Calcium in PDB 3rrd: Native Structure of Dioclea Virgata Lectin

The structure of Native Structure of Dioclea Virgata Lectin, PDB code: 3rrd was solved by P.Delatorre, R.B.Nobrega, C.A.A.Gadelha, T.Santi-Gadelha, D.L.Farias, B.A.M.Rocha, B.S.Cavada, C.S.Nagano, E.H.S.Bezerra, M.J.Bezerra, K.L.Alencar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.35 / 2.46
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.890, 87.670, 88.780, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 22.6

The structure of Native Structure of Dioclea Virgata Lectin also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

The binding sites of Calcium atom in the Native Structure of Dioclea Virgata Lectin (pdb code 3rrd). 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 Native Structure of Dioclea Virgata Lectin, PDB code: 3rrd:

Calcium binding site 1 out of 1 in the Native Structure of Dioclea Virgata Lectin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Native Structure of Dioclea Virgata Lectin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca239 b:21.1 occ:1.00 O A:HOH299 2.2 14.3 1.0 OD2 A:ASP19 2.4 19.2 1.0 O A:TYR12 2.4 16.3 1.0 OD1 A:ASP10 2.4 13.6 1.0 OD1 A:ASN14 2.5 18.5 1.0 OD2 A:ASP10 2.6 17.2 1.0 CG A:ASP10 2.8 13.8 1.0 CG A:ASN14 3.5 16.7 1.0 CG A:ASP19 3.6 19.3 1.0 C A:TYR12 3.6 15.3 1.0 N A:ASN14 3.8 16.5 1.0 CB A:ASN14 3.9 16.2 1.0 OD1 A:ASP19 4.1 16.7 1.0 MN A:MN238 4.2 20.1 1.0 CB A:ASP10 4.3 12.0 1.0 CA A:TYR12 4.4 15.1 1.0 CE1 A:HIS24 4.5 14.4 1.0 CA A:ASN14 4.5 16.3 1.0 C A:PRO13 4.6 16.2 1.0 CB A:ARG228 4.6 17.9 1.0 O A:ARG228 4.6 18.3 1.0 CA A:PRO13 4.6 16.0 1.0 N A:PRO13 4.6 15.6 1.0 CB A:TYR12 4.6 16.0 1.0 N A:TYR12 4.6 14.2 1.0 O A:ASP208 4.7 18.6 1.0 NE2 A:HIS24 4.7 14.6 1.0 ND2 A:ASN14 4.7 15.5 1.0 CB A:ASP19 4.7 19.2 1.0 CA A:ARG228 4.8 18.0 1.0 OD1 A:ASP208 4.9 21.2 1.0

R.Batista Da Nobrega, B.A.Rocha, C.A.Gadelha, T.Santi-Gadelha, A.F.Pires, A.M.Assreuy, K.S.Nascimento, C.S.Nagano, A.H.Sampaio, B.S.Cavada, P.Delatorre. Structure of Dioclea Virgata Lectin: Relations Between Carbohydrate Binding Site and Nitric Oxide Production. Biochimie V. 94 900 2012.
ISSN: ISSN 0300-9084
PubMed: 22198239
DOI: 10.1016/J.BIOCHI.2011.12.009