Manganese 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:

Calcium

(Ca)

2 atoms

The binding sites of Manganese 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 Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Canavalia Virosa Lectin in Complex with Alpha- Methyl-Mannoside, PDB code: 5f5q:
Jump to Manganese binding site number: 1; 2;

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:38.3 occ:1.00 OD1 A:ASP19 2.2 22.7 1.0 OD2 A:ASP10 2.2 18.4 1.0 O A:HOH405 2.3 15.2 1.0 NE2 A:HIS24 2.3 19.4 1.0 OE1 A:GLU8 2.3 19.2 1.0 O A:HOH430 2.3 12.2 1.0 CG A:ASP19 3.0 22.3 1.0 CE1 A:HIS24 3.2 18.8 1.0 CD A:GLU8 3.3 18.1 1.0 CG A:ASP10 3.3 18.0 1.0 CD2 A:HIS24 3.3 18.8 1.0 OD2 A:ASP19 3.4 20.0 1.0 OE2 A:GLU8 3.6 17.0 1.0 CB A:ASP10 3.7 19.2 1.0 O A:HOH422 3.9 9.6 1.0 O A:HOH434 3.9 26.1 1.0 CA A:CA301 4.1 19.6 1.0 OG A:SER34 4.2 14.6 1.0 CB A:ASP19 4.2 23.0 1.0 O A:HOH446 4.3 23.8 1.0 OD1 A:ASP10 4.3 16.8 1.0 ND1 A:HIS24 4.4 18.3 1.0 CG A:HIS24 4.4 18.6 1.0 O A:VAL32 4.5 15.8 1.0 CG A:GLU8 4.6 17.9 1.0 CA A:ASP19 4.6 23.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:48.9 occ:1.00 OD2 B:ASP10 1.8 25.0 1.0 O B:HOH405 2.1 31.6 1.0 O B:HOH418 2.2 27.2 1.0 NE2 B:HIS24 2.4 27.2 1.0 OE1 B:GLU8 2.6 27.7 1.0 OD2 B:ASP19 2.6 58.0 1.0 CG B:ASP10 3.0 25.3 1.0 CG B:ASP19 3.1 51.0 1.0 CE1 B:HIS24 3.3 27.2 1.0 CD B:GLU8 3.4 27.9 1.0 CD2 B:HIS24 3.5 29.3 1.0 OD1 B:ASP19 3.5 58.2 1.0 OE2 B:GLU8 3.6 25.6 1.0 CB B:ASP10 3.8 26.6 1.0 OG B:SER34 3.9 26.3 1.0 OD1 B:ASP10 4.0 22.9 1.0 CB B:ASP19 4.0 46.2 1.0 O B:HOH411 4.1 32.5 1.0 O B:VAL32 4.3 27.4 1.0 CA B:CA301 4.4 37.5 1.0 ND1 B:HIS24 4.4 29.8 1.0 CA B:ASP19 4.6 42.3 1.0 CG B:HIS24 4.6 30.5 1.0 CG B:GLU8 4.8 28.0 1.0 CD B:PRO20 4.9 39.2 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