Calcium in PDB 6cj9: Crystal Structure of Lectin From Dioclea Lasiophylla Seeds (Dlyl) Complexed with X-Man

The structure of Crystal Structure of Lectin From Dioclea Lasiophylla Seeds (Dlyl) Complexed with X-Man, PDB code: 6cj9 was solved by V.R.Pinto-Junior, M.Q.Santiago, V.J.S.Osterne, D.A.Araripe, A.H.B.Neco, J.C.Silva-Filho, R.B.Leal, C.R.C.Rocha, 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)	27.86 / 1.70
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	64.100, 86.930, 92.820, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 21.5

The structure of Crystal Structure of Lectin From Dioclea Lasiophylla Seeds (Dlyl) Complexed with X-Man also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Bromine	(Br)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Calcium atom in the Crystal Structure of Lectin From Dioclea Lasiophylla Seeds (Dlyl) Complexed with X-Man (pdb code 6cj9). 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 Lectin From Dioclea Lasiophylla Seeds (Dlyl) Complexed with X-Man, PDB code: 6cj9:

Calcium binding site 1 out of 1 in the Crystal Structure of Lectin From Dioclea Lasiophylla Seeds (Dlyl) 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 Crystal Structure of Lectin From Dioclea Lasiophylla Seeds (Dlyl) Complexed with X-Man within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:20.4 occ:1.00 O A:HOH487 2.3 21.4 1.0 OD2 A:ASP19 2.3 26.2 1.0 O A:TYR12 2.3 22.0 1.0 OD1 A:ASN14 2.4 22.6 1.0 OD1 A:ASP10 2.4 19.0 1.0 O A:HOH414 2.5 19.1 1.0 OD2 A:ASP10 2.5 16.5 1.0 CG A:ASP10 2.8 18.2 1.0 CG A:ASP19 3.4 26.5 1.0 CG A:ASN14 3.5 29.7 1.0 C A:TYR12 3.6 18.2 1.0 OD1 A:ASP19 3.9 20.3 1.0 N A:ASN14 3.9 20.3 1.0 MN A:MN302 4.1 23.7 1.0 CB A:ASN14 4.2 27.8 1.0 CB A:ASP10 4.3 17.4 1.0 CA A:TYR12 4.4 21.5 1.0 CE1 A:HIS24 4.4 21.2 1.0 N A:TYR12 4.5 20.8 1.0 O A:HOH418 4.5 21.5 1.0 N A:PRO13 4.5 21.5 1.0 CA A:PRO13 4.5 21.9 1.0 CB A:TYR12 4.6 22.4 1.0 ND2 A:ASN14 4.6 26.2 1.0 C A:PRO13 4.6 27.5 1.0 OD1 A:ASP208 4.7 21.2 1.0 CB A:ASP19 4.7 23.1 1.0 O A:ARG228 4.7 21.4 1.0 CA A:ASN14 4.7 24.7 1.0 O A:ASP208 4.7 16.4 1.0 CB A:ARG228 4.7 25.1 1.0 NE2 A:HIS24 4.8 20.6 1.0 CA A:ARG228 4.8 18.5 1.0 CD2 A:TYR12 5.0 21.9 1.0

R.B.Leal, V.R.Pinto-Junior, V.J.S.Osterne, I.A.V.Wolin, A.P.M.Nascimento, A.H.B.Neco, D.A.Araripe, P.G.Welter, C.C.Neto, J.L.A.Correia, C.R.C.Rocha, K.S.Nascimento, B.S.Cavada. Crystal Structure of Dlyl, A Mannose-Specific Lectin From Dioclea Lasiophylla Mart. Ex Benth Seeds That Display Cytotoxic Effects Against C6 Glioma Cells. Int. J. Biol. Macromol. V. 114 64 2018.
ISSN: ISSN 1879-0003
PubMed: 29559315
DOI: 10.1016/J.IJBIOMAC.2018.03.080