Calcium in PDB 6v95: Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt)

The structure of Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt), PDB code: 6v95 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)	26.06 / 1.78
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.941, 124.553, 127.484, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.3

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

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt) (pdb code 6v95). 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 Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt), PDB code: 6v95:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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- Tartaramidoyl Derivative (Dingt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:25.2 occ:1.00 O A:TYR125 2.2 25.6 1.0 O A:HOH436 2.3 17.5 1.0 OD2 A:ASP132 2.4 30.3 1.0 OD1 A:ASP123 2.4 29.0 1.0 OD1 A:ASN127 2.5 25.3 1.0 O A:HOH406 2.5 22.2 1.0 OD2 A:ASP123 2.5 20.2 1.0 CG A:ASP123 2.8 27.0 1.0 C A:TYR125 3.4 26.5 1.0 CG A:ASP132 3.4 31.2 1.0 CG A:ASN127 3.5 35.6 1.0 OD1 A:ASP132 3.9 29.4 1.0 N A:ASN127 4.0 27.2 1.0 CB A:ASN127 4.1 24.1 1.0 MN A:MN302 4.2 33.8 1.0 CA A:TYR125 4.2 23.1 1.0 N A:TYR125 4.3 24.3 1.0 CB A:ASP123 4.3 21.0 1.0 O A:HOH415 4.3 19.5 1.0 N A:SER126 4.4 23.8 1.0 CB A:TYR125 4.5 23.7 1.0 CA A:SER126 4.5 24.5 1.0 ND2 A:ASN127 4.6 30.7 1.0 CA A:GLY104 4.6 23.9 1.0 CB A:ASP132 4.6 26.5 1.0 C A:SER126 4.6 30.9 1.0 CA A:ASN127 4.7 26.6 1.0 OD2 A:ASP83 4.7 25.9 1.0 O A:ASP83 4.7 21.6 1.0 CE1 A:HIS137 4.8 27.3 1.0 O A:GLY104 4.8 26.3 1.0 CD2 A:TYR125 4.9 26.6 1.0

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


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- Tartaramidoyl Derivative (Dingt) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:22.9 occ:1.00 O B:HOH449 2.3 17.2 1.0 O B:TYR125 2.3 22.7 1.0 O B:HOH402 2.4 19.3 1.0 OD2 B:ASP132 2.4 26.6 1.0 OD1 B:ASN127 2.5 21.2 1.0 OD1 B:ASP123 2.5 22.4 1.0 OD2 B:ASP123 2.6 18.0 1.0 CG B:ASP123 2.8 21.0 1.0 CG B:ASP132 3.5 24.8 1.0 CG B:ASN127 3.5 35.3 1.0 C B:TYR125 3.5 25.1 1.0 OD1 B:ASP132 3.9 21.8 1.0 CB B:ASN127 4.0 21.5 1.0 N B:ASN127 4.0 23.1 1.0 MN B:MN302 4.2 32.9 1.0 O B:HOH423 4.3 21.5 1.0 CA B:GLY104 4.4 20.2 1.0 CA B:TYR125 4.4 21.0 1.0 CB B:ASP123 4.4 18.7 1.0 N B:TYR125 4.4 22.6 1.0 N B:SER126 4.5 22.8 1.0 OD2 B:ASP83 4.6 23.3 1.0 CB B:TYR125 4.6 20.9 1.0 ND2 B:ASN127 4.6 21.1 1.0 O B:GLY104 4.7 21.8 1.0 CA B:SER126 4.7 22.8 1.0 CA B:ASN127 4.7 22.2 1.0 O B:ASP83 4.7 19.3 1.0 CB B:ASP132 4.7 21.7 1.0 C B:SER126 4.8 27.3 1.0 CE1 B:HIS137 4.9 20.3 1.0 CD2 B:TYR125 4.9 22.7 1.0

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


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- Tartaramidoyl Derivative (Dingt) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:44.4 occ:1.00 O C:HOH403 2.1 31.8 1.0 OD1 C:ASN127 2.2 55.4 1.0 OD2 C:ASP132 2.2 43.4 1.0 O C:TYR125 2.4 55.0 1.0 O C:HOH406 2.4 48.2 1.0 OD2 C:ASP123 2.6 41.8 1.0 OD1 C:ASP123 2.7 39.9 1.0 CG C:ASP123 3.0 41.6 1.0 CG C:ASN127 3.2 59.5 1.0 CG C:ASP132 3.3 42.1 1.0 C C:TYR125 3.4 55.4 1.0 N C:ASN127 3.7 53.9 1.0 CB C:ASN127 3.8 51.9 1.0 OD1 C:ASP132 3.9 41.6 1.0 MN C:MN302 4.2 53.1 1.0 O C:HOH407 4.2 34.0 1.0 CA C:TYR125 4.3 50.5 1.0 CB C:TYR125 4.3 53.4 1.0 N C:SER126 4.3 52.4 1.0 ND2 C:ASN127 4.3 43.9 1.0 CA C:ASN127 4.4 53.6 1.0 N C:TYR125 4.4 49.1 1.0 CA C:SER126 4.4 52.3 1.0 C C:SER126 4.5 57.5 1.0 CB C:ASP123 4.5 36.1 1.0 OD2 C:ASP83 4.5 58.0 1.0 CB C:ASP132 4.5 46.4 1.0 CA C:GLY104 4.5 49.4 1.0 CD2 C:TYR125 4.6 59.1 1.0 O C:GLY104 4.8 50.2 1.0 CE1 C:HIS137 4.9 40.0 1.0 O C:ASP83 5.0 44.4 1.0

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


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 Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:26.8 occ:1.00 OD1 D:ASP123 2.3 20.5 1.0 O D:TYR125 2.4 25.4 1.0 OD2 D:ASP123 2.4 20.0 1.0 O D:HOH446 2.4 25.9 1.0 OD2 D:ASP132 2.4 26.4 1.0 O D:HOH431 2.5 26.0 1.0 OD1 D:ASN127 2.5 26.0 1.0 CG D:ASP123 2.7 17.8 1.0 CG D:ASP132 3.5 29.3 1.0 C D:TYR125 3.5 26.8 1.0 CG D:ASN127 3.6 34.6 1.0 OD1 D:ASP132 3.9 29.4 1.0 N D:ASN127 4.0 25.7 1.0 CB D:ASN127 4.1 29.3 1.0 MN D:MN302 4.2 35.6 1.0 CB D:ASP123 4.2 20.3 1.0 O D:HOH406 4.3 21.4 1.0 CA D:TYR125 4.3 23.1 1.0 N D:TYR125 4.3 23.5 1.0 N D:SER126 4.5 24.5 1.0 CB D:TYR125 4.5 25.9 1.0 CA D:GLY104 4.6 25.3 1.0 CA D:SER126 4.7 24.0 1.0 O D:ASP83 4.7 28.1 1.0 ND2 D:ASN127 4.7 29.6 1.0 CA D:ASN127 4.7 26.5 1.0 CB D:ASP132 4.7 26.9 1.0 C D:SER126 4.8 27.8 1.0 OD2 D:ASP83 4.8 29.5 1.0 CE1 D:HIS137 4.8 23.2 1.0 O D:GLY104 4.8 23.9 1.0 CD1 D:TYR125 4.9 30.9 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