Calcium in PDB 6vc3: Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg)

The structure of Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg), PDB code: 6vc3 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)	49.03 / 1.95
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.190, 125.418, 128.112, 90.00, 90.00, 90.00
R / Rfree (%)	26.7 / 28.3

The structure of Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg) 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 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg) (pdb code 6vc3). 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 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg), PDB code: 6vc3:
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 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg)


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 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:26.7 occ:1.00 O A:TYR125 2.2 27.4 1.0 O A:HOH477 2.3 16.5 1.0 O A:HOH415 2.3 15.8 1.0 OD2 A:ASP132 2.3 32.4 1.0 OD1 A:ASN127 2.4 37.4 1.0 OD1 A:ASP123 2.6 29.8 1.0 OD2 A:ASP123 2.6 24.3 1.0 CG A:ASP123 2.9 25.0 1.0 C A:TYR125 3.4 27.0 1.0 CG A:ASP132 3.4 31.8 1.0 CG A:ASN127 3.4 41.3 1.0 N A:ASN127 3.9 22.6 1.0 CB A:ASN127 3.9 16.4 1.0 OD1 A:ASP132 3.9 30.2 1.0 MN A:MN302 4.1 39.6 1.0 CA A:TYR125 4.2 22.8 1.0 N A:TYR125 4.3 22.8 1.0 N A:SER126 4.3 23.3 1.0 O A:HOH405 4.4 16.8 1.0 CB A:TYR125 4.4 24.2 1.0 CB A:ASP123 4.4 23.4 1.0 CA A:SER126 4.5 24.0 1.0 CA A:ASN127 4.5 21.6 1.0 C A:SER126 4.6 27.2 1.0 CB A:ASP132 4.6 30.9 1.0 CD1 A:TYR125 4.6 27.6 1.0 ND2 A:ASN127 4.6 36.3 1.0 OD2 A:ASP83 4.7 33.4 1.0 CA A:GLY104 4.7 21.5 1.0 O A:ASP83 4.8 27.8 1.0

Calcium binding site 2 out of 4 in the Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg)


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 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg) within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:25.1 occ:1.00 OD2 B:ASP132 2.3 15.6 1.0 O B:HOH434 2.4 20.1 1.0 O B:TYR125 2.5 21.2 1.0 O B:HOH416 2.5 28.0 1.0 OD1 B:ASP123 2.5 26.7 1.0 OD1 B:ASN127 2.6 24.9 1.0 OD2 B:ASP123 2.7 24.2 1.0 CG B:ASP123 2.9 22.4 1.0 CG B:ASP132 3.4 16.9 1.0 CG B:ASN127 3.6 32.4 1.0 C B:TYR125 3.6 23.0 1.0 OD1 B:ASP132 3.8 16.2 1.0 CB B:ASN127 3.9 14.8 1.0 N B:ASN127 4.0 23.7 1.0 O B:HOH443 4.0 16.5 1.0 MN B:MN302 4.1 37.0 1.0 CB B:ASP123 4.4 22.5 1.0 CA B:GLY104 4.4 21.0 1.0 CA B:TYR125 4.5 21.0 1.0 N B:SER126 4.6 19.5 1.0 CB B:ASP132 4.6 20.9 1.0 N B:TYR125 4.6 21.4 1.0 CA B:ASN127 4.6 22.1 1.0 CA B:SER126 4.7 20.1 1.0 CB B:TYR125 4.7 23.2 1.0 C B:SER126 4.7 27.6 1.0 ND2 B:ASN127 4.8 26.5 1.0 O B:GLY104 4.8 22.7 1.0 OD2 B:ASP83 4.9 24.4 1.0 O B:ASP83 4.9 29.7 1.0 CE1 B:HIS137 5.0 21.6 1.0

Calcium binding site 3 out of 4 in the Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg)


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 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg) within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:35.3 occ:1.00 O C:HOH418 2.2 45.0 1.0 OD2 C:ASP132 2.2 70.3 1.0 O C:TYR125 2.4 62.9 1.0 OD2 C:ASP123 2.4 55.0 1.0 OD1 C:ASN127 2.6 85.5 1.0 OD1 C:ASP123 2.6 52.2 1.0 O C:HOH411 2.7 25.7 1.0 CG C:ASP123 2.8 50.4 1.0 CG C:ASP132 3.3 66.2 1.0 C C:TYR125 3.5 63.4 1.0 CG C:ASN127 3.6 90.2 1.0 OD1 C:ASP132 3.8 65.9 1.0 N C:ASN127 3.9 65.0 1.0 CB C:ASN127 4.0 67.7 1.0 MN C:MN301 4.1 47.5 1.0 O C:HOH401 4.2 32.2 1.0 CA C:TYR125 4.3 58.8 1.0 CB C:ASP123 4.3 39.7 1.0 N C:TYR125 4.4 57.4 1.0 N C:SER126 4.4 60.8 1.0 CB C:TYR125 4.4 61.4 1.0 CA C:SER126 4.5 60.7 1.0 CB C:ASP132 4.5 60.6 1.0 CA C:ASN127 4.6 66.1 1.0 CA C:GLY104 4.6 92.8 1.0 C C:SER126 4.6 66.0 1.0 OD2 C:ASP83 4.6 66.9 1.0 CD2 C:TYR125 4.7 66.4 1.0 O C:ASP83 4.8 55.1 1.0 ND2 C:ASN127 4.8 81.5 1.0 CE1 C:HIS137 4.8 36.4 1.0 O C:GLY104 4.9 95.1 1.0 NE2 C:HIS137 5.0 35.9 1.0

Calcium binding site 4 out of 4 in the Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg)


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 6-Deoxy-6- S-Propynyl-Beta-D-Glucopyranoside (Stg) within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca303 b:30.2 occ:1.00 O D:HOH445 2.3 19.9 1.0 OD2 D:ASP132 2.4 30.9 1.0 OD1 D:ASP123 2.4 27.7 1.0 OD1 D:ASN127 2.4 25.4 1.0 O D:HOH407 2.5 31.5 1.0 OD2 D:ASP123 2.5 32.8 1.0 O D:TYR125 2.5 29.6 1.0 CG D:ASP123 2.8 27.9 1.0 CG D:ASP132 3.5 32.1 1.0 CG D:ASN127 3.6 36.6 1.0 C D:TYR125 3.6 31.0 1.0 OD1 D:ASP132 3.9 31.8 1.0 N D:ASN127 4.1 33.1 1.0 CB D:ASN127 4.2 33.7 1.0 O D:HOH401 4.2 22.7 1.0 CB D:ASP123 4.3 24.5 1.0 CA D:TYR125 4.4 27.5 1.0 MN D:MN302 4.4 46.0 1.0 CA D:GLY104 4.4 27.9 1.0 N D:TYR125 4.4 26.9 1.0 CB D:TYR125 4.6 30.2 1.0 N D:SER126 4.6 28.6 1.0 ND2 D:ASN127 4.7 27.3 1.0 O D:GLY104 4.7 33.0 1.0 CB D:ASP132 4.7 32.6 1.0 CA D:SER126 4.8 28.8 1.0 O D:ASP83 4.8 26.3 1.0 CA D:ASN127 4.8 33.8 1.0 C D:SER126 4.8 34.4 1.0 CD2 D:TYR125 4.9 35.0 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