLU280 4.7 16.4 1.0 CB A:GLU280 4.8 13.1 1.0

I.Moustafa, H.Connaris, M.Taylor, V.Zaitsev, J.C.Wilsonm, 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