Calcium in PDB 4up4: Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE

The structure of Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE, PDB code: 4up4 was solved by A.Audfray, M.Beljoudi, A.Hurbin, A.Varrot, A.Breiman, B.Busser, J.Lependu, J.L.Coll, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.814, 97.468, 158.650, 90.00, 90.00, 90.00
R / Rfree (%)	19.002 / 23.694

The binding sites of Calcium atom in the Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE (pdb code 4up4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE, PDB code: 4up4:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca500 b:13.8 occ:1.00 O A:CYS349 2.3 12.3 1.0 O A:HOH2413 2.3 14.3 1.0 OD1 A:ASP347 2.4 13.7 1.0 OD1 A:ASP343 2.4 13.4 1.0 OG1 A:THR345 2.5 11.6 1.0 OD2 A:ASP351 2.5 12.2 1.0 OD1 A:ASP351 2.7 14.4 1.0 CG A:ASP351 2.9 11.8 1.0 CG A:ASP347 3.4 14.2 1.0 C A:CYS349 3.5 12.2 1.0 CG A:ASP343 3.5 13.5 1.0 CB A:THR345 3.6 12.8 1.0 OD2 A:ASP347 3.8 12.7 1.0 CG2 A:THR345 3.8 13.7 1.0 N A:THR345 4.0 12.8 1.0 N A:CYS349 4.1 12.8 1.0 CA A:CYS349 4.1 12.6 1.0 OD2 A:ASP343 4.3 14.3 1.0 O A:HOH2412 4.3 12.2 1.0 CA A:THR345 4.3 12.9 1.0 CB A:CYS349 4.3 13.6 1.0 CB A:ASP351 4.4 13.2 1.0 N A:LEU344 4.4 13.4 1.0 CA A:ASP343 4.4 13.0 1.0 C A:ALA350 4.5 11.8 1.0 N A:ASP351 4.5 12.0 1.0 N A:ASP347 4.5 11.6 1.0 CB A:ASP343 4.5 13.3 1.0 CB A:ASN365 4.5 14.2 1.0 N A:ALA350 4.5 11.7 1.0 N A:GLY346 4.6 12.1 1.0 CB A:ASP347 4.6 13.2 1.0 CA A:ALA350 4.7 12.2 1.0 C A:THR345 4.7 13.5 1.0 O A:ALA350 4.8 11.6 1.0 O A:ASN365 4.9 16.9 1.0 C A:ASP343 4.9 13.1 1.0 CA A:ASP351 4.9 12.5 1.0 N A:GLY348 5.0 12.8 1.0

Calcium binding site 2 out of 6 in the Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:24.1 occ:1.00 OD1 A:ASP233 2.4 10.9 1.0 O A:LYS239 2.4 12.5 1.0 OD1 A:ASP237 2.5 18.5 1.0 OG1 A:THR235 2.5 12.9 1.0 OD2 A:ASP241 2.5 12.6 1.0 O A:HOH2329 2.7 24.4 1.0 CG A:ASP241 3.4 12.9 1.0 CG A:ASP233 3.4 12.7 1.0 CG A:ASP237 3.5 18.6 1.0 OD1 A:ASP241 3.5 13.2 1.0 C A:LYS239 3.5 14.9 1.0 CB A:THR235 3.7 16.3 1.0 N A:THR235 3.8 14.8 1.0 OD2 A:ASP237 4.0 18.6 1.0 N A:LYS239 4.0 15.8 1.0 N A:LEU234 4.0 12.9 1.0 CG2 A:THR235 4.1 17.1 1.0 CA A:LYS239 4.1 14.8 1.0 CA A:ASP233 4.1 12.3 1.0 O A:HOH2332 4.1 24.0 1.0 OD2 A:ASP233 4.2 13.5 1.0 CB A:ASP233 4.2 12.1 1.0 CA A:THR235 4.2 15.9 1.0 CB A:LYS239 4.2 16.6 1.0 N A:ASP237 4.3 16.4 1.0 O A:HOH2328 4.4 36.9 1.0 N A:GLY236 4.4 15.4 1.0 C A:ASP233 4.5 11.8 1.0 N A:ALA240 4.6 13.7 1.0 N A:ASP241 4.6 13.0 1.0 C A:THR235 4.7 17.5 1.0 CB A:ASP237 4.7 17.1 1.0 N A:ARG238 4.7 18.1 1.0 C A:ALA240 4.7 13.9 1.0 CB A:ASP241 4.8 13.0 1.0 C A:LEU234 4.8 14.2 1.0 CA A:ASP237 4.8 16.4 1.0 CA A:ALA240 4.9 13.9 1.0 C A:ASP237 4.9 17.5 1.0 CA A:LEU234 5.0 13.6 1.0

Calcium binding site 3 out of 6 in the Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca502 b:29.6 occ:1.00 OD1 A:ASP181 2.4 18.7 1.0 O A:LEU183 2.4 14.5 1.0 OD1 A:ASP177 2.4 12.2 1.0 OG1 A:THR179 2.6 16.6 1.0 OD2 A:ASP185 2.6 14.4 1.0 O A:HOH2276 2.6 17.6 1.0 OD1 A:ASP185 3.1 15.1 1.0 CG A:ASP185 3.1 15.1 1.0 CG A:ASP181 3.3 20.9 1.0 CG A:ASP177 3.3 12.6 1.0 C A:LEU183 3.4 15.1 1.0 OD2 A:ASP181 3.6 21.7 1.0 N A:LEU183 3.7 15.7 1.0 CB A:THR179 3.8 17.4 1.0 N A:THR179 3.9 15.8 1.0 CA A:LEU183 3.9 15.3 1.0 CA A:ASP177 4.0 12.4 1.0 CB A:LEU183 4.0 15.7 1.0 OD2 A:ASP177 4.1 11.2 1.0 CB A:ASP177 4.1 12.2 1.0 CG2 A:THR179 4.1 19.2 1.0 N A:VAL178 4.2 14.6 1.0 CA A:THR179 4.3 17.8 1.0 N A:ASP181 4.3 20.2 1.0 N A:GLY180 4.4 19.8 1.0 N A:GLY182 4.5 18.5 1.0 C A:ASP177 4.5 13.7 1.0 CB A:ASP181 4.5 20.1 1.0 CB A:ASP185 4.6 14.5 1.0 N A:ASP185 4.6 12.4 1.0 N A:LEU184 4.6 14.4 1.0 C A:THR179 4.8 18.4 1.0 CA A:ASP181 4.8 19.6 1.0 C A:GLY182 4.8 16.3 1.0 C A:ASP181 4.9 20.4 1.0 C A:LEU184 4.9 14.1 1.0 C A:VAL178 4.9 15.8 1.0 CA A:LEU184 5.0 13.8 1.0

Calcium binding site 4 out of 6 in the Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca500 b:15.2 occ:1.00 O B:HOH2350 2.3 18.4 1.0 OG1 B:THR345 2.3 14.2 1.0 O B:CYS349 2.4 14.1 1.0 OD1 B:ASP343 2.4 16.8 1.0 OD1 B:ASP347 2.5 17.3 1.0 OD2 B:ASP351 2.5 13.9 1.0 OD1 B:ASP351 2.7 14.3 1.0 CG B:ASP351 2.9 15.0 1.0 CG B:ASP347 3.5 17.2 1.0 CB B:THR345 3.5 14.0 1.0 C B:CYS349 3.5 15.8 1.0 CG B:ASP343 3.5 15.7 1.0 CG2 B:THR345 3.8 13.8 1.0 OD2 B:ASP347 3.9 18.8 1.0 N B:THR345 3.9 13.6 1.0 O B:HOH2349 4.1 18.1 1.0 N B:CYS349 4.1 15.6 1.0 CA B:THR345 4.2 14.5 1.0 CA B:CYS349 4.2 15.8 1.0 OD2 B:ASP343 4.3 15.4 1.0 CB B:CYS349 4.4 17.1 1.0 CB B:ASP351 4.4 14.6 1.0 N B:LEU344 4.4 13.5 1.0 CA B:ASP343 4.4 14.1 1.0 N B:ASP351 4.5 14.9 1.0 N B:ASP347 4.5 14.4 1.0 C B:ALA350 4.5 17.1 1.0 CB B:ASP343 4.5 14.7 1.0 CB B:ASN365 4.5 14.7 1.0 N B:ALA350 4.6 15.1 1.0 N B:GLY346 4.6 14.7 1.0 C B:THR345 4.6 14.5 1.0 CB B:ASP347 4.7 15.7 1.0 CA B:ALA350 4.7 16.3 1.0 O B:ALA350 4.8 16.9 1.0 O B:ASN365 4.8 18.5 1.0 C B:ASP343 4.9 13.5 1.0 CA B:ASP351 4.9 15.4 1.0 N B:GLY348 5.0 13.9 1.0

Calcium binding site 5 out of 6 in the Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:33.5 occ:1.00 O B:HOH2268 2.3 18.6 1.0 O B:LYS239 2.3 20.1 1.0 OD1 B:ASP233 2.4 18.6 1.0 OD2 B:ASP241 2.5 16.9 1.0 OG1 B:THR235 2.6 19.4 1.0 OD1 B:ASP237 2.6 19.3 1.0 CG B:ASP241 3.3 18.9 1.0 OD1 B:ASP241 3.4 20.3 1.0 C B:LYS239 3.4 20.3 1.0 CG B:ASP233 3.4 20.0 1.0 CG B:ASP237 3.6 21.5 1.0 CB B:THR235 3.8 20.8 1.0 N B:THR235 3.8 20.1 1.0 N B:LYS239 4.0 19.6 1.0 N B:LEU234 4.0 18.4 1.0 OD2 B:ASP237 4.1 21.4 1.0 CA B:LYS239 4.1 21.9 1.0 CA B:ASP233 4.1 17.2 1.0 CG2 B:THR235 4.1 21.4 1.0 CB B:LYS239 4.2 23.9 1.0 CB B:ASP233 4.2 18.3 1.0 CA B:THR235 4.3 21.2 1.0 OD2 B:ASP233 4.3 22.6 1.0 N B:ASP237 4.5 20.4 1.0 N B:GLY236 4.5 19.2 1.0 C B:ASP233 4.5 17.2 1.0 N B:ALA240 4.5 19.2 1.0 N B:ASP241 4.6 18.0 1.0 C B:ALA240 4.6 17.6 1.0 CB B:ASP241 4.7 19.0 1.0 C B:THR235 4.7 20.9 1.0 CA B:ALA240 4.8 18.3 1.0 C B:LEU234 4.8 20.4 1.0 CB B:ASP237 4.8 21.2 1.0 N B:ARG238 4.9 22.6 1.0 CB B:ASN255 4.9 20.1 1.0 CA B:LEU234 4.9 19.2 1.0

Calcium binding site 6 out of 6 in the Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of the Recombinant Lectin Pvl From Psathyrella Velutina in Complex with Glcnacb-D-1,3GALACTOSIDE within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca502 b:31.0 occ:1.00 O B:LEU183 2.3 16.1 1.0 OD1 B:ASP177 2.4 17.4 1.0 OD2 B:ASP185 2.5 20.4 1.0 OD1 B:ASP181 2.5 16.1 1.0 OG1 B:THR179 2.6 23.9 1.0 O B:HOH2227 2.7 31.1 1.0 OD1 B:ASP185 3.0 18.1 1.0 CG B:ASP185 3.0 19.6 1.0 CG B:ASP177 3.2 16.8 1.0 C B:LEU183 3.4 17.9 1.0 CG B:ASP181 3.4 19.4 1.0 N B:LEU183 3.8 17.2 1.0 OD2 B:ASP181 3.8 19.9 1.0 CB B:THR179 3.9 24.2 1.0 N B:THR179 3.9 21.4 1.0 CA B:ASP177 3.9 16.0 1.0 CA B:LEU183 3.9 17.9 1.0 OD2 B:ASP177 4.0 16.8 1.0 CB B:ASP177 4.0 16.8 1.0 CB B:LEU183 4.1 17.8 1.0 N B:VAL178 4.2 19.3 1.0 CG2 B:THR179 4.2 24.0 1.0 CA B:THR179 4.4 23.1 1.0 N B:ASP181 4.4 22.5 1.0 C B:ASP177 4.4 17.0 1.0 N B:ASP185 4.4 14.5 1.0 N B:GLY180 4.4 24.6 1.0 CB B:ASP185 4.5 18.4 1.0 N B:LEU184 4.5 14.5 1.0 N B:GLY182 4.5 18.7 1.0 CB B:ASP181 4.7 19.7 1.0 C B:LEU184 4.7 14.5 1.0 CA B:LEU184 4.8 14.4 1.0 C B:THR179 4.8 25.6 1.0 C B:GLY182 4.8 18.7 1.0 CA B:ASP181 4.9 20.1 1.0 C B:VAL178 4.9 21.8 1.0 C B:ASP181 4.9 19.1 1.0 CA B:ASP185 5.0 16.0 1.0

A.Audfray, M.Beljoudi, A.Hurbin, A.Varrot, A.Breiman, B.Busser, J.Lependu, J.L.Coll, A.Imberty. New Recombinant Lectin For Lung Cancer Diagnosis To Be Published.