Calcium in PDB 5f5q: Crystal Structure of Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside

The structure of Crystal Structure of Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside, PDB code: 5f5q was solved by V.J.S.Osterne, J.C.Silva-Filho, V.R.Pinto-Junior, M.Q.Santiago, C.F.Lossio, P.Delatorre, 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)	36.99 / 2.52
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	60.250, 81.740, 86.930, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 25.1

The structure of Crystal Structure of Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Calcium atom in the Crystal Structure of Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside (pdb code 5f5q). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside, PDB code: 5f5q:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside


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 Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:19.6 occ:1.00 OD1 A:ASN14 2.3 18.4 1.0 O A:HOH414 2.3 14.6 1.0 O A:HOH422 2.4 9.6 1.0 OD2 A:ASP19 2.4 20.0 1.0 OD1 A:ASP10 2.4 16.8 1.0 OD2 A:ASP10 2.4 18.4 1.0 O A:TYR12 2.5 19.3 1.0 CG A:ASP10 2.8 18.0 1.0 CG A:ASN14 3.5 18.9 1.0 CG A:ASP19 3.5 22.3 1.0 C A:TYR12 3.7 20.2 1.0 N A:ASN14 4.0 21.4 1.0 OD1 A:ASP19 4.0 22.7 1.0 MN A:MN302 4.1 38.3 1.0 CB A:ASN14 4.2 19.6 1.0 CB A:ASP10 4.3 19.2 1.0 ND2 A:ASN14 4.5 18.6 1.0 CE1 A:HIS24 4.5 18.8 1.0 CA A:TYR12 4.5 20.1 1.0 CB A:ARG228 4.6 19.9 1.0 N A:TYR12 4.6 21.1 1.0 N A:PRO13 4.6 20.4 1.0 CB A:TYR12 4.6 20.0 1.0 O A:HOH430 4.6 12.2 1.0 CA A:PRO13 4.6 21.0 1.0 OD2 A:ASP208 4.7 13.7 1.0 CB A:ASP19 4.7 23.0 1.0 CA A:ARG228 4.7 19.9 1.0 CA A:ASN14 4.7 21.1 1.0 O A:ASP208 4.7 15.5 1.0 C A:PRO13 4.7 21.1 1.0 NE2 A:HIS24 4.7 19.4 1.0 O A:ARG228 4.8 19.4 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:37.5 occ:1.00 O B:HOH411 2.1 32.5 1.0 OD1 B:ASP10 2.3 22.9 1.0 O B:HOH413 2.3 18.9 1.0 O B:TYR12 2.3 31.4 1.0 OD1 B:ASN14 2.4 45.0 1.0 OD2 B:ASP19 2.7 58.0 1.0 CG B:ASP10 3.0 25.3 1.0 OD2 B:ASP10 3.1 25.0 1.0 C B:TYR12 3.5 33.4 1.0 CG B:ASN14 3.5 39.3 1.0 CG B:ASP19 3.8 51.0 1.0 N B:ASN14 3.9 36.2 1.0 CB B:ASN14 4.2 38.1 1.0 CA B:PRO13 4.3 33.4 1.0 MN B:MN302 4.4 48.9 1.0 N B:PRO13 4.4 32.5 1.0 OD1 B:ASP19 4.4 58.2 1.0 C B:PRO13 4.4 33.8 1.0 CA B:TYR12 4.5 36.4 1.0 CB B:ASP10 4.5 26.6 1.0 N B:TYR12 4.5 37.1 1.0 O B:ARG228 4.5 30.7 1.0 CB B:ARG228 4.6 32.6 1.0 ND2 B:ASN14 4.6 39.3 1.0 O B:HOH418 4.6 27.2 1.0 CE1 B:HIS24 4.6 27.2 1.0 CA B:ARG228 4.7 31.6 1.0 CB B:TYR12 4.7 39.4 1.0 CB B:ASP19 4.7 46.2 1.0 CA B:ASN14 4.7 37.3 1.0 O B:ASP208 4.7 32.6 1.0 OD2 B:ASP208 4.7 30.4 1.0 CD2 B:TYR12 4.9 42.2 1.0

V.J.Osterne, J.C.Silva-Filho, M.Q.Santiago, V.R.Pinto-Junior, A.C.Almeida, A.A.Barreto, I.A.Wolin, A.P.Nascimento, R.M.Amorim, B.A.Rocha, P.Delatorre, C.S.Nagano, R.B.Leal, A.M.Assreuy, K.S.Nascimento, B.S.Cavada. Structural Characterization of A Lectin From Canavalia Virosa Seeds with Inflammatory and Cytotoxic Activities. Int.J.Biol.Macromol. V. 94 271 2016.
ISSN: ISSN 0141-8130
PubMed: 27737777
DOI: 10.1016/J.IJBIOMAC.2016.10.020