Calcium in PDB 5u38: Crystal Structure of Native Lectin From Platypodium Elegans Seeds (Pela) Complexed with MAN1-3MAN-Ome.

The structure of Crystal Structure of Native Lectin From Platypodium Elegans Seeds (Pela) Complexed with MAN1-3MAN-Ome., PDB code: 5u38 was solved by I.B.Silva, D.A.Araripe, A.H.B.Neco, V.R.Pinto-Junior, V.J.S.Osterne, M.Q.Santiago, 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)	26.62 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	53.240, 87.510, 120.120, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.8

The structure of Crystal Structure of Native Lectin From Platypodium Elegans Seeds (Pela) Complexed with MAN1-3MAN-Ome. also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Native Lectin From Platypodium Elegans Seeds (Pela) Complexed with MAN1-3MAN-Ome. (pdb code 5u38). 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 Platypodium Elegans Seeds (Pela) Complexed with MAN1-3MAN-Ome., PDB code: 5u38:

Calcium binding site 1 out of 1 in the Crystal Structure of Native Lectin From Platypodium Elegans Seeds (Pela) Complexed with MAN1-3MAN-Ome.


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 Platypodium Elegans Seeds (Pela) Complexed with MAN1-3MAN-Ome. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:14.6 occ:1.00 OD2 A:ASP142 2.3 9.4 1.0 O A:PHE133 2.3 5.9 1.0 O A:HOH478 2.4 4.5 1.0 ND2 A:ASN139 2.4 5.9 1.0 O A:HOH435 2.4 4.0 1.0 OD1 A:ASP131 2.4 10.1 1.0 OD2 A:ASP131 2.5 8.4 1.0 CG A:ASP131 2.8 5.7 1.0 CG A:ASP142 3.4 6.3 1.0 C A:PHE133 3.5 6.8 1.0 CG A:ASN139 3.6 11.3 1.0 OD1 A:ASP142 3.9 7.6 1.0 CB A:ASN139 4.1 8.4 1.0 MN A:MN302 4.1 14.6 1.0 CB A:ASP131 4.3 5.7 1.0 CA A:PHE133 4.4 6.5 1.0 N A:PHE133 4.4 5.7 1.0 N A:PHE134 4.5 5.0 1.0 NE1 A:TRP141 4.5 9.1 1.0 O A:HOH430 4.5 4.7 1.0 O A:GLY107 4.5 8.3 1.0 CA A:PHE134 4.6 7.7 1.0 OD1 A:ASN139 4.6 12.7 1.0 CB A:ASP142 4.6 6.7 1.0 CB A:PHE133 4.6 8.5 1.0 CA A:GLY107 4.7 8.9 1.0 OD1 A:ASP87 4.7 9.4 1.0 CE1 A:HIS147 4.7 7.4 1.0 O A:ASP87 4.7 5.8 1.0

B.S.Cavada, D.A.Araripe, I.B.Silva, V.R.Pinto-Junior, V.J.S.Osterne, A.H.B.Neco, E.P.P.Laranjeira, C.F.Lossio, J.L.A.Correia, A.F.Pires, A.M.S.Assreuy, K.S.Nascimento. Structural Studies and Nociceptive Activity of A Native Lectin From Platypodium Elegans Seeds (Npela). Int. J. Biol. Macromol. V. 107 236 2018.
ISSN: ISSN 1879-0003
PubMed: 28867234
DOI: 10.1016/J.IJBIOMAC.2017.08.174