Calcium in PDB 3ax4: Three-Dimensional Structure of Lectin From Dioclea Violacea and Comparative Vasorelaxant Effects with Dioclea Rostrata

The structure of Three-Dimensional Structure of Lectin From Dioclea Violacea and Comparative Vasorelaxant Effects with Dioclea Rostrata, PDB code: 3ax4 was solved by M.J.B.Bezerra, G.A.Bezerra, J.L.Martins, K.S.Nascimento, C.S.Nagano, K.Gruber, A.M.Assereuy, P.Delatorre, B.A.M.Rocha, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.32 / 2.61
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.340, 66.110, 106.690, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 27.4

The structure of Three-Dimensional Structure of Lectin From Dioclea Violacea and Comparative Vasorelaxant Effects with Dioclea Rostrata 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 Three-Dimensional Structure of Lectin From Dioclea Violacea and Comparative Vasorelaxant Effects with Dioclea Rostrata (pdb code 3ax4). 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 Three-Dimensional Structure of Lectin From Dioclea Violacea and Comparative Vasorelaxant Effects with Dioclea Rostrata, PDB code: 3ax4:

Calcium binding site 1 out of 1 in the Three-Dimensional Structure of Lectin From Dioclea Violacea and Comparative Vasorelaxant Effects with Dioclea Rostrata


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Three-Dimensional Structure of Lectin From Dioclea Violacea and Comparative Vasorelaxant Effects with Dioclea Rostrata within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:37.9 occ:1.00 OD1 A:ASN14 2.1 21.8 1.0 O A:TYR12 2.4 24.8 1.0 OD1 A:ASP10 2.6 19.3 1.0 OD2 A:ASP19 2.6 22.4 1.0 OD2 A:ASP10 2.7 18.3 1.0 O A:HOH284 2.9 27.8 1.0 CG A:ASP10 3.0 17.4 1.0 CG A:ASN14 3.2 23.6 1.0 HB2 A:ASN14 3.3 30.4 1.0 HA A:ARG228 3.4 25.0 1.0 HB3 A:TYR12 3.5 28.1 1.0 C A:TYR12 3.6 23.5 1.0 HB2 A:ARG228 3.6 25.0 1.0 H A:ASN14 3.6 28.9 1.0 CG A:ASP19 3.6 23.5 1.0 CB A:ASN14 3.8 25.7 1.0 H A:TYR12 3.9 24.3 1.0 N A:ASN14 4.0 24.4 1.0 HB3 A:ARG228 4.0 25.0 1.0 OD1 A:ASP19 4.0 25.7 1.0 HD2 A:TYR12 4.1 31.1 1.0 CB A:ARG228 4.1 21.2 1.0 CA A:ARG228 4.1 21.2 1.0 HE1 A:HIS24 4.3 20.6 1.0 CB A:TYR12 4.3 23.7 1.0 CA A:TYR12 4.3 21.5 1.0 ND2 A:ASN14 4.3 27.8 1.0 HB3 A:ASP208 4.4 22.9 1.0 O A:ARG228 4.4 15.5 1.0 MN A:MN238 4.4 36.4 1.0 O A:ASP208 4.4 16.7 1.0 HA A:PRO13 4.5 27.1 1.0 C A:PRO13 4.5 23.6 1.0 HD21 A:ASN14 4.5 32.9 1.0 N A:TYR12 4.5 20.6 1.0 CB A:ASP10 4.5 18.4 1.0 CA A:ASN14 4.5 24.1 1.0 HD21 A:LEU230 4.6 16.6 1.0 OD1 A:ASP208 4.6 20.4 1.0 HB3 A:ASN14 4.6 30.4 1.0 N A:PRO13 4.6 25.4 1.0 O A:HOH277 4.7 29.4 1.0 CD2 A:TYR12 4.7 26.3 1.0 CA A:PRO13 4.7 22.9 1.0 HD11 A:ILE17 4.7 25.4 1.0 C A:ARG228 4.8 19.0 1.0 HB2 A:ASP10 4.8 21.7 1.0 CB A:ASP19 4.9 22.9 1.0 CG A:TYR12 4.9 26.5 1.0 HA A:ASP10 4.9 18.7 1.0 HB3 A:ASP10 4.9 21.7 1.0 HB2 A:ASP19 5.0 27.1 1.0 HB3 A:ASP19 5.0 27.1 1.0

M.J.B.Bezerra, N.V.F.C.Rodrigues, A.F.Pires, G.A.Bezerra, C.B.Nobre, K.L.L.Alencar, P.M.G.Soares, K.S.Nascimento, C.S.Nagano, J.L.Martins, K.Gruber, A.H.Sampaio, P.Delatorre, B.A.M.Rocha, A.M.S.Assreuy, B.S.Cavada. Crystal Structure of Dioclea Violacea Lectin and A Comparative Study of Vasorelaxant Properties with Dioclea Rostrata Lectin Int.J.Biochem.Cell Biol. V. 45 807 2013.
ISSN: ISSN 1357-2725
PubMed: 23353644
DOI: 10.1016/J.BIOCEL.2013.01.012