Calcium in PDB 8ux7: Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man

The structure of Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man, PDB code: 8ux7 was solved by M.V.Oliveira, G.De Sloover, V.J.S.Osterne, V.R.Pinto-Junior, J.C.Sacramento-Neto, E.J.M.Van Damme, K.S.Nascimento, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.66 / 2.20
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	89.35, 109.414, 126.364, 90, 90, 90
R / Rfree (%)	20.1 / 24.8

The structure of Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	2 atoms
Bromine	(Br)	2 atoms
Manganese	(Mn)	2 atoms

The binding sites of Calcium atom in the Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man (pdb code 8ux7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man, PDB code: 8ux7:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:40.5 occ:1.00 O A:TYR12 2.3 37.3 1.0 O A:HOH412 2.3 40.9 1.0 OD1 A:ASP10 2.3 36.7 1.0 OD2 A:ASP19 2.3 43.4 1.0 O A:HOH416 2.4 35.6 1.0 OD1 A:ASN14 2.4 49.8 1.0 OD2 A:ASP10 2.5 41.0 1.0 CG A:ASP10 2.7 40.5 1.0 CG A:ASP19 3.5 44.4 1.0 CG A:ASN14 3.5 47.3 1.0 C A:TYR12 3.5 44.8 1.0 OD1 A:ASP19 4.0 40.3 1.0 N A:ASN14 4.0 40.5 1.0 MN A:MN301 4.1 39.8 1.0 CB A:ASN14 4.2 43.8 1.0 CB A:ASP10 4.2 41.2 1.0 CA A:TYR12 4.4 41.0 1.0 CB A:TYR12 4.5 48.2 1.0 N A:TYR12 4.5 50.1 1.0 O A:HOH408 4.5 34.9 1.0 N A:PRO13 4.5 44.6 1.0 CE1 A:HIS24 4.5 44.7 1.0 CB A:ARG228 4.6 46.0 1.0 O A:ARG228 4.6 40.5 1.0 CA A:PRO13 4.6 45.4 1.0 ND2 A:ASN14 4.6 44.8 1.0 C A:PRO13 4.6 43.0 1.0 O A:ASP208 4.6 43.8 1.0 CA A:ARG228 4.7 43.5 1.0 CB A:ASP19 4.7 47.2 1.0 OD1 A:ASP208 4.7 46.7 1.0 CA A:ASN14 4.7 41.1 1.0 CD2 A:TYR12 4.9 49.4 1.0 NE2 A:HIS24 4.9 42.1 1.0

Calcium binding site 2 out of 2 in the Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:51.7 occ:1.00 O B:HOH413 2.0 37.6 1.0 O B:TYR12 2.3 41.4 1.0 OD2 B:ASP19 2.4 47.2 1.0 OD1 B:ASN14 2.5 63.3 1.0 OD2 B:ASP10 2.5 44.7 1.0 O B:HOH425 2.5 46.4 1.0 OD1 B:ASP10 2.5 53.6 1.0 CG B:ASP10 2.8 53.4 1.0 C B:TYR12 3.5 52.6 1.0 CG B:ASP19 3.5 49.0 1.0 CG B:ASN14 3.5 60.7 1.0 N B:ASN14 3.8 50.1 1.0 OD1 B:ASP19 3.9 66.0 1.0 CB B:ASN14 4.0 50.9 1.0 MN B:MN301 4.1 47.3 1.0 CA B:TYR12 4.3 53.4 1.0 CB B:ASP10 4.4 54.5 1.0 N B:TYR12 4.4 50.8 1.0 N B:PRO13 4.4 50.9 1.0 C B:PRO13 4.5 47.3 1.0 CA B:PRO13 4.5 52.9 1.0 O B:HOH415 4.5 31.4 1.0 CB B:TYR12 4.5 53.5 1.0 CA B:ASN14 4.6 46.6 1.0 CE1 B:HIS24 4.6 47.4 1.0 ND2 B:ASN14 4.7 60.8 1.0 CB B:ASP19 4.7 54.6 1.0 O B:ARG228 4.8 63.2 1.0 CB B:ARG228 4.8 58.6 1.0 OD1 B:ASP208 4.8 59.8 1.0 O B:ASP208 4.8 53.3 1.0 CA B:ARG228 4.9 63.9 1.0 CD2 B:TYR12 5.0 57.1 1.0

M.V.Oliveira, G.De Sloover, V.J.S.Osterne, V.R.Pinto-Junior, J.C.Sacramento-Neto, E.J.M.Van Damme, K.S.Nascimento, B.S.Cavada. Dioclea Megacarpa Lectin (Dmega) Complexed with X-Man To Be Published.