Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese 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 Manganese binding site number: 1; 2; 3; 4;

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:39.6 occ:1.00 OD2 A:ASP123 2.1 24.3 1.0 O A:HOH405 2.1 16.8 1.0 OD1 A:ASP132 2.1 30.2 1.0 NE2 A:HIS137 2.2 23.2 1.0 O A:HOH439 2.2 18.2 1.0 OE2 A:GLU121 2.3 24.2 1.0 CG A:ASP123 3.0 25.0 1.0 CE1 A:HIS137 3.1 23.5 1.0 CG A:ASP132 3.1 31.8 1.0 CD A:GLU121 3.2 23.6 1.0 CD2 A:HIS137 3.3 24.7 1.0 CB A:ASP123 3.4 23.4 1.0 OE1 A:GLU121 3.5 12.0 1.0 OD2 A:ASP132 3.6 32.4 1.0 O A:HOH477 4.0 16.5 1.0 OD1 A:ASP123 4.1 29.8 1.0 CA A:CA303 4.1 26.7 1.0 O A:HOH499 4.2 25.5 1.0 ND1 A:HIS137 4.3 24.1 1.0 CB A:ASP132 4.3 30.9 1.0 CG A:HIS137 4.4 23.8 1.0 O A:VAL145 4.4 28.2 1.0 OG A:SER147 4.6 25.5 1.0 CG A:GLU121 4.6 22.9 1.0 CA A:ASP132 4.7 30.5 1.0 CD A:PRO133 4.8 31.8 1.0 CA A:ASP123 4.9 21.8 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:37.0 occ:1.00 O B:HOH443 2.0 16.5 1.0 OD2 B:ASP123 2.0 24.2 1.0 OD1 B:ASP132 2.1 16.2 1.0 O B:HOH415 2.2 38.4 1.0 NE2 B:HIS137 2.3 21.6 1.0 OE2 B:GLU121 2.4 15.0 1.0 CE1 B:HIS137 3.1 21.6 1.0 CG B:ASP132 3.1 16.9 1.0 CG B:ASP123 3.1 22.4 1.0 CD B:GLU121 3.4 33.7 1.0 CD2 B:HIS137 3.5 23.0 1.0 OD2 B:ASP132 3.6 15.6 1.0 OE1 B:GLU121 3.6 20.4 1.0 CB B:ASP123 3.7 22.5 1.0 O B:HOH434 4.0 20.1 1.0 CA B:CA303 4.1 25.1 1.0 O B:VAL145 4.1 20.6 1.0 O B:HOH497 4.1 26.3 1.0 OD1 B:ASP123 4.2 26.7 1.0 CB B:ASP132 4.3 20.9 1.0 ND1 B:HIS137 4.3 22.9 1.0 OG B:SER147 4.3 39.7 1.0 CG B:HIS137 4.5 22.1 1.0 CA B:ASP132 4.7 21.4 1.0 CD B:PRO133 4.7 26.4 1.0 CG B:GLU121 4.8 28.1 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn301 b:47.5 occ:1.00 O C:HOH415 2.0 22.0 1.0 OD1 C:ASP132 2.0 65.9 1.0 NE2 C:HIS137 2.3 35.9 1.0 OD2 C:ASP123 2.3 55.0 1.0 OE2 C:GLU121 2.3 28.9 1.0 O C:HOH401 2.6 32.2 1.0 CG C:ASP132 3.1 66.2 1.0 CD2 C:HIS137 3.2 36.9 1.0 CE1 C:HIS137 3.3 36.4 1.0 CG C:ASP123 3.3 50.4 1.0 CD C:GLU121 3.3 42.5 1.0 OD2 C:ASP132 3.5 70.3 1.0 OE1 C:GLU121 3.6 25.6 1.0 CB C:ASP123 3.6 39.7 1.0 CA C:CA302 4.1 35.3 1.0 O C:HOH411 4.1 25.7 1.0 O C:VAL145 4.1 44.5 1.0 CB C:ASP132 4.2 60.6 1.0 OG C:SER147 4.4 31.2 1.0 CG C:HIS137 4.4 35.5 1.0 ND1 C:HIS137 4.4 36.6 1.0 OD1 C:ASP123 4.4 52.2 1.0 CA C:ASP132 4.6 58.9 1.0 CG C:GLU121 4.7 29.4 1.0 CD C:PRO133 4.7 55.8 1.0 O C:HOH457 5.0 44.6 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:46.0 occ:1.00 O D:HOH433 2.0 15.7 1.0 OE2 D:GLU121 2.1 16.1 1.0 OD1 D:ASP132 2.3 31.8 1.0 NE2 D:HIS137 2.3 26.0 1.0 OD2 D:ASP123 2.3 32.8 1.0 O D:HOH401 2.6 22.7 1.0 CD D:GLU121 3.1 21.2 1.0 CD2 D:HIS137 3.1 26.8 1.0 CG D:ASP123 3.3 27.9 1.0 CG D:ASP132 3.4 32.1 1.0 CE1 D:HIS137 3.4 26.1 1.0 OE1 D:GLU121 3.4 28.1 1.0 CB D:ASP123 3.6 24.5 1.0 OD2 D:ASP132 3.9 30.9 1.0 OG D:SER147 4.0 29.0 1.0 O D:HOH445 4.1 19.9 1.0 O D:VAL145 4.1 24.4 1.0 O D:HOH404 4.2 28.6 1.0 CG D:HIS137 4.3 26.8 1.0 CA D:CA303 4.4 30.2 1.0 CG D:GLU121 4.4 22.5 1.0 OD1 D:ASP123 4.4 27.7 1.0 ND1 D:HIS137 4.4 27.3 1.0 CB D:ASP132 4.5 32.6 1.0 CD D:PRO133 4.7 33.7 1.0 CA D:ASP132 4.8 31.3 1.0 CG2 D:THR150 4.9 29.4 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