Manganese 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:

Calcium

(Ca)

4 atoms

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Peanut Lectin Complexed with S-Beta-D-Thiogalactopyranosyl Beta-D- Glucopyranoside Derivative (Stgd), PDB code: 6vc4:
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 Beta-D- Glucopyranoside Derivative (Stgd)


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 Beta-D- Glucopyranoside Derivative (Stgd) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:35.8 occ:1.00 NE2 A:HIS137 2.1 25.4 1.0 OD2 A:ASP123 2.1 21.1 1.0 O A:HOH442 2.2 20.8 1.0 OE2 A:GLU121 2.3 16.4 1.0 OD1 A:ASP132 2.3 26.5 1.0 O A:HOH403 2.5 20.9 1.0 CE1 A:HIS137 3.0 24.5 1.0 CG A:ASP123 3.1 22.5 1.0 CD2 A:HIS137 3.1 25.8 1.0 CG A:ASP132 3.2 27.9 1.0 CD A:GLU121 3.2 25.1 1.0 CB A:ASP123 3.4 20.1 1.0 OE1 A:GLU121 3.5 17.5 1.0 OD2 A:ASP132 3.7 23.3 1.0 ND1 A:HIS137 4.1 25.4 1.0 O A:HOH413 4.2 16.4 1.0 CA A:CA303 4.2 22.8 1.0 CG A:HIS137 4.2 24.2 1.0 OD1 A:ASP123 4.2 27.7 1.0 OG A:SER147 4.3 34.0 1.0 O A:HOH482 4.3 22.9 1.0 CB A:ASP132 4.4 25.9 1.0 O A:VAL145 4.4 25.5 1.0 CG A:GLU121 4.6 22.2 1.0 CD A:PRO133 4.6 28.0 1.0 CA A:ASP132 4.7 26.6 1.0 CA A:ASP123 4.9 20.0 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:34.7 occ:1.00 OD2 B:ASP123 2.0 19.0 1.0 O B:HOH432 2.1 19.7 1.0 NE2 B:HIS137 2.1 23.0 1.0 O B:HOH458 2.1 22.4 1.0 OD1 B:ASP132 2.2 18.5 1.0 OE2 B:GLU121 2.3 14.0 1.0 CE1 B:HIS137 3.0 22.1 1.0 CG B:ASP123 3.1 19.7 1.0 CG B:ASP132 3.2 22.9 1.0 CD2 B:HIS137 3.2 23.8 1.0 CD B:GLU121 3.3 37.0 1.0 CB B:ASP123 3.6 18.5 1.0 OE1 B:GLU121 3.6 17.3 1.0 OD2 B:ASP132 3.6 22.6 1.0 O B:HOH418 4.0 20.7 1.0 CA B:CA303 4.1 23.5 1.0 O B:VAL145 4.2 25.1 1.0 OD1 B:ASP123 4.2 20.5 1.0 OG B:SER147 4.2 25.5 1.0 ND1 B:HIS137 4.2 23.9 1.0 CG B:HIS137 4.3 23.3 1.0 CB B:ASP132 4.4 22.6 1.0 O B:HOH461 4.4 22.4 1.0 CG B:GLU121 4.6 26.5 1.0 CA B:ASP132 4.7 23.4 1.0 CD B:PRO133 4.8 24.4 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:54.8 occ:1.00 O C:HOH417 2.0 32.6 1.0 OE2 C:GLU121 2.2 32.2 1.0 OD1 C:ASP132 2.2 52.9 1.0 OD2 C:ASP123 2.2 34.2 1.0 NE2 C:HIS137 2.3 38.3 1.0 O C:HOH402 2.4 31.8 1.0 CG C:ASP132 3.2 52.5 1.0 CD C:GLU121 3.2 47.1 1.0 CG C:ASP123 3.2 37.3 1.0 CE1 C:HIS137 3.3 37.8 1.0 CD2 C:HIS137 3.3 38.9 1.0 OE1 C:GLU121 3.5 36.6 1.0 CB C:ASP123 3.6 32.0 1.0 OD2 C:ASP132 3.6 55.8 1.0 O C:HOH413 4.1 35.4 1.0 OG C:SER147 4.2 35.0 1.0 O C:VAL145 4.2 43.5 1.0 O C:HOH412 4.2 38.9 1.0 CA C:CA303 4.2 40.8 1.0 OD1 C:ASP123 4.4 37.5 1.0 CB C:ASP132 4.4 48.0 1.0 ND1 C:HIS137 4.4 38.1 1.0 CG C:HIS137 4.5 36.6 1.0 CG C:GLU121 4.5 34.3 1.0 CD C:PRO133 4.7 46.1 1.0 CA C:ASP132 4.7 46.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:42.9 occ:1.00 O D:HOH416 2.1 21.6 1.0 OD2 D:ASP123 2.2 21.2 1.0 NE2 D:HIS137 2.2 24.5 1.0 OE2 D:GLU121 2.2 21.4 1.0 OD1 D:ASP132 2.2 28.2 1.0 O D:HOH402 2.4 24.4 1.0 CD2 D:HIS137 3.1 24.8 1.0 CG D:ASP123 3.1 19.0 1.0 CD D:GLU121 3.2 28.2 1.0 CE1 D:HIS137 3.2 24.3 1.0 CG D:ASP132 3.2 29.4 1.0 OE1 D:GLU121 3.5 22.5 1.0 CB D:ASP123 3.5 21.4 1.0 OD2 D:ASP132 3.7 30.0 1.0 O D:HOH450 4.0 26.4 1.0 OG D:SER147 4.1 28.7 1.0 OD1 D:ASP123 4.2 23.1 1.0 O D:VAL145 4.3 26.0 1.0 CA D:CA303 4.3 23.5 1.0 CG D:HIS137 4.3 24.1 1.0 O D:HOH410 4.3 24.5 1.0 ND1 D:HIS137 4.3 24.9 1.0 CB D:ASP132 4.4 28.8 1.0 CG D:GLU121 4.5 20.6 1.0 CD D:PRO133 4.7 33.7 1.0 CA D:ASP132 4.7 27.4 1.0 CG2 D:THR150 5.0 23.5 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