Calcium in PDB 5u3e: Crystal Structure of Native Lectin From Canavalia Bonariensis Seeds (Cabo) Complexed with Alpha-Methyl-D-Mannoside

The structure of Crystal Structure of Native Lectin From Canavalia Bonariensis Seeds (Cabo) Complexed with Alpha-Methyl-D-Mannoside, PDB code: 5u3e was solved by M.T.L.Silva, V.J.S.Osterne, V.R.Pinto-Junior, M.Q.Santiago, D.A.Araripe, A.H.B.Neco, J.C.Silva-Filho, J.L.Martins, C.R.C.Rocha, R.B.Leal, 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)	36.09 / 2.30
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.169, 70.030, 111.649, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 28.3

The structure of Crystal Structure of Native Lectin From Canavalia Bonariensis Seeds (Cabo) Complexed with Alpha-Methyl-D-Mannoside also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Native Lectin From Canavalia Bonariensis Seeds (Cabo) Complexed with Alpha-Methyl-D-Mannoside (pdb code 5u3e). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Crystal Structure of Native Lectin From Canavalia Bonariensis Seeds (Cabo) Complexed with Alpha-Methyl-D-Mannoside, PDB code: 5u3e:

Calcium binding site 1 out of 1 in the Crystal Structure of Native Lectin From Canavalia Bonariensis Seeds (Cabo) Complexed with Alpha-Methyl-D-Mannoside


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 Native Lectin From Canavalia Bonariensis Seeds (Cabo) Complexed with Alpha-Methyl-D-Mannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:19.9 occ:1.00 ND2 A:ASN14 2.2 22.0 1.0 O A:HOH448 2.3 13.7 1.0 O A:TYR12 2.4 18.8 1.0 OD1 A:ASP10 2.4 22.0 1.0 OD2 A:ASP19 2.4 15.1 1.0 OD2 A:ASP10 2.4 15.9 1.0 O A:HOH421 2.5 13.5 1.0 CG A:ASP10 2.8 17.0 1.0 CG A:ASN14 3.3 19.1 1.0 CG A:ASP19 3.5 15.4 1.0 C A:TYR12 3.6 15.7 1.0 N A:ASN14 3.8 19.6 1.0 CB A:ASN14 3.9 15.7 1.0 OD1 A:ASP19 4.1 21.7 1.0 MN A:MN302 4.1 25.1 1.0 CB A:ASP10 4.3 16.4 1.0 OD1 A:ASN14 4.3 26.4 1.0 CA A:TYR12 4.4 22.7 1.0 N A:TYR12 4.4 22.7 1.0 C A:PRO13 4.4 18.6 1.0 CA A:ASN14 4.5 18.8 1.0 N A:PRO13 4.5 18.9 1.0 CE1 A:HIS24 4.5 20.2 1.0 CA A:PRO13 4.5 16.6 1.0 CB A:TYR12 4.5 21.1 1.0 O A:HOH419 4.5 16.6 1.0 O A:ASP208 4.6 22.1 1.0 OD1 A:ASP208 4.6 24.6 1.0 CB A:ASP19 4.7 20.5 1.0 O A:ARG228 4.7 22.0 1.0 CB A:ARG228 4.9 24.9 1.0 NE2 A:HIS24 4.9 17.8 1.0 CD2 A:TYR12 4.9 22.7 1.0 CA A:ARG228 4.9 22.2 1.0

B.S.Cavada, M.T.L.Silva, V.J.S.Osterne, V.R.Pinto-Junior, A.P.M.Nascimento, I.A.V.Wolin, I.A.Heinrich, C.A.S.Nobre, C.G.Moreira, C.F.Lossio, C.R.C.Rocha, J.L.Martins, K.S.Nascimento, R.B.Leal. Canavalia Bonariensis Lectin: Molecular Bases of Glycoconjugates Interaction and Antiglioma Potential. Int. J. Biol. Macromol. V. 106 369 2018.
ISSN: ISSN 1879-0003
PubMed: 28803976
DOI: 10.1016/J.IJBIOMAC.2017.08.023