Manganese in PDB 6v95: Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt)

The structure of Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt), PDB code: 6v95 was solved by L.H.Otero, E.D.Primo, A.J.Cagnoni, 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)	26.06 / 1.78
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.941, 124.553, 127.484, 90.00, 90.00, 90.00
R / Rfree (%)	22.2 / 24.3

The structure of Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt) (pdb code 6v95). 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 N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt), PDB code: 6v95:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt)


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 N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:33.8 occ:1.00 NE2 A:HIS137 2.1 27.9 1.0 O A:HOH471 2.1 20.0 1.0 OD1 A:ASP132 2.1 29.4 1.0 OD2 A:ASP123 2.2 20.2 1.0 OE2 A:GLU121 2.3 16.9 1.0 O A:HOH415 2.4 19.5 1.0 CE1 A:HIS137 3.0 27.3 1.0 CD2 A:HIS137 3.1 28.1 1.0 CG A:ASP132 3.1 31.2 1.0 CG A:ASP123 3.2 27.0 1.0 CD A:GLU121 3.3 28.8 1.0 CB A:ASP123 3.5 21.0 1.0 OE1 A:GLU121 3.6 18.9 1.0 OD2 A:ASP132 3.6 30.3 1.0 O A:HOH406 4.1 22.2 1.0 ND1 A:HIS137 4.2 28.2 1.0 CA A:CA303 4.2 25.2 1.0 CG A:HIS137 4.2 26.6 1.0 O A:HOH508 4.2 24.8 1.0 OG A:SER147 4.2 26.6 1.0 OD1 A:ASP123 4.3 29.0 1.0 CB A:ASP132 4.3 26.5 1.0 O A:VAL145 4.3 24.3 1.0 CD A:PRO133 4.6 26.6 1.0 CG A:GLU121 4.6 17.0 1.0 CA A:ASP132 4.7 26.0 1.0

Manganese binding site 2 out of 4 in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt)


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 N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:32.9 occ:1.00 OD2 B:ASP123 2.1 18.0 1.0 O B:HOH415 2.1 24.4 1.0 O B:HOH423 2.2 21.5 1.0 NE2 B:HIS137 2.2 20.8 1.0 OD1 B:ASP132 2.2 21.8 1.0 OE2 B:GLU121 2.2 14.8 1.0 CG B:ASP123 3.1 21.0 1.0 CE1 B:HIS137 3.1 20.3 1.0 CG B:ASP132 3.2 24.8 1.0 CD2 B:HIS137 3.2 21.3 1.0 CD B:GLU121 3.2 33.4 1.0 CB B:ASP123 3.5 18.7 1.0 OE1 B:GLU121 3.6 18.2 1.0 OD2 B:ASP132 3.7 26.6 1.0 O B:HOH402 4.0 19.3 1.0 OG B:SER147 4.2 22.3 1.0 O B:VAL145 4.2 23.7 1.0 CA B:CA303 4.2 22.9 1.0 OD1 B:ASP123 4.2 22.4 1.0 ND1 B:HIS137 4.3 22.2 1.0 O B:HOH506 4.3 21.6 1.0 CG B:HIS137 4.3 21.0 1.0 CB B:ASP132 4.4 21.7 1.0 CG B:GLU121 4.6 21.9 1.0 CD B:PRO133 4.7 24.1 1.0 CA B:ASP132 4.7 22.0 1.0

Manganese binding site 3 out of 4 in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt)


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 N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:53.1 occ:1.00 O C:HOH432 2.0 31.4 1.0 OE2 C:GLU121 2.1 32.4 1.0 OD1 C:ASP132 2.2 41.6 1.0 NE2 C:HIS137 2.2 40.3 1.0 OD2 C:ASP123 2.2 41.8 1.0 O C:HOH407 2.4 34.0 1.0 CD C:GLU121 3.1 44.3 1.0 CE1 C:HIS137 3.2 40.0 1.0 CG C:ASP132 3.2 42.1 1.0 CG C:ASP123 3.2 41.6 1.0 CD2 C:HIS137 3.3 40.6 1.0 OE1 C:GLU121 3.4 27.9 1.0 CB C:ASP123 3.5 36.1 1.0 OD2 C:ASP132 3.6 43.4 1.0 O C:HOH406 4.2 48.2 1.0 OG C:SER147 4.2 46.2 1.0 O C:VAL145 4.2 46.8 1.0 CA C:CA303 4.2 44.4 1.0 O C:HOH424 4.2 45.8 1.0 OD1 C:ASP123 4.4 39.9 1.0 ND1 C:HIS137 4.4 40.3 1.0 CG C:HIS137 4.4 38.2 1.0 CB C:ASP132 4.4 46.4 1.0 CG C:GLU121 4.5 28.8 1.0 CD C:PRO133 4.8 47.4 1.0 CA C:ASP132 4.8 45.2 1.0

Manganese binding site 4 out of 4 in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt)


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 N-Beta-D-Galactopyranosyl-L- Tartaramidoyl Derivative (Dingt) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:35.6 occ:1.00 O D:HOH401 2.0 21.6 1.0 OE2 D:GLU121 2.1 20.9 1.0 NE2 D:HIS137 2.2 23.1 1.0 OD2 D:ASP123 2.2 20.0 1.0 OD1 D:ASP132 2.3 29.4 1.0 O D:HOH406 2.3 21.4 1.0 CG D:ASP123 3.1 17.8 1.0 CE1 D:HIS137 3.1 23.2 1.0 CD D:GLU121 3.1 31.5 1.0 CD2 D:HIS137 3.2 23.3 1.0 CG D:ASP132 3.3 29.3 1.0 CB D:ASP123 3.4 20.3 1.0 OE1 D:GLU121 3.5 24.4 1.0 OD2 D:ASP132 3.8 26.4 1.0 OG D:SER147 4.1 25.9 1.0 O D:HOH431 4.1 26.0 1.0 CA D:CA303 4.2 26.8 1.0 OD1 D:ASP123 4.2 20.5 1.0 O D:VAL145 4.3 25.2 1.0 ND1 D:HIS137 4.3 24.2 1.0 CG D:HIS137 4.3 23.4 1.0 O D:HOH417 4.4 25.5 1.0 CG D:GLU121 4.4 21.4 1.0 CB D:ASP132 4.5 26.9 1.0 CD D:PRO133 4.7 30.8 1.0 CA D:ASP132 4.8 25.2 1.0 CA D:ASP123 5.0 20.1 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