Calcium in PDB 5eyx: Monoclinic Form of Centrolobium Tomentosum Seed Lectin (Ctl) Complexed with MAN1-3MAN-Ome.

The structure of Monoclinic Form of Centrolobium Tomentosum Seed Lectin (Ctl) Complexed with MAN1-3MAN-Ome., PDB code: 5eyx was solved by A.C.Almeida, V.J.S.Osterne, M.Q.Santiago, V.R.Pinto-Junior, J.C.Silva-Filho, C.F.Lossio, R.P.H.Almeida, C.S.Teixeira, P.Delatorre, B.A.M.Rocha, K.S.Santiago, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.92 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	145.840, 41.550, 94.640, 90.00, 102.40, 90.00
R / Rfree (%)	18.6 / 23.7

The structure of Monoclinic Form of Centrolobium Tomentosum Seed Lectin (Ctl) Complexed with MAN1-3MAN-Ome. also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Monoclinic Form of Centrolobium Tomentosum Seed Lectin (Ctl) Complexed with MAN1-3MAN-Ome. (pdb code 5eyx). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Monoclinic Form of Centrolobium Tomentosum Seed Lectin (Ctl) Complexed with MAN1-3MAN-Ome., PDB code: 5eyx:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Monoclinic Form of Centrolobium Tomentosum Seed Lectin (Ctl) 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 Monoclinic Form of Centrolobium Tomentosum Seed Lectin (Ctl) Complexed with MAN1-3MAN-Ome. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:15.2 occ:1.00 OD2 A:ASP141 2.2 18.6 1.0 O A:HOH443 2.2 10.7 1.0 O A:PHE132 2.3 16.7 1.0 ND2 A:ASN138 2.4 13.0 1.0 OD2 A:ASP130 2.4 13.1 1.0 O A:HOH452 2.5 12.6 1.0 OD1 A:ASP130 2.5 20.5 1.0 CG A:ASP130 2.8 17.0 1.0 CG A:ASP141 3.3 16.7 1.0 CG A:ASN138 3.5 20.7 1.0 C A:PHE132 3.5 16.9 1.0 OD1 A:ASP141 3.8 17.5 1.0 CB A:ASN138 3.8 16.1 1.0 MN A:MN302 4.0 19.1 1.0 NE1 A:TRP140 4.2 14.7 1.0 CB A:ASP130 4.3 14.9 1.0 CA A:PHE132 4.4 13.0 1.0 N A:TYR133 4.4 15.1 1.0 N A:PHE132 4.4 14.6 1.0 CB A:ASP141 4.5 14.5 1.0 CA A:TYR133 4.5 15.8 1.0 O A:HOH425 4.5 13.4 1.0 OD1 A:ASN138 4.6 26.1 1.0 CE1 A:HIS146 4.6 13.9 1.0 O A:GLY106 4.6 18.6 1.0 O A:ASP86 4.6 16.5 1.0 CB A:PHE132 4.7 12.3 1.0 CA A:GLY106 4.8 18.1 1.0 OD2 A:ASP86 4.9 16.8 1.0 NE2 A:HIS146 5.0 16.8 1.0 CD1 A:TRP140 5.0 12.3 1.0

Calcium binding site 2 out of 2 in the Monoclinic Form of Centrolobium Tomentosum Seed Lectin (Ctl) 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 2 of Monoclinic Form of Centrolobium Tomentosum Seed Lectin (Ctl) Complexed with MAN1-3MAN-Ome. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:16.4 occ:1.00 OD2 B:ASP142 2.3 14.7 1.0 O B:HOH401 2.4 13.6 1.0 O B:PHE133 2.4 17.4 1.0 OD1 B:ASN139 2.4 18.7 1.0 O B:HOH409 2.5 11.3 1.0 OD1 B:ASP131 2.5 30.0 1.0 OD2 B:ASP131 2.6 30.0 1.0 CG B:ASP131 2.8 30.0 1.0 CG B:ASP142 3.4 19.4 1.0 CG B:ASN139 3.4 17.2 1.0 C B:PHE133 3.5 16.4 1.0 OD1 B:ASP142 3.9 20.7 1.0 CB B:ASN139 3.9 15.9 1.0 CB B:ASP131 4.1 30.0 1.0 MN B:MN302 4.1 20.9 1.0 NE1 B:TRP141 4.3 19.1 1.0 N B:PHE133 4.4 16.6 1.0 CA B:PHE133 4.4 16.1 1.0 N B:TYR134 4.4 16.6 1.0 O B:GLY107 4.5 19.2 1.0 CA B:TYR134 4.5 17.1 1.0 ND2 B:ASN139 4.6 14.8 1.0 O B:HOH404 4.6 14.5 1.0 CA B:GLY107 4.6 12.8 1.0 CE1 B:HIS147 4.6 16.6 1.0 CB B:ASP142 4.6 19.7 1.0 O B:ASP87 4.7 16.1 1.0 CB B:PHE133 4.7 17.0 1.0 OD1 B:ASP87 4.8 14.6 1.0 NE2 B:HIS147 4.9 22.0 1.0 CD1 B:PHE133 4.9 18.0 1.0

A.C.Almeida, V.J.Osterne, M.Q.Santiago, V.R.Pinto-Junior, J.C.Silva-Filho, C.F.Lossio, F.L.Nascimento, R.P.Almeida, C.S.Teixeira, R.B.Leal, P.Delatorre, B.A.Rocha, A.M.Assreuy, K.S.Nascimento, B.S.Cavada. Structural Analysis of Centrolobium Tomentosum Seed Lectin with Inflammatory Activity. Arch.Biochem.Biophys. V. 596 73 2016.
ISSN: ESSN 1096-0384
PubMed: 26946944
DOI: 10.1016/J.ABB.2016.03.001