Manganese in PDB 4wv8: Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose

The structure of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose, PDB code: 4wv8 was solved by B.L.Sousa, J.C.Silva-Filho, P.Kumar, A.Lyskowski, G.A.Bezerra, P.Delatorre, B.A.M.Rocha, R.M.S.Cunha, C.S.Nagano, K.Gruber, B.S.Cavada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	82.05 / 1.83
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	152.644, 97.427, 78.667, 90.00, 94.68, 90.00
R / Rfree (%)	15.7 / 19.5

The structure of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose (pdb code 4wv8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose, PDB code: 4wv8:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose


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 A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:20.2 occ:1.00 O A:HOH454 2.1 10.1 1.0 OD2 A:ASP126 2.1 8.2 1.0 OE2 A:GLU124 2.1 7.6 1.0 OD1 A:ASP133 2.2 9.3 1.0 O A:HOH452 2.2 8.6 1.0 NE2 A:HIS138 2.3 9.8 1.0 CD A:GLU124 3.1 9.4 1.0 CG A:ASP133 3.1 10.6 1.0 CG A:ASP126 3.2 8.8 1.0 CE1 A:HIS138 3.3 9.8 1.0 CD2 A:HIS138 3.3 9.3 1.0 OE1 A:GLU124 3.5 9.1 1.0 CB A:ASP126 3.6 8.3 1.0 OD2 A:ASP133 3.6 11.0 1.0 O A:HOH460 3.9 8.6 1.0 CA A:CA301 4.2 8.6 1.0 OG A:SER148 4.2 9.4 1.0 OD1 A:ASP126 4.2 7.6 1.0 CB A:ASP133 4.3 11.1 1.0 O A:ILE146 4.4 10.8 1.0 ND1 A:HIS138 4.4 9.7 1.0 O A:HOH462 4.4 14.4 1.0 CG A:GLU124 4.4 8.3 1.0 NE1 A:TRP132 4.5 11.2 1.0 CG A:HIS138 4.5 9.2 1.0 CD1 A:TRP132 4.6 11.1 1.0 CA A:ASP133 4.8 11.0 1.0 CD A:PRO134 5.0 12.6 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose


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 A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:22.0 occ:1.00 O B:HOH485 2.0 11.7 1.0 OD2 B:ASP126 2.1 10.5 1.0 OE2 B:GLU124 2.1 8.4 1.0 OD1 B:ASP133 2.2 11.4 1.0 NE2 B:HIS138 2.2 10.2 1.0 O B:HOH467 2.3 9.8 1.0 CG B:ASP133 3.1 11.8 1.0 CD B:GLU124 3.1 9.5 1.0 CE1 B:HIS138 3.1 10.6 1.0 CG B:ASP126 3.2 10.2 1.0 CD2 B:HIS138 3.2 10.4 1.0 OE1 B:GLU124 3.5 10.7 1.0 OD2 B:ASP133 3.6 12.3 1.0 CB B:ASP126 3.7 10.2 1.0 O B:HOH475 3.8 12.8 1.0 OG B:SER148 4.2 10.4 1.0 CA B:CA301 4.2 10.8 1.0 OD1 B:ASP126 4.3 10.1 1.0 ND1 B:HIS138 4.3 10.8 1.0 CB B:ASP133 4.3 11.8 1.0 CG B:HIS138 4.4 10.7 1.0 O B:HOH439 4.4 16.3 1.0 O B:ILE146 4.4 12.3 1.0 CG B:GLU124 4.5 9.0 1.0 NE1 B:TRP132 4.5 13.5 1.0 CD1 B:TRP132 4.7 13.6 1.0 CA B:ASP133 4.7 13.1 1.0 CD B:PRO134 4.9 16.0 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:23.7 occ:1.00 OD2 C:ASP126 2.1 9.3 1.0 OE2 C:GLU124 2.2 8.5 1.0 OD1 C:ASP133 2.2 10.7 1.0 O C:HOH427 2.2 13.9 1.0 O C:HOH434 2.2 12.5 1.0 NE2 C:HIS138 2.3 10.8 1.0 CD C:GLU124 3.1 10.3 1.0 CG C:ASP133 3.1 12.7 1.0 CG C:ASP126 3.1 10.4 1.0 CE1 C:HIS138 3.2 10.5 1.0 CD2 C:HIS138 3.3 10.6 1.0 OE1 C:GLU124 3.5 10.5 1.0 OD2 C:ASP133 3.6 12.4 1.0 CB C:ASP126 3.6 10.4 1.0 O C:HOH471 3.9 14.2 1.0 CA C:CA301 4.2 14.0 1.0 OD1 C:ASP126 4.2 10.5 1.0 OG C:SER148 4.3 10.7 1.0 CB C:ASP133 4.3 12.6 1.0 ND1 C:HIS138 4.4 10.5 1.0 O C:ILE146 4.4 13.3 1.0 NE1 C:TRP132 4.4 16.0 1.0 CG C:GLU124 4.4 8.7 1.0 O C:HOH432 4.5 15.7 1.0 CG C:HIS138 4.5 10.6 1.0 CD1 C:TRP132 4.6 15.7 1.0 CA C:ASP133 4.8 13.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:24.7 occ:1.00 O D:HOH434 2.1 12.8 1.0 OD2 D:ASP126 2.2 12.9 1.0 OE2 D:GLU124 2.2 9.9 1.0 O D:HOH422 2.2 11.2 1.0 OD1 D:ASP133 2.3 11.9 1.0 NE2 D:HIS138 2.3 12.6 1.0 CG D:ASP133 3.1 14.4 1.0 CG D:ASP126 3.2 13.3 1.0 CE1 D:HIS138 3.2 11.8 1.0 CD D:GLU124 3.2 11.0 1.0 CD2 D:HIS138 3.3 11.9 1.0 OE1 D:GLU124 3.6 12.0 1.0 OD2 D:ASP133 3.6 15.5 1.0 CB D:ASP126 3.6 12.1 1.0 O D:HOH493 3.9 15.4 1.0 OG D:SER148 4.2 12.6 1.0 CA D:CA301 4.2 12.9 1.0 OD1 D:ASP126 4.3 12.7 1.0 CB D:ASP133 4.3 15.6 1.0 ND1 D:HIS138 4.3 12.6 1.0 O D:ILE146 4.4 14.0 1.0 CG D:HIS138 4.4 12.1 1.0 O D:HOH452 4.4 16.2 1.0 NE1 D:TRP132 4.4 15.8 1.0 CD1 D:TRP132 4.5 16.5 1.0 CG D:GLU124 4.6 9.9 1.0 CA D:ASP133 4.8 15.9 1.0

B.L.Sousa, J.C.Silva-Filho, P.Kumar, M.A.Graewert, R.I.Pereira, R.M.Cunha, K.S.Nascimento, G.A.Bezerra, P.Delatorre, K.Djinovic-Carugo, C.S.Nagano, K.Gruber, B.S.Cavada. Structural Characterization of A Vatairea Macrocarpa Lectin in Complex with A Tumor-Associated Antigen: A New Tool For Cancer Research. Int.J.Biochem.Cell Biol. V. 72 27 2016.
ISSN: ISSN 1357-2725
PubMed: 26751394
DOI: 10.1016/J.BIOCEL.2015.12.016