Calcium in PDB 5byn: Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid

The structure of Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid, PDB code: 5byn was solved by R.B.Nobrega, J.C.Silva-Filho, C.Y.Kawasoko, O.E.D.Rodrigues, R.S.Schwab, A.L.Braga, P.Delatorre, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.91 / 2.65
Space group	F 2 3
Cell size a, b, c (Å), α, β, γ (°)	190.640, 190.640, 190.640, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 27.8

The structure of Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid also contains other interesting chemical elements:

Manganese	(Mn)	2 atoms
Cadmium	(Cd)	1 atom

The binding sites of Calcium atom in the Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid (pdb code 5byn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid, PDB code: 5byn:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:43.0 occ:1.00 O A:HOH412 1.9 33.4 1.0 OD2 A:ASP10 2.4 39.8 1.0 OD1 A:ASP10 2.4 41.5 1.0 OD1 A:ASN14 2.4 47.5 1.0 O A:HOH408 2.4 36.7 1.0 O A:TYR12 2.5 48.2 1.0 OD2 A:ASP19 2.6 40.8 1.0 CG A:ASP10 2.7 40.4 1.0 CG A:ASN14 3.4 48.1 1.0 C A:TYR12 3.6 48.1 1.0 CG A:ASP19 3.8 43.8 1.0 CB A:ASN14 3.9 48.4 1.0 N A:ASN14 4.1 49.0 1.0 MN A:MN302 4.1 28.7 1.0 CB A:ASP10 4.2 38.9 1.0 OD1 A:ASP19 4.3 44.8 1.0 O A:HOH406 4.3 27.8 1.0 CA A:TYR12 4.3 47.9 1.0 ND2 A:ASN14 4.4 50.4 1.0 N A:TYR12 4.4 45.5 1.0 CB A:TYR12 4.5 49.7 1.0 O A:ARG228 4.5 45.1 1.0 O A:ASP208 4.6 40.7 1.0 CA A:ASN14 4.6 49.5 1.0 CB A:ARG228 4.7 48.0 1.0 N A:PRO13 4.7 49.6 1.0 CA A:ARG228 4.7 46.2 1.0 CD1 A:ILE17 4.8 45.5 1.0 OD1 A:ASP208 4.9 52.0 1.0 CB A:ASP19 4.9 44.4 1.0 C A:PRO13 4.9 50.1 1.0 CA A:ASP10 5.0 38.8 1.0 CA A:PRO13 5.0 48.9 1.0 CE1 A:HIS24 5.0 40.7 1.0

Calcium binding site 2 out of 2 in the Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:46.3 occ:1.00 O B:HOH417 2.0 34.9 1.0 O B:HOH406 2.1 34.7 1.0 OD1 B:ASP10 2.3 40.7 1.0 ND2 B:ASN14 2.4 50.1 1.0 OD2 B:ASP10 2.4 37.4 1.0 O B:TYR12 2.5 50.0 1.0 OD2 B:ASP19 2.5 43.8 1.0 CG B:ASP10 2.6 39.8 1.0 CG B:ASN14 3.5 52.3 1.0 C B:TYR12 3.7 50.0 1.0 CG B:ASP19 3.7 46.6 1.0 MN B:MN303 4.0 29.8 1.0 N B:ASN14 4.0 52.5 1.0 CB B:ASP10 4.0 40.3 1.0 CB B:ASN14 4.1 52.1 1.0 O B:HOH408 4.4 31.1 1.0 CA B:TYR12 4.4 49.7 1.0 N B:TYR12 4.5 47.4 1.0 OD1 B:ASP19 4.5 47.5 1.0 OD1 B:ASN14 4.5 56.9 1.0 CB B:TYR12 4.5 51.3 1.0 CE1 B:HIS24 4.6 42.9 1.0 O B:ARG228 4.6 45.4 1.0 CB B:ASP19 4.6 47.8 1.0 CB B:ARG228 4.7 50.7 1.0 CA B:ASN14 4.7 53.5 1.0 N B:PRO13 4.7 51.9 1.0 CA B:ARG228 4.8 48.7 1.0 CA B:ASP10 4.8 39.8 1.0 CA B:PRO13 4.8 51.7 1.0 NE2 B:HIS24 4.8 39.9 1.0 C B:PRO13 4.9 53.4 1.0

R.B.Nobrega, J.C.Silva-Filho, C.Y.Kawasoko, O.E.D.Rodrigues, R.S.Schwab, A.L.Braga, P.Delatorre, B.S.Cavada. Canavalia Maritima Lectin Complexed with Synthetic Selenoamino Acid To Be Published.