Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Concanavalin A Bound to An Octa-Alpha-Mannosyl- Octasilsesquioxane Cluster, PDB code: 3qlq:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn239 b:23.2 occ:1.00 O A:HOH259 1.4 19.1 1.0 OE2 A:GLU8 2.1 20.1 1.0 O A:HOH262 2.1 14.7 1.0 O A:HOH297 2.3 24.1 1.0 OD1 A:ASP19 2.4 25.0 1.0 OD2 A:ASP10 2.6 12.4 1.0 NE2 A:HIS24 2.7 16.3 1.0 CD A:GLU8 2.9 13.2 1.0 OE1 A:GLU8 3.1 15.0 1.0 CG A:ASP19 3.1 27.3 1.0 CD2 A:HIS24 3.4 19.3 1.0 OD2 A:ASP19 3.5 28.8 1.0 CG A:ASP10 3.5 18.1 1.0 CB A:ASP10 3.8 19.7 1.0 CE1 A:HIS24 3.8 25.3 1.0 O A:HOH275 3.8 15.7 1.0 OG A:SER34 3.9 17.7 1.0 CA A:CA238 4.3 22.2 1.0 CG A:GLU8 4.3 15.3 1.0 CB A:ASP19 4.3 29.2 1.0 O A:VAL32 4.3 20.8 1.0 O A:HOH266 4.6 28.1 1.0 CA A:ASP19 4.7 30.8 1.0 CG A:HIS24 4.7 24.6 1.0 OD1 A:ASP10 4.7 18.4 1.0 ND1 A:HIS24 4.8 20.4 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:25.3 occ:1.00 O B:HOH283 1.9 21.0 1.0 OD2 B:ASP10 2.0 13.4 1.0 OE2 B:GLU8 2.1 19.2 1.0 O B:HOH259 2.2 23.1 1.0 OD1 B:ASP19 2.3 24.5 1.0 NE2 B:HIS24 2.5 23.3 1.0 CG B:ASP10 3.0 21.1 1.0 CD B:GLU8 3.1 12.6 1.0 CG B:ASP19 3.1 25.6 1.0 CD2 B:HIS24 3.3 25.9 1.0 OE1 B:GLU8 3.3 13.8 1.0 OD2 B:ASP19 3.4 24.4 1.0 CB B:ASP10 3.5 20.8 1.0 CE1 B:HIS24 3.6 23.8 1.0 O B:HOH258 4.0 20.7 1.0 OD1 B:ASP10 4.0 15.2 1.0 OG B:SER34 4.1 20.8 1.0 CA B:CA239 4.2 23.1 1.0 CB B:ASP19 4.4 29.0 1.0 O B:HOH282 4.4 27.2 1.0 O B:VAL32 4.5 20.6 1.0 CG B:GLU8 4.5 15.3 1.0 CG B:HIS24 4.5 24.6 1.0 ND1 B:HIS24 4.6 24.4 1.0 CA B:ASP19 4.7 29.9 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn238 b:22.5 occ:1.00 OD2 C:ASP10 2.0 12.1 1.0 OE2 C:GLU8 2.2 19.5 1.0 OD1 C:ASP19 2.3 19.9 1.0 O C:HOH255 2.3 16.7 1.0 NE2 C:HIS24 2.3 22.0 1.0 O C:HOH297 2.4 23.3 1.0 CG C:ASP19 3.0 25.2 1.0 CG C:ASP10 3.1 15.8 1.0 CE1 C:HIS24 3.2 22.2 1.0 CD C:GLU8 3.2 15.0 1.0 CD2 C:HIS24 3.3 23.2 1.0 OD2 C:ASP19 3.4 25.9 1.0 CB C:ASP10 3.5 18.0 1.0 OE1 C:GLU8 3.6 17.6 1.0 O C:HOH298 4.0 19.4 1.0 OG C:SER34 4.0 21.4 1.0 CA C:CA239 4.2 20.3 1.0 OD1 C:ASP10 4.2 19.1 1.0 CB C:ASP19 4.2 28.6 1.0 ND1 C:HIS24 4.4 23.9 1.0 O C:HOH244 4.4 26.9 1.0 CG C:HIS24 4.4 22.8 1.0 CG C:GLU8 4.5 15.0 1.0 O C:VAL32 4.6 18.4 1.0 CA C:ASP19 4.6 29.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn239 b:24.4 occ:1.00 O D:HOH251 1.7 26.9 1.0 OD2 D:ASP10 1.9 13.8 1.0 O D:HOH286 2.2 22.6 1.0 OE2 D:GLU8 2.2 19.1 1.0 NE2 D:HIS24 2.3 29.9 1.0 OD1 D:ASP19 2.3 18.2 1.0 CG D:ASP10 3.0 21.2 1.0 CD D:GLU8 3.1 19.5 1.0 CG D:ASP19 3.2 26.0 1.0 CD2 D:HIS24 3.2 29.4 1.0 CE1 D:HIS24 3.3 26.7 1.0 CB D:ASP10 3.5 20.3 1.0 OE1 D:GLU8 3.5 21.1 1.0 OD2 D:ASP19 3.6 22.3 1.0 O D:HOH253 4.0 18.3 1.0 OD1 D:ASP10 4.1 19.5 1.0 CA D:CA238 4.1 23.2 1.0 OG D:SER34 4.2 20.2 1.0 CB D:ASP19 4.3 29.1 1.0 CG D:HIS24 4.4 28.2 1.0 ND1 D:HIS24 4.4 25.5 1.0 CG D:GLU8 4.4 18.2 1.0 O D:VAL32 4.5 22.0 1.0 CA D:ASP19 4.6 30.3 1.0 CA D:ASP10 5.0 21.6 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