Calcium in PDB 6vaw: Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs)

The structure of Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs), PDB code: 6vaw 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)	45.42 / 1.75
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.222, 125.052, 126.844, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 23.2

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

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs) (pdb code 6vaw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs), PDB code: 6vaw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs)


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 N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:23.6 occ:1.00 O A:TYR125 2.2 26.6 1.0 O A:HOH418 2.3 19.7 1.0 OD2 A:ASP132 2.4 28.3 1.0 O A:HOH426 2.4 21.2 1.0 OD1 A:ASP123 2.5 23.4 1.0 OD1 A:ASN127 2.5 28.4 1.0 OD2 A:ASP123 2.6 19.9 1.0 CG A:ASP123 2.9 22.2 1.0 C A:TYR125 3.4 27.5 1.0 CG A:ASP132 3.4 31.5 1.0 CG A:ASN127 3.6 36.5 1.0 OD1 A:ASP132 3.9 30.1 1.0 N A:ASN127 4.0 26.9 1.0 CB A:ASN127 4.2 26.4 1.0 MN A:MN302 4.2 37.3 1.0 CA A:TYR125 4.2 24.6 1.0 N A:TYR125 4.3 26.4 1.0 N A:SER126 4.3 24.8 1.0 CB A:ASP123 4.3 21.9 1.0 O A:HOH401 4.4 21.5 1.0 CB A:TYR125 4.5 25.4 1.0 CA A:GLY104 4.5 27.8 1.0 CA A:SER126 4.5 26.0 1.0 CB A:ASP132 4.6 26.6 1.0 C A:SER126 4.6 31.1 1.0 ND2 A:ASN127 4.7 32.1 1.0 OD2 A:ASP83 4.7 25.5 1.0 CA A:ASN127 4.7 25.7 1.0 O A:ASP83 4.8 23.6 1.0 O A:GLY104 4.8 28.0 1.0 CD1 A:TYR125 4.8 27.6 1.0 CE1 A:HIS137 4.8 27.2 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs)


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 N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:21.3 occ:1.00 O B:TYR125 2.3 21.7 1.0 O B:HOH443 2.3 16.0 1.0 OD2 B:ASP132 2.4 24.8 1.0 O B:HOH403 2.4 17.7 1.0 OD1 B:ASN127 2.5 20.3 1.0 OD1 B:ASP123 2.5 20.0 1.0 OD2 B:ASP123 2.5 17.8 1.0 CG B:ASP123 2.9 20.4 1.0 CG B:ASP132 3.5 26.3 1.0 C B:TYR125 3.5 25.2 1.0 CG B:ASN127 3.5 34.9 1.0 OD1 B:ASP132 3.9 21.5 1.0 N B:ASN127 4.1 25.4 1.0 CB B:ASN127 4.1 24.1 1.0 O B:HOH422 4.2 23.0 1.0 MN B:MN302 4.2 34.7 1.0 CA B:TYR125 4.3 21.3 1.0 N B:TYR125 4.3 22.9 1.0 CB B:ASP123 4.4 18.8 1.0 CA B:GLY104 4.4 22.3 1.0 CB B:TYR125 4.5 20.8 1.0 N B:SER126 4.5 24.3 1.0 OD2 B:ASP83 4.6 27.8 1.0 ND2 B:ASN127 4.6 20.8 1.0 CB B:ASP132 4.7 24.6 1.0 O B:GLY104 4.7 24.4 1.0 CA B:SER126 4.7 24.0 1.0 CA B:ASN127 4.7 24.8 1.0 O B:ASP83 4.8 22.1 1.0 C B:SER126 4.9 29.6 1.0 CE1 B:HIS137 4.9 20.8 1.0 CD1 B:TYR125 4.9 24.6 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs)


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 N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:42.7 occ:1.00 O C:HOH407 2.1 38.9 1.0 OD2 C:ASP132 2.2 52.0 1.0 O C:TYR125 2.2 53.4 1.0 OD1 C:ASN127 2.2 56.7 1.0 O C:HOH409 2.4 43.2 1.0 OD2 C:ASP123 2.5 43.4 1.0 OD1 C:ASP123 2.8 44.3 1.0 CG C:ASP123 3.0 43.5 1.0 CG C:ASP132 3.3 49.1 1.0 CG C:ASN127 3.3 63.1 1.0 C C:TYR125 3.4 53.7 1.0 N C:ASN127 3.7 53.8 1.0 CB C:ASN127 3.8 50.9 1.0 OD1 C:ASP132 3.8 48.5 1.0 MN C:MN302 4.2 55.1 1.0 O C:HOH404 4.3 34.9 1.0 CA C:TYR125 4.3 47.8 1.0 N C:SER126 4.3 51.1 1.0 CA C:ASN127 4.4 53.6 1.0 CB C:TYR125 4.4 49.8 1.0 N C:TYR125 4.4 46.9 1.0 CA C:SER126 4.4 51.3 1.0 CB C:ASP132 4.5 48.0 1.0 ND2 C:ASN127 4.5 53.2 1.0 C C:SER126 4.5 56.9 1.0 OD2 C:ASP83 4.5 56.6 1.0 CB C:ASP123 4.5 34.8 1.0 CA C:GLY104 4.5 49.2 1.0 CD1 C:TYR125 4.7 54.7 1.0 O C:GLY104 4.8 49.7 1.0 O C:ASP83 5.0 42.3 1.0 CE1 C:HIS137 5.0 38.4 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:25.8 occ:1.00 OD1 D:ASP123 2.2 21.8 1.0 OD1 D:ASN127 2.3 26.0 1.0 O D:TYR125 2.3 27.4 1.0 O D:HOH440 2.4 27.7 1.0 OD2 D:ASP123 2.4 22.6 1.0 OD2 D:ASP132 2.5 29.1 1.0 O D:HOH418 2.5 30.6 1.0 CG D:ASP123 2.6 21.1 1.0 CG D:ASP132 3.5 28.8 1.0 C D:TYR125 3.5 29.3 1.0 CG D:ASN127 3.5 34.0 1.0 OD1 D:ASP132 3.9 31.3 1.0 MN D:MN302 4.1 36.6 1.0 N D:ASN127 4.1 29.6 1.0 CB D:ASP123 4.1 21.4 1.0 N D:TYR125 4.3 25.6 1.0 CA D:TYR125 4.3 25.2 1.0 O D:HOH402 4.3 21.9 1.0 CB D:ASN127 4.3 29.3 1.0 CB D:TYR125 4.5 27.5 1.0 ND2 D:ASN127 4.5 31.2 1.0 N D:SER126 4.5 25.9 1.0 CA D:GLY104 4.6 27.2 1.0 O D:ASP83 4.6 24.8 1.0 CA D:SER126 4.7 25.2 1.0 CB D:ASP132 4.7 27.3 1.0 OD2 D:ASP83 4.7 32.2 1.0 CE1 D:HIS137 4.8 25.3 1.0 O D:GLY104 4.8 24.0 1.0 CA D:ASN127 4.9 29.9 1.0 C D:SER126 4.9 30.5 1.0 CD1 D:TYR125 4.9 33.1 1.0 O D:HOH492 5.0 30.6 1.0 CA D:ASP123 5.0 20.7 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