Manganese in PDB 1azd: Concanavalin From Canavalia Brasiliensis

The structure of Concanavalin From Canavalia Brasiliensis, PDB code: 1azd was solved by J.Sanz-Aparicio, J.Hermoso, T.B.Grangeiro, J.J.Calvete, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	8.00 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.290, 71.650, 190.960, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 24

The structure of Concanavalin From Canavalia Brasiliensis also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Concanavalin From Canavalia Brasiliensis (pdb code 1azd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Concanavalin From Canavalia Brasiliensis, PDB code: 1azd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Concanavalin From Canavalia Brasiliensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Concanavalin From Canavalia Brasiliensis within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn239 b:16.1 occ:1.00 OE2 A:GLU8 2.1 18.9 1.0 OD2 A:ASP10 2.2 7.0 1.0 NE2 A:HIS24 2.3 10.0 1.0 OD1 A:ASP19 2.7 31.7 1.0 CD A:GLU8 3.2 11.6 1.0 CE1 A:HIS24 3.2 13.8 1.0 CG A:ASP10 3.3 13.3 1.0 CD2 A:HIS24 3.3 12.2 1.0 CG A:ASP19 3.4 25.5 1.0 OD2 A:ASP19 3.6 29.1 1.0 OE1 A:GLU8 3.6 8.7 1.0 CB A:ASP10 3.7 10.9 1.0 OG A:SER34 3.9 7.4 1.0 CA A:CA238 4.3 11.8 1.0 OD1 A:ASP10 4.4 20.1 1.0 ND1 A:HIS24 4.4 12.1 1.0 CG A:HIS24 4.4 12.3 1.0 CG A:GLU8 4.5 9.2 1.0 O A:VAL32 4.6 18.7 1.0 CB A:ASP19 4.7 19.6 1.0 CA A:ASP19 5.0 15.8 1.0

Manganese binding site 2 out of 4 in the Concanavalin From Canavalia Brasiliensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Concanavalin From Canavalia Brasiliensis within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn239 b:12.1 occ:1.00 OE2 B:GLU8 2.2 15.5 1.0 OD2 B:ASP10 2.3 13.0 1.0 NE2 B:HIS24 2.3 2.0 1.0 OD1 B:ASP19 2.6 26.8 1.0 CD B:GLU8 3.2 11.5 1.0 CE1 B:HIS24 3.2 2.2 1.0 CD2 B:HIS24 3.3 4.9 1.0 CG B:ASP10 3.4 16.3 1.0 CG B:ASP19 3.4 23.7 1.0 OD2 B:ASP19 3.6 22.0 1.0 OE1 B:GLU8 3.6 15.2 1.0 CB B:ASP10 3.8 13.8 1.0 OG B:SER34 3.8 15.8 1.0 O B:HOH248 4.1 42.5 1.0 ND1 B:HIS24 4.4 6.6 1.0 CG B:HIS24 4.4 5.7 1.0 OD1 B:ASP10 4.4 24.8 1.0 CA B:CA238 4.5 20.5 1.0 CG B:GLU8 4.5 5.7 1.0 O B:VAL32 4.5 23.3 1.0 CB B:ASP19 4.6 21.3 1.0 CA B:ASP19 4.9 15.6 1.0

Manganese binding site 3 out of 4 in the Concanavalin From Canavalia Brasiliensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Concanavalin From Canavalia Brasiliensis within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn239 b:9.6 occ:1.00 OE2 C:GLU8 2.2 16.0 1.0 OD2 C:ASP10 2.2 26.3 1.0 NE2 C:HIS24 2.2 2.0 1.0 OD1 C:ASP19 2.6 33.7 1.0 CE1 C:HIS24 3.2 5.6 1.0 CD2 C:HIS24 3.2 13.3 1.0 CD C:GLU8 3.2 13.1 1.0 CG C:ASP10 3.3 22.9 1.0 CG C:ASP19 3.4 30.3 1.0 OD2 C:ASP19 3.6 28.2 1.0 OE1 C:GLU8 3.6 10.3 1.0 CB C:ASP10 3.7 15.5 1.0 OG C:SER34 3.9 7.6 1.0 O C:HOH318 4.0 44.8 1.0 ND1 C:HIS24 4.3 13.7 1.0 CG C:HIS24 4.4 10.1 1.0 OD1 C:ASP10 4.4 24.8 1.0 CA C:CA238 4.4 27.8 1.0 CG C:GLU8 4.5 10.5 1.0 CB C:ASP19 4.6 26.1 1.0 O C:VAL32 4.6 22.8 1.0 CA C:ASP19 4.9 22.1 1.0

Manganese binding site 4 out of 4 in the Concanavalin From Canavalia Brasiliensis


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Concanavalin From Canavalia Brasiliensis within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn239 b:16.6 occ:1.00 OE2 D:GLU8 2.1 19.8 1.0 OD2 D:ASP10 2.3 13.1 1.0 NE2 D:HIS24 2.4 9.5 1.0 OD1 D:ASP19 2.7 29.8 1.0 CD D:GLU8 3.2 14.5 1.0 CE1 D:HIS24 3.3 11.1 1.0 CD2 D:HIS24 3.3 11.2 1.0 CG D:ASP10 3.4 19.4 1.0 CG D:ASP19 3.4 25.9 1.0 OE1 D:GLU8 3.5 12.8 1.0 OD2 D:ASP19 3.6 29.0 1.0 O D:HOH277 3.8 32.1 1.0 OG D:SER34 3.8 13.5 1.0 CB D:ASP10 3.8 14.8 1.0 CA D:CA238 4.4 10.6 1.0 ND1 D:HIS24 4.5 11.6 1.0 O D:VAL32 4.5 18.4 1.0 OD1 D:ASP10 4.5 23.9 1.0 CG D:GLU8 4.5 9.8 1.0 CG D:HIS24 4.5 12.5 1.0 CB D:ASP19 4.7 18.5 1.0 CA D:ASP19 5.0 17.4 1.0

J.Sanz-Aparicio, J.Hermoso, T.B.Grangeiro, J.J.Calvete, B.S.Cavada. The Crystal Structure of Canavalia Brasiliensis Lectin Suggests A Correlation Between Its Quaternary Conformation and Its Distinct Biological Properties From Concanavalin A. Febs Lett. V. 405 114 1997.
ISSN: ISSN 0014-5793
PubMed: 9094437
DOI: 10.1016/S0014-5793(97)00137-3