Calcium in PDB 6vc4: Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl Beta-D- Glucopyranoside Derivative (Stgd)

The structure of Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl Beta-D- Glucopyranoside Derivative (Stgd), PDB code: 6vc4 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)	56.64 / 1.90
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.067, 124.562, 127.188, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.4

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

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl Beta-D- Glucopyranoside Derivative (Stgd) (pdb code 6vc4). 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 S-Beta-D-Thiogalactopyranosyl Beta-D- Glucopyranoside Derivative (Stgd), PDB code: 6vc4:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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 S-Beta-D-Thiogalactopyranosyl Beta-D- Glucopyranoside Derivative (Stgd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:22.8 occ:1.00 O A:HOH419 2.2 18.4 1.0 O A:TYR125 2.2 24.4 1.0 OD2 A:ASP132 2.3 23.3 1.0 O A:HOH413 2.5 16.4 1.0 OD2 A:ASP123 2.5 21.1 1.0 OD1 A:ASP123 2.5 27.7 1.0 OD1 A:ASN127 2.5 24.4 1.0 CG A:ASP123 2.8 22.5 1.0 CG A:ASP132 3.4 27.9 1.0 C A:TYR125 3.5 25.7 1.0 CG A:ASN127 3.6 32.3 1.0 OD1 A:ASP132 3.9 26.5 1.0 N A:ASN127 4.0 23.6 1.0 CB A:ASN127 4.1 17.7 1.0 MN A:MN302 4.2 35.8 1.0 CA A:TYR125 4.3 22.4 1.0 N A:TYR125 4.3 22.2 1.0 O A:HOH403 4.3 20.9 1.0 CB A:ASP123 4.3 20.1 1.0 N A:SER126 4.4 22.7 1.0 CB A:TYR125 4.5 23.6 1.0 CA A:GLY104 4.5 21.9 1.0 CA A:SER126 4.6 22.4 1.0 CB A:ASP132 4.7 25.9 1.0 CA A:ASN127 4.7 22.6 1.0 O A:ASP83 4.7 20.9 1.0 C A:SER126 4.7 27.8 1.0 ND2 A:ASN127 4.7 28.4 1.0 OD2 A:ASP83 4.8 25.6 1.0 CD2 A:TYR125 4.8 25.0 1.0 O A:GLY104 4.8 25.5 1.0 CE1 A:HIS137 4.9 24.5 1.0

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


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 S-Beta-D-Thiogalactopyranosyl Beta-D- Glucopyranoside Derivative (Stgd) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:23.5 occ:1.00 O B:HOH426 2.3 16.5 1.0 OD2 B:ASP132 2.3 22.6 1.0 O B:HOH418 2.4 20.7 1.0 O B:TYR125 2.4 21.8 1.0 OD1 B:ASN127 2.5 17.9 1.0 OD2 B:ASP123 2.6 19.0 1.0 OD1 B:ASP123 2.6 20.5 1.0 CG B:ASP123 2.9 19.7 1.0 CG B:ASP132 3.4 22.9 1.0 CG B:ASN127 3.6 26.5 1.0 C B:TYR125 3.6 22.0 1.0 OD1 B:ASP132 3.9 18.5 1.0 CB B:ASN127 4.0 18.2 1.0 O B:HOH432 4.0 19.7 1.0 N B:ASN127 4.1 22.1 1.0 MN B:MN302 4.1 34.7 1.0 CA B:GLY104 4.3 18.7 1.0 CA B:TYR125 4.4 19.6 1.0 N B:TYR125 4.5 20.4 1.0 CB B:ASP123 4.5 18.5 1.0 CB B:TYR125 4.6 21.1 1.0 N B:SER126 4.6 19.9 1.0 OD2 B:ASP83 4.6 24.1 1.0 O B:GLY104 4.6 16.7 1.0 CB B:ASP132 4.7 22.6 1.0 CA B:ASN127 4.7 20.6 1.0 ND2 B:ASN127 4.7 16.5 1.0 CA B:SER126 4.7 20.1 1.0 O B:ASP83 4.8 23.9 1.0 C B:SER126 4.9 26.8 1.0 CD1 B:TYR125 4.9 24.0 1.0 CE1 B:HIS137 4.9 22.1 1.0

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


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 S-Beta-D-Thiogalactopyranosyl Beta-D- Glucopyranoside Derivative (Stgd) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:40.8 occ:1.00 O C:HOH411 2.1 31.3 1.0 OD2 C:ASP132 2.1 55.8 1.0 OD1 C:ASN127 2.3 57.1 1.0 O C:HOH413 2.4 35.4 1.0 O C:TYR125 2.4 51.5 1.0 OD2 C:ASP123 2.6 34.2 1.0 OD1 C:ASP123 2.8 37.5 1.0 CG C:ASP123 3.1 37.3 1.0 CG C:ASP132 3.2 52.5 1.0 CG C:ASN127 3.3 60.0 1.0 C C:TYR125 3.5 52.3 1.0 N C:ASN127 3.7 52.6 1.0 CB C:ASN127 3.8 49.9 1.0 OD1 C:ASP132 3.8 52.9 1.0 MN C:MN302 4.2 54.8 1.0 O C:HOH402 4.3 31.8 1.0 CA C:TYR125 4.4 47.5 1.0 CA C:ASN127 4.4 52.5 1.0 N C:SER126 4.4 49.5 1.0 CB C:ASP132 4.4 48.0 1.0 CA C:SER126 4.5 49.8 1.0 CB C:TYR125 4.5 49.8 1.0 C C:SER126 4.5 56.0 1.0 N C:TYR125 4.5 46.5 1.0 ND2 C:ASN127 4.5 46.9 1.0 CA C:GLY104 4.5 45.7 1.0 CD2 C:TYR125 4.6 54.2 1.0 CB C:ASP123 4.6 32.0 1.0 O C:GLY104 4.8 46.1 1.0 OD2 C:ASP83 4.8 63.0 1.0 O C:ASP83 5.0 45.7 1.0 CE1 C:HIS137 5.0 37.8 1.0

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


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 S-Beta-D-Thiogalactopyranosyl Beta-D- Glucopyranoside Derivative (Stgd) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:23.5 occ:1.00 O D:HOH403 2.2 28.3 1.0 O D:TYR125 2.4 21.7 1.0 OD1 D:ASN127 2.4 20.7 1.0 OD2 D:ASP132 2.4 30.0 1.0 OD1 D:ASP123 2.4 23.1 1.0 O D:HOH450 2.5 26.4 1.0 OD2 D:ASP123 2.6 21.2 1.0 CG D:ASP123 2.8 19.0 1.0 CG D:ASP132 3.5 29.4 1.0 C D:TYR125 3.5 24.8 1.0 CG D:ASN127 3.6 30.7 1.0 OD1 D:ASP132 3.9 28.2 1.0 N D:ASN127 4.1 26.9 1.0 CB D:ASN127 4.2 26.1 1.0 CA D:TYR125 4.2 21.7 1.0 N D:TYR125 4.3 22.4 1.0 MN D:MN302 4.3 42.9 1.0 O D:HOH402 4.3 24.4 1.0 CB D:ASP123 4.4 21.4 1.0 CB D:TYR125 4.5 23.1 1.0 N D:SER126 4.5 23.3 1.0 CA D:GLY104 4.6 25.9 1.0 ND2 D:ASN127 4.6 22.7 1.0 OD2 D:ASP83 4.7 30.3 1.0 CA D:SER126 4.7 23.7 1.0 CB D:ASP132 4.7 28.8 1.0 O D:GLY104 4.7 27.4 1.0 CD1 D:TYR125 4.7 27.1 1.0 O D:ASP83 4.8 26.2 1.0 CA D:ASN127 4.8 27.9 1.0 C D:SER126 4.8 28.2 1.0 CE1 D:HIS137 4.9 24.3 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