Calcium in PDB 3qlq: Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster

The structure of Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster, PDB code: 3qlq was solved by E.J.Sundberg, D.A.Bonsor, B.Trastoy, J.L.Chiara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.84 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.890, 63.680, 125.800, 90.00, 93.23, 90.00
R / Rfree (%)	21.8 / 24.8

The structure of Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster (pdb code 3qlq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster, PDB code: 3qlq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca238 b:22.2 occ:1.00 O A:HOH275 1.9 15.7 1.0 O A:TYR12 2.2 20.1 1.0 OD2 A:ASP10 2.3 12.4 1.0 OD2 A:ASP19 2.4 28.8 1.0 OD1 A:ASN14 2.4 22.4 1.0 O A:HOH281 2.4 24.3 1.0 OD1 A:ASP10 2.5 18.4 1.0 CG A:ASP10 2.8 18.1 1.0 O A:HOH259 3.5 19.1 1.0 C A:TYR12 3.5 25.0 1.0 CG A:ASP19 3.5 27.3 1.0 CG A:ASN14 3.5 29.2 1.0 N A:ASN14 3.9 27.5 1.0 OD1 A:ASP19 4.0 25.0 1.0 CB A:ASN14 4.1 27.5 1.0 CB A:ASP10 4.2 19.7 1.0 CA A:TYR12 4.3 25.1 1.0 MN A:MN239 4.3 23.2 1.0 N A:TYR12 4.4 25.1 1.0 N A:PRO13 4.5 25.7 1.0 CA A:PRO13 4.5 27.1 1.0 C A:PRO13 4.5 27.8 1.0 CB A:TYR12 4.5 25.9 1.0 CA A:ASN14 4.6 27.9 1.0 O A:ASP208 4.6 19.6 1.0 CB A:ARG228 4.6 22.6 1.0 ND2 A:ASN14 4.6 26.0 1.0 CE1 A:HIS24 4.7 25.3 1.0 CB A:ASP19 4.7 29.2 1.0 OD1 A:ASP208 4.7 21.9 1.0 CA A:ARG228 4.7 22.1 1.0 NE2 A:HIS24 4.8 16.3 1.0 O A:HOH297 4.8 24.1 1.0 O A:ARG228 4.8 21.8 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca239 b:23.1 occ:1.00 O B:TYR12 2.2 23.0 1.0 O B:HOH258 2.3 20.7 1.0 O B:HOH276 2.4 23.9 1.0 OD1 B:ASP10 2.4 15.2 1.0 OD1 B:ASN14 2.5 23.2 1.0 OD2 B:ASP19 2.5 24.4 1.0 OD2 B:ASP10 2.6 13.4 1.0 CG B:ASP10 2.9 21.1 1.0 C B:TYR12 3.4 23.2 1.0 CG B:ASN14 3.6 29.3 1.0 CG B:ASP19 3.6 25.6 1.0 N B:ASN14 3.9 27.8 1.0 OD1 B:ASP19 4.1 24.5 1.0 CB B:ASN14 4.2 28.1 1.0 MN B:MN238 4.2 25.3 1.0 CA B:TYR12 4.3 23.4 1.0 CB B:ASP10 4.4 20.8 1.0 O B:HOH259 4.4 23.1 1.0 N B:PRO13 4.4 25.5 1.0 N B:TYR12 4.4 23.2 1.0 CB B:TYR12 4.4 25.2 1.0 O B:ASP208 4.6 20.6 1.0 CA B:PRO13 4.6 26.3 1.0 C B:PRO13 4.6 27.0 1.0 OD1 B:ASP208 4.6 21.9 1.0 CE1 B:HIS24 4.7 23.8 1.0 ND2 B:ASN14 4.7 26.5 1.0 CA B:ASN14 4.7 28.6 1.0 O B:ARG228 4.8 21.5 1.0 CB B:ARG228 4.8 25.9 1.0 CA B:ARG228 4.8 23.6 1.0 CB B:ASP19 4.8 29.0 1.0 NE2 B:HIS24 4.8 23.3 1.0 CD1 B:TYR12 4.9 31.4 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca239 b:20.3 occ:1.00 O C:HOH298 2.2 19.4 1.0 O C:TYR12 2.2 20.7 1.0 OD1 C:ASP10 2.4 19.1 1.0 OD2 C:ASP19 2.4 25.9 1.0 OD1 C:ASN14 2.5 19.1 1.0 O C:HOH262 2.5 16.4 1.0 OD2 C:ASP10 2.5 12.1 1.0 CG C:ASP10 2.8 15.8 1.0 C C:TYR12 3.5 24.5 1.0 CG C:ASP19 3.6 25.2 1.0 CG C:ASN14 3.6 25.4 1.0 N C:ASN14 3.9 27.7 1.0 OD1 C:ASP19 4.1 19.9 1.0 CB C:ASN14 4.2 27.4 1.0 MN C:MN238 4.2 22.5 1.0 CA C:TYR12 4.3 23.4 1.0 CB C:ASP10 4.3 18.0 1.0 N C:TYR12 4.4 23.9 1.0 N C:PRO13 4.4 25.4 1.0 CB C:TYR12 4.5 23.6 1.0 CA C:PRO13 4.5 26.8 1.0 O C:HOH297 4.5 23.3 1.0 C C:PRO13 4.6 27.5 1.0 O C:ASP208 4.6 19.0 1.0 CE1 C:HIS24 4.6 22.2 1.0 ND2 C:ASN14 4.7 20.4 1.0 CA C:ASN14 4.7 27.4 1.0 CB C:ARG228 4.7 21.7 1.0 OD1 C:ASP208 4.7 22.8 1.0 CB C:ASP19 4.7 28.6 1.0 CA C:ARG228 4.8 20.1 1.0 O C:ARG228 4.9 20.0 1.0 CD1 C:TYR12 4.9 30.6 1.0 NE2 C:HIS24 4.9 22.0 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca238 b:23.2 occ:1.00 OD2 D:ASP19 2.2 22.3 1.0 O D:TYR12 2.3 23.1 1.0 O D:HOH253 2.4 18.3 1.0 OD1 D:ASN14 2.5 23.3 1.0 OD1 D:ASP10 2.5 19.5 1.0 O D:HOH266 2.6 26.7 1.0 OD2 D:ASP10 2.6 13.8 1.0 CG D:ASP10 2.8 21.2 1.0 CG D:ASP19 3.3 26.0 1.0 C D:TYR12 3.5 24.0 1.0 CG D:ASN14 3.6 30.6 1.0 OD1 D:ASP19 3.7 18.2 1.0 N D:ASN14 3.9 30.9 1.0 MN D:MN239 4.1 24.4 1.0 CB D:ASN14 4.1 30.3 1.0 O D:HOH286 4.3 22.6 1.0 CB D:ASP10 4.4 20.3 1.0 N D:PRO13 4.4 26.4 1.0 CA D:TYR12 4.5 24.3 1.0 CA D:PRO13 4.5 27.5 1.0 N D:TYR12 4.6 23.3 1.0 C D:PRO13 4.6 28.6 1.0 CE1 D:HIS24 4.6 26.7 1.0 CB D:ASP19 4.6 29.1 1.0 O D:ASP208 4.6 23.4 1.0 CB D:TYR12 4.7 24.9 1.0 CA D:ASN14 4.7 30.8 1.0 CB D:ARG228 4.7 23.8 1.0 ND2 D:ASN14 4.7 31.1 1.0 OD1 D:ASP208 4.8 24.0 1.0 O D:ARG228 4.8 25.4 1.0 CA D:ARG228 4.8 23.7 1.0 NE2 D:HIS24 4.8 29.9 1.0

B.Trastoy, D.A.Bonsor, M.E.Perez-Ojeda, E.J.Sundberg, M.L.Jimeno, J.M.Garcia-Fernandez, J.L.Chiara. Synthesis and Biophysical Study of Disassembling Nano Hybrid Bioconjugates with A Cubic Octasilsesquioxane Core Adv Funct Mater V. 22 3191 2012.
ISSN: ISSN 1616-301X
DOI: 10.1002/ADFM.201200423