Calcium 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:

Manganese

(Mn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of A Recombinant Vatairea Macrocarpa Seed Lectin Complexed with Lactose, PDB code: 4wv8:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca301 b:8.6 occ:1.00 O A:PHE128 2.3 10.4 1.0 O A:HOH460 2.4 8.6 1.0 OD2 A:ASP133 2.4 11.0 1.0 OD1 A:ASP126 2.4 7.6 1.0 O A:HOH468 2.4 9.3 1.0 ND2 A:ASN130 2.5 8.2 1.0 OD2 A:ASP126 2.5 8.2 1.0 CG A:ASP126 2.8 8.8 1.0 CG A:ASP133 3.4 10.6 1.0 C A:PHE128 3.5 9.8 1.0 CG A:ASN130 3.6 11.7 1.0 OD1 A:ASP133 3.9 9.3 1.0 N A:ASN130 4.0 10.5 1.0 CB A:ASN130 4.1 11.6 1.0 MN A:MN302 4.2 20.2 1.0 CA A:PHE128 4.3 9.6 1.0 CB A:ASP126 4.3 8.3 1.0 O A:HOH452 4.3 8.6 1.0 N A:PHE128 4.4 9.4 1.0 NE1 A:TRP132 4.5 11.2 1.0 N A:SER129 4.5 10.8 1.0 CB A:PHE128 4.5 9.5 1.0 O A:GLY106 4.5 9.2 1.0 O A:ASP88 4.6 7.9 1.0 CA A:SER129 4.6 11.4 1.0 CB A:ASP133 4.6 11.1 1.0 OD1 A:ASN130 4.7 14.5 1.0 OD1 A:ASP88 4.7 9.2 1.0 CA A:GLY106 4.7 8.9 1.0 CA A:ASN130 4.7 12.2 1.0 C A:SER129 4.7 11.7 1.0 CD2 A:PHE128 4.8 10.1 1.0 CE1 A:HIS138 4.9 9.8 1.0 CZ2 A:TRP132 5.0 11.4 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca301 b:10.8 occ:1.00 O B:PHE128 2.3 11.6 1.0 OD2 B:ASP133 2.3 12.3 1.0 O B:HOH441 2.4 10.4 1.0 O B:HOH475 2.4 12.8 1.0 OD1 B:ASP126 2.4 10.1 1.0 ND2 B:ASN130 2.5 9.7 1.0 OD2 B:ASP126 2.6 10.5 1.0 CG B:ASP126 2.8 10.2 1.0 CG B:ASP133 3.4 11.8 1.0 C B:PHE128 3.5 13.9 1.0 CG B:ASN130 3.7 12.9 1.0 OD1 B:ASP133 3.9 11.4 1.0 N B:ASN130 4.0 13.0 1.0 CB B:ASN130 4.2 12.6 1.0 MN B:MN302 4.2 22.0 1.0 CA B:PHE128 4.3 12.6 1.0 CB B:ASP126 4.3 10.2 1.0 O B:HOH467 4.3 9.8 1.0 N B:PHE128 4.3 12.0 1.0 NE1 B:TRP132 4.5 13.5 1.0 N B:SER129 4.5 13.5 1.0 O B:GLY106 4.5 10.6 1.0 O B:ASP88 4.6 9.3 1.0 CB B:ASP133 4.6 11.8 1.0 CA B:SER129 4.6 13.4 1.0 CB B:PHE128 4.6 12.5 1.0 OD1 B:ASP88 4.7 10.5 1.0 OD1 B:ASN130 4.7 15.1 1.0 CA B:ASN130 4.7 14.1 1.0 C B:SER129 4.7 15.0 1.0 CE1 B:HIS138 4.8 10.6 1.0 CA B:GLY106 4.8 11.3 1.0 CD1 B:PHE128 4.9 13.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca301 b:14.0 occ:1.00 O C:HOH471 2.3 14.2 1.0 OD2 C:ASP133 2.4 12.4 1.0 O C:PHE128 2.4 15.9 1.0 ND2 C:ASN130 2.4 11.9 1.0 O C:HOH458 2.4 12.7 1.0 OD1 C:ASP126 2.5 10.5 1.0 OD2 C:ASP126 2.5 9.3 1.0 CG C:ASP126 2.8 10.4 1.0 CG C:ASP133 3.4 12.7 1.0 C C:PHE128 3.6 13.4 1.0 CG C:ASN130 3.6 14.9 1.0 OD1 C:ASP133 4.0 10.7 1.0 N C:ASN130 4.0 14.5 1.0 CB C:ASN130 4.1 15.2 1.0 MN C:MN302 4.2 23.7 1.0 O C:HOH434 4.3 12.5 1.0 CB C:ASP126 4.4 10.4 1.0 CA C:PHE128 4.4 14.6 1.0 N C:PHE128 4.4 14.5 1.0 NE1 C:TRP132 4.4 16.0 1.0 O C:GLY106 4.6 15.2 1.0 N C:SER129 4.6 13.2 1.0 O C:ASP88 4.6 13.5 1.0 CB C:PHE128 4.6 14.1 1.0 OD1 C:ASN130 4.7 18.0 1.0 OD1 C:ASP88 4.7 17.1 1.0 CB C:ASP133 4.7 12.6 1.0 CA C:SER129 4.7 13.7 1.0 CA C:ASN130 4.7 15.2 1.0 CA C:GLY106 4.7 16.0 1.0 C C:SER129 4.8 15.4 1.0 CD2 C:PHE128 4.8 14.8 1.0 O C:HOH529 4.9 24.3 1.0 CE1 C:HIS138 4.9 10.5 1.0 CZ2 C:TRP132 5.0 15.8 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca301 b:12.9 occ:1.00 O D:HOH415 2.3 14.7 1.0 O D:PHE128 2.3 15.5 1.0 O D:HOH493 2.3 15.4 1.0 OD2 D:ASP133 2.3 15.5 1.0 ND2 D:ASN130 2.4 12.6 1.0 OD2 D:ASP126 2.4 12.9 1.0 OD1 D:ASP126 2.5 12.7 1.0 CG D:ASP126 2.8 13.3 1.0 CG D:ASP133 3.4 14.4 1.0 C D:PHE128 3.5 14.3 1.0 CG D:ASN130 3.6 16.2 1.0 OD1 D:ASP133 3.9 11.9 1.0 N D:ASN130 4.0 15.2 1.0 CB D:ASN130 4.1 15.5 1.0 MN D:MN302 4.2 24.7 1.0 O D:HOH422 4.3 11.2 1.0 CB D:ASP126 4.3 12.1 1.0 CA D:PHE128 4.3 15.0 1.0 N D:PHE128 4.4 14.5 1.0 NE1 D:TRP132 4.4 15.8 1.0 N D:SER129 4.5 14.5 1.0 CB D:PHE128 4.6 14.8 1.0 O D:ASP88 4.6 13.4 1.0 CB D:ASP133 4.6 15.6 1.0 O D:GLY106 4.6 17.9 1.0 CA D:SER129 4.6 16.1 1.0 OD1 D:ASN130 4.7 20.3 1.0 CA D:ASN130 4.7 15.6 1.0 OD1 D:ASP88 4.7 17.1 1.0 CA D:GLY106 4.7 17.9 1.0 C D:SER129 4.8 16.4 1.0 CE1 D:HIS138 4.9 11.8 1.0 CD2 D:PHE128 4.9 16.1 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