Calcium in PDB 6vgf: Peanut Lectin Complexed with Divalent S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd)

The structure of Peanut Lectin Complexed with Divalent S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd), PDB code: 6vgf was solved by L.H.Otero, E.D.Primo, A.J.Cagnoni, M.E.Cano, 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)	26.79 / 1.83
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.059, 125.041, 126.961, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.3

The structure of Peanut Lectin Complexed with Divalent S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd) also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Peanut Lectin Complexed with Divalent S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd) (pdb code 6vgf). 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 S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd), PDB code: 6vgf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Peanut Lectin Complexed with Divalent S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd)


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 S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:25.5 occ:1.00 O A:TYR125 2.2 27.0 1.0 O A:HOH463 2.3 19.0 1.0 OD2 A:ASP132 2.3 27.1 1.0 OD1 A:ASP123 2.4 27.8 1.0 OD1 A:ASN127 2.5 27.9 1.0 O A:HOH453 2.5 22.2 1.0 OD2 A:ASP123 2.5 24.4 1.0 CG A:ASP123 2.8 25.5 1.0 C A:TYR125 3.4 27.4 1.0 CG A:ASP132 3.4 32.7 1.0 CG A:ASN127 3.5 38.4 1.0 OD1 A:ASP132 3.9 31.7 1.0 N A:ASN127 4.0 28.0 1.0 CB A:ASN127 4.1 24.9 1.0 MN A:MN302 4.2 35.2 1.0 CA A:TYR125 4.2 24.1 1.0 N A:TYR125 4.3 25.2 1.0 CB A:ASP123 4.3 22.6 1.0 N A:SER126 4.3 24.5 1.0 O A:HOH406 4.4 18.4 1.0 CB A:TYR125 4.5 24.8 1.0 CA A:SER126 4.5 24.2 1.0 CB A:ASP132 4.6 28.1 1.0 ND2 A:ASN127 4.6 31.5 1.0 CA A:GLY104 4.6 25.9 1.0 C A:SER126 4.6 30.8 1.0 CA A:ASN127 4.7 27.0 1.0 OD1 A:ASP83 4.7 27.6 1.0 O A:ASP83 4.7 23.5 1.0 CE1 A:HIS137 4.8 26.0 1.0 CD1 A:TYR125 4.8 28.5 1.0 O A:GLY104 4.9 28.9 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin Complexed with Divalent S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd)


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 S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:23.7 occ:1.00 O B:HOH489 2.2 17.6 1.0 O B:HOH441 2.3 20.7 1.0 OD2 B:ASP132 2.4 24.0 1.0 O B:TYR125 2.4 20.8 1.0 OD1 B:ASP123 2.5 19.6 1.0 OD1 B:ASN127 2.5 19.8 1.0 OD2 B:ASP123 2.6 16.8 1.0 CG B:ASP123 2.9 19.3 1.0 CG B:ASP132 3.5 25.4 1.0 CG B:ASN127 3.5 27.8 1.0 C B:TYR125 3.6 23.5 1.0 OD1 B:ASP132 3.9 22.8 1.0 CB B:ASN127 4.0 20.7 1.0 N B:ASN127 4.1 25.6 1.0 MN B:MN302 4.2 31.5 1.0 O B:HOH403 4.3 19.9 1.0 CA B:TYR125 4.4 21.3 1.0 CA B:GLY104 4.4 21.6 1.0 CB B:ASP123 4.4 18.4 1.0 N B:TYR125 4.4 23.2 1.0 N B:SER126 4.6 22.4 1.0 CB B:TYR125 4.6 21.7 1.0 OD2 B:ASP83 4.6 24.4 1.0 ND2 B:ASN127 4.7 17.5 1.0 O B:GLY104 4.7 23.6 1.0 CB B:ASP132 4.7 22.9 1.0 CA B:SER126 4.7 21.8 1.0 CA B:ASN127 4.7 24.0 1.0 O B:ASP83 4.8 21.7 1.0 C B:SER126 4.8 29.4 1.0 CD1 B:TYR125 4.9 24.3 1.0 CE1 B:HIS137 4.9 23.8 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin Complexed with Divalent S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd)


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 S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:49.3 occ:1.00 O C:HOH433 2.1 30.7 1.0 OD1 C:ASN127 2.1 50.6 1.0 OD2 C:ASP132 2.2 52.6 1.0 O C:TYR125 2.4 51.0 1.0 OD2 C:ASP123 2.6 44.3 1.0 O C:HOH412 2.6 41.1 1.0 OD1 C:ASP123 2.8 43.9 1.0 CG C:ASP123 3.0 43.3 1.0 CG C:ASN127 3.2 59.2 1.0 CG C:ASP132 3.3 49.9 1.0 C C:TYR125 3.5 51.1 1.0 N C:ASN127 3.7 54.1 1.0 CB C:ASN127 3.8 51.2 1.0 OD1 C:ASP132 3.9 50.8 1.0 MN C:MN302 4.2 48.6 1.0 O C:HOH409 4.3 34.6 1.0 CA C:TYR125 4.3 45.2 1.0 ND2 C:ASN127 4.4 50.8 1.0 N C:SER126 4.4 48.6 1.0 CA C:ASN127 4.4 54.0 1.0 CB C:TYR125 4.4 47.6 1.0 N C:TYR125 4.5 44.1 1.0 CA C:SER126 4.5 49.3 1.0 C C:SER126 4.5 56.7 1.0 CA C:GLY104 4.5 54.0 1.0 CB C:ASP132 4.5 46.2 1.0 CB C:ASP123 4.5 33.3 1.0 CD1 C:TYR125 4.6 53.5 1.0 OD2 C:ASP83 4.7 60.4 1.0 O C:GLY104 4.8 53.2 1.0 O C:ASP83 4.9 43.0 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin Complexed with Divalent S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd)


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 S-Beta-D-Thiogalactopyranosyl Beta-D-Glucopyranoside Derivative (Distgd) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:26.2 occ:1.00 OD1 D:ASP123 2.2 19.3 1.0 OD2 D:ASP123 2.4 24.8 1.0 O D:TYR125 2.4 25.9 1.0 OD2 D:ASP132 2.4 27.6 1.0 O D:HOH424 2.4 25.9 1.0 O D:HOH423 2.4 27.0 1.0 OD1 D:ASN127 2.5 26.6 1.0 CG D:ASP123 2.6 18.8 1.0 CG D:ASP132 3.4 29.2 1.0 C D:TYR125 3.6 27.7 1.0 CG D:ASN127 3.6 34.7 1.0 OD1 D:ASP132 3.9 30.7 1.0 CB D:ASP123 4.1 23.2 1.0 N D:ASN127 4.1 29.8 1.0 MN D:MN302 4.1 36.3 1.0 O D:HOH401 4.2 21.2 1.0 CB D:ASN127 4.2 32.3 1.0 CA D:TYR125 4.4 23.6 1.0 N D:TYR125 4.4 24.6 1.0 N D:SER126 4.6 25.8 1.0 CB D:TYR125 4.6 25.5 1.0 CA D:GLY104 4.6 26.4 1.0 O D:ASP83 4.6 25.3 1.0 CB D:ASP132 4.7 27.1 1.0 ND2 D:ASN127 4.7 27.0 1.0 CA D:SER126 4.8 26.0 1.0 CE1 D:HIS137 4.8 26.0 1.0 CA D:ASN127 4.8 29.9 1.0 O D:GLY104 4.8 25.9 1.0 OD2 D:ASP83 4.8 28.6 1.0 C D:SER126 4.9 30.1 1.0 CD1 D:TYR125 4.9 29.1 1.0 NE2 D:HIS137 5.0 26.0 1.0 CA D:ASP123 5.0 22.5 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