Calcium in PDB 6vav: Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings)

The structure of Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings), PDB code: 6vav was solved by L.H.Otero, E.D.Primo, A.J.Cagnoni, S.Klinke, F.A.Goldbaum, M.L.Uhrig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.09 / 1.85
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.760, 124.640, 128.375, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 22.5

The structure of Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings) also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Calcium atom in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings) (pdb code 6vav). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings), PDB code: 6vav:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:20.6 occ:1.00 O A:HOH460 2.2 19.4 1.0 O A:HOH530 2.2 17.3 1.0 O A:TYR125 2.3 22.1 1.0 OD2 A:ASP132 2.3 20.8 1.0 OD1 A:ASN127 2.4 23.5 1.0 OD1 A:ASP123 2.5 23.5 1.0 OD2 A:ASP123 2.6 17.6 1.0 CG A:ASP123 2.9 21.9 1.0 CG A:ASP132 3.4 23.9 1.0 C A:TYR125 3.5 22.4 1.0 CG A:ASN127 3.5 30.3 1.0 OD1 A:ASP132 3.9 22.3 1.0 N A:ASN127 4.0 21.4 1.0 CB A:ASN127 4.0 18.7 1.0 MN A:MN302 4.1 38.6 1.0 CA A:TYR125 4.3 19.9 1.0 N A:TYR125 4.3 20.6 1.0 CB A:ASP123 4.4 20.0 1.0 O A:HOH402 4.4 15.9 1.0 N A:SER126 4.5 19.3 1.0 CA A:GLY104 4.5 21.2 1.0 CB A:TYR125 4.5 20.8 1.0 CA A:SER126 4.6 19.7 1.0 CB A:ASP132 4.6 25.1 1.0 ND2 A:ASN127 4.6 24.9 1.0 CA A:ASN127 4.6 21.8 1.0 OD2 A:ASP83 4.7 23.6 1.0 C A:SER126 4.7 24.7 1.0 O A:ASP83 4.7 19.5 1.0 CD1 A:TYR125 4.8 27.2 1.0 O A:GLY104 4.8 23.7 1.0 CE1 A:HIS137 4.9 23.2 1.0

Calcium binding site 2 out of 3 in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:20.3 occ:1.00 OD2 B:ASP132 2.3 19.7 1.0 O B:HOH485 2.3 17.7 1.0 O B:TYR125 2.3 24.0 1.0 O B:HOH516 2.4 19.0 1.0 OD1 B:ASN127 2.5 18.2 1.0 OD2 B:ASP123 2.5 18.9 1.0 OD1 B:ASP123 2.5 20.9 1.0 CG B:ASP123 2.9 19.9 1.0 CG B:ASP132 3.4 21.9 1.0 CG B:ASN127 3.5 26.6 1.0 C B:TYR125 3.5 23.5 1.0 OD1 B:ASP132 3.9 18.3 1.0 N B:ASN127 4.0 22.4 1.0 CB B:ASN127 4.0 19.9 1.0 MN B:MN302 4.1 40.4 1.0 O B:HOH403 4.3 19.7 1.0 CA B:TYR125 4.4 19.8 1.0 CB B:ASP123 4.4 18.9 1.0 N B:TYR125 4.4 20.6 1.0 CA B:GLY104 4.5 18.5 1.0 N B:SER126 4.5 19.7 1.0 CB B:TYR125 4.6 20.6 1.0 CB B:ASP132 4.6 20.9 1.0 CA B:SER126 4.6 19.3 1.0 O B:ASP83 4.7 15.6 1.0 CA B:ASN127 4.7 22.0 1.0 ND2 B:ASN127 4.7 16.2 1.0 C B:SER126 4.7 25.1 1.0 OD1 B:ASP83 4.8 23.6 1.0 O B:GLY104 4.8 21.6 1.0 CE1 B:HIS137 4.9 23.1 1.0 CD1 B:TYR125 4.9 22.8 1.0

Calcium binding site 3 out of 3 in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:24.4 occ:1.00 OD1 D:ASP123 2.2 21.4 1.0 O D:HOH464 2.3 20.6 1.0 OD2 D:ASP123 2.4 19.6 1.0 O D:TYR125 2.4 21.4 1.0 OD2 D:ASP132 2.4 21.8 1.0 O D:HOH414 2.5 25.0 1.0 OD1 D:ASN127 2.6 24.9 1.0 CG D:ASP123 2.6 20.6 1.0 CG D:ASP132 3.5 25.3 1.0 C D:TYR125 3.6 24.9 1.0 CG D:ASN127 3.7 32.0 1.0 OD1 D:ASP132 3.9 27.5 1.0 N D:ASN127 4.1 23.9 1.0 CB D:ASP123 4.1 19.2 1.0 MN D:MN302 4.1 36.8 1.0 O D:HOH401 4.2 20.0 1.0 CB D:ASN127 4.2 26.2 1.0 N D:TYR125 4.3 21.5 1.0 CA D:TYR125 4.3 21.6 1.0 CB D:TYR125 4.6 23.7 1.0 N D:SER126 4.6 23.4 1.0 CA D:GLY104 4.6 22.9 1.0 O D:ASP83 4.6 25.4 1.0 CB D:ASP132 4.7 24.9 1.0 CA D:SER126 4.7 23.1 1.0 CE1 D:HIS137 4.7 22.4 1.0 ND2 D:ASN127 4.8 24.0 1.0 OD2 D:ASP83 4.8 26.2 1.0 CA D:ASN127 4.8 24.8 1.0 C D:SER126 4.8 27.1 1.0 O D:GLY104 4.9 25.5 1.0 CD1 D:TYR125 5.0 30.6 1.0 CA D:ASP123 5.0 18.2 1.0

A.J.Cagnoni, E.D.Primo, S.Klinke, M.E.Cano, W.Giordano, K.V.Marino, J.Kovensky, F.A.Goldbaum, M.L.Uhrig, L.H.Otero. Crystal Structures of Peanut Lectin in the Presence of Synthetic Beta-N- and Beta-S-Galactosides Disclose Evidence For the Recognition of Different Glycomimetic Ligands. Acta Crystallogr D Struct V. 76 1080 2020BIOL.
ISSN: ISSN 2059-7983
PubMed: 33135679
DOI: 10.1107/S2059798320012371