Manganese 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:

Calcium

(Ca)

4 atoms

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

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:35.2 occ:1.00 NE2 A:HIS137 2.1 26.6 1.0 OD2 A:ASP123 2.1 24.4 1.0 O A:HOH474 2.1 20.5 1.0 OE2 A:GLU121 2.2 18.6 1.0 OD1 A:ASP132 2.2 31.7 1.0 O A:HOH406 2.4 18.4 1.0 CE1 A:HIS137 3.0 26.0 1.0 CD2 A:HIS137 3.1 26.7 1.0 CG A:ASP123 3.1 25.5 1.0 CG A:ASP132 3.1 32.7 1.0 CD A:GLU121 3.2 29.1 1.0 CB A:ASP123 3.5 22.6 1.0 OE1 A:GLU121 3.5 20.8 1.0 OD2 A:ASP132 3.6 27.1 1.0 O A:HOH453 4.1 22.2 1.0 ND1 A:HIS137 4.2 26.8 1.0 CA A:CA303 4.2 25.5 1.0 CG A:HIS137 4.2 25.4 1.0 O A:HOH555 4.2 22.5 1.0 OD1 A:ASP123 4.2 27.8 1.0 OG A:SER147 4.3 27.8 1.0 CB A:ASP132 4.3 28.1 1.0 O A:VAL145 4.4 24.6 1.0 CG A:GLU121 4.5 23.0 1.0 CD A:PRO133 4.7 27.4 1.0 CA A:ASP132 4.7 28.2 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:31.5 occ:1.00 O B:HOH425 2.1 27.1 1.0 OD2 B:ASP123 2.1 16.8 1.0 O B:HOH403 2.2 19.9 1.0 OD1 B:ASP132 2.2 22.8 1.0 NE2 B:HIS137 2.2 24.2 1.0 OE2 B:GLU121 2.3 17.7 1.0 CG B:ASP123 3.1 19.3 1.0 CE1 B:HIS137 3.2 23.8 1.0 CG B:ASP132 3.2 25.4 1.0 CD B:GLU121 3.2 33.0 1.0 CD2 B:HIS137 3.3 24.8 1.0 OE1 B:GLU121 3.5 17.8 1.0 CB B:ASP123 3.6 18.4 1.0 OD2 B:ASP132 3.6 24.0 1.0 O B:HOH441 4.0 20.7 1.0 O B:VAL145 4.2 24.6 1.0 OG B:SER147 4.2 23.4 1.0 CA B:CA303 4.2 23.7 1.0 O B:HOH514 4.2 22.2 1.0 OD1 B:ASP123 4.2 19.6 1.0 ND1 B:HIS137 4.3 25.0 1.0 CG B:HIS137 4.4 23.5 1.0 CB B:ASP132 4.4 22.9 1.0 CG B:GLU121 4.6 20.6 1.0 CA B:ASP132 4.7 24.4 1.0 CD B:PRO133 4.8 25.5 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:48.6 occ:1.00 O C:HOH445 2.0 40.2 1.0 OE2 C:GLU121 2.1 35.8 1.0 OD1 C:ASP132 2.2 50.8 1.0 OD2 C:ASP123 2.2 44.3 1.0 O C:HOH409 2.4 34.6 1.0 NE2 C:HIS137 2.4 37.2 1.0 CD C:GLU121 3.1 48.8 1.0 CG C:ASP132 3.1 49.9 1.0 CG C:ASP123 3.2 43.3 1.0 CE1 C:HIS137 3.4 36.9 1.0 CD2 C:HIS137 3.4 37.9 1.0 OE1 C:GLU121 3.5 39.5 1.0 CB C:ASP123 3.6 33.3 1.0 OD2 C:ASP132 3.6 52.6 1.0 O C:HOH412 4.1 41.1 1.0 O C:VAL145 4.2 41.7 1.0 OG C:SER147 4.2 42.4 1.0 O C:HOH418 4.2 42.3 1.0 CA C:CA303 4.2 49.3 1.0 CB C:ASP132 4.4 46.2 1.0 OD1 C:ASP123 4.4 43.9 1.0 CG C:GLU121 4.5 32.0 1.0 CG C:HIS137 4.5 36.1 1.0 ND1 C:HIS137 4.5 37.4 1.0 CA C:ASP132 4.7 44.9 1.0 CD C:PRO133 4.8 45.7 1.0

Manganese 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 Manganese with other atoms in the Mn 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:Mn302 b:36.3 occ:1.00 O D:HOH402 2.0 23.5 1.0 OE2 D:GLU121 2.1 22.9 1.0 OD2 D:ASP123 2.1 24.8 1.0 NE2 D:HIS137 2.2 26.0 1.0 OD1 D:ASP132 2.2 30.7 1.0 O D:HOH401 2.3 21.2 1.0 CG D:ASP123 3.1 18.8 1.0 CD D:GLU121 3.1 32.3 1.0 CE1 D:HIS137 3.2 26.0 1.0 CD2 D:HIS137 3.2 26.2 1.0 CG D:ASP132 3.2 29.2 1.0 CB D:ASP123 3.5 23.2 1.0 OE1 D:GLU121 3.5 24.0 1.0 OD2 D:ASP132 3.7 27.6 1.0 O D:HOH424 4.1 25.9 1.0 CA D:CA303 4.1 26.2 1.0 OG D:SER147 4.1 31.4 1.0 OD1 D:ASP123 4.2 19.3 1.0 O D:VAL145 4.2 26.0 1.0 CG D:HIS137 4.3 25.8 1.0 O D:HOH417 4.3 23.1 1.0 ND1 D:HIS137 4.3 26.8 1.0 CB D:ASP132 4.4 27.1 1.0 CG D:GLU121 4.4 19.6 1.0 CA D:ASP132 4.7 25.3 1.0 CD D:PRO133 4.8 33.6 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