Manganese in PDB 6vav: Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings)

The structure of Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings), PDB code: 6vav 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)	27.09 / 1.85
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.760, 124.640, 128.375, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 22.5

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

Calcium

(Ca)

3 atoms

The binding sites of Manganese atom in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings) (pdb code 6vav). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings), PDB code: 6vav:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings)


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- Succinamoyl Derivative (Dings) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:38.6 occ:1.00 OD2 A:ASP123 2.0 17.6 1.0 OD1 A:ASP132 2.1 22.3 1.0 NE2 A:HIS137 2.1 24.1 1.0 O A:HOH426 2.1 18.3 1.0 OE2 A:GLU121 2.3 17.2 1.0 O A:HOH402 2.4 15.9 1.0 CE1 A:HIS137 3.0 23.2 1.0 CG A:ASP123 3.0 21.9 1.0 CG A:ASP132 3.1 23.9 1.0 CD2 A:HIS137 3.2 24.1 1.0 CD A:GLU121 3.4 29.6 1.0 CB A:ASP123 3.5 20.0 1.0 OD2 A:ASP132 3.5 20.8 1.0 OE1 A:GLU121 3.7 19.4 1.0 O A:HOH530 4.0 17.3 1.0 CA A:CA303 4.1 20.6 1.0 OD1 A:ASP123 4.2 23.5 1.0 ND1 A:HIS137 4.2 24.2 1.0 CB A:ASP132 4.2 25.1 1.0 CG A:HIS137 4.3 22.7 1.0 O A:HOH523 4.3 18.2 1.0 OG A:SER147 4.3 24.8 1.0 O A:VAL145 4.4 22.6 1.0 CA A:ASP132 4.6 24.5 1.0 CD A:PRO133 4.7 29.4 1.0 CG A:GLU121 4.7 23.4 1.0 CA A:ASP123 5.0 18.9 1.0

Manganese binding site 2 out of 3 in the Peanut Lectin Complexed with Divalent N-Beta-D-Galactopyranosyl-L- Succinamoyl Derivative (Dings)


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- Succinamoyl Derivative (Dings) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:40.4 occ:1.00 OD2 B:ASP123 2.1 18.9 1.0 OD1 B:ASP132 2.1 18.3 1.0 NE2 B:HIS137 2.2 23.7 1.0 O B:HOH403 2.3 19.7 1.0 O B:HOH405 2.3 22.6 1.0 OE2 B:GLU121 2.3 16.2 1.0 CG B:ASP132 3.1 21.9 1.0 CE1 B:HIS137 3.1 23.1 1.0 CG B:ASP123 3.1 19.9 1.0 CD2 B:HIS137 3.3 24.1 1.0 CD B:GLU121 3.3 31.0 1.0 CB B:ASP123 3.5 18.9 1.0 OD2 B:ASP132 3.5 19.7 1.0 OE1 B:GLU121 3.6 18.4 1.0 O B:HOH485 4.0 17.7 1.0 CA B:CA303 4.1 20.3 1.0 OD1 B:ASP123 4.2 20.9 1.0 O B:VAL145 4.3 24.0 1.0 OG B:SER147 4.3 23.0 1.0 ND1 B:HIS137 4.3 24.3 1.0 CB B:ASP132 4.3 20.9 1.0 O B:HOH541 4.3 18.5 1.0 CG B:HIS137 4.4 23.6 1.0 CG B:GLU121 4.7 18.5 1.0 CA B:ASP132 4.7 21.0 1.0 CD B:PRO133 4.7 22.3 1.0

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


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- Succinamoyl Derivative (Dings) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:36.8 occ:1.00 OE2 D:GLU121 2.0 21.8 1.0 O D:HOH420 2.1 23.3 1.0 OD2 D:ASP123 2.1 19.6 1.0 NE2 D:HIS137 2.2 22.4 1.0 OD1 D:ASP132 2.3 27.5 1.0 O D:HOH401 2.4 20.0 1.0 CD D:GLU121 3.0 26.9 1.0 CG D:ASP123 3.1 20.6 1.0 CE1 D:HIS137 3.1 22.4 1.0 CD2 D:HIS137 3.2 23.0 1.0 CG D:ASP132 3.3 25.3 1.0 OE1 D:GLU121 3.3 23.4 1.0 CB D:ASP123 3.4 19.2 1.0 OD2 D:ASP132 3.8 21.8 1.0 OG D:SER147 4.1 24.3 1.0 O D:HOH414 4.1 25.0 1.0 CA D:CA303 4.1 24.4 1.0 OD1 D:ASP123 4.2 21.4 1.0 ND1 D:HIS137 4.3 23.0 1.0 CG D:HIS137 4.3 22.3 1.0 O D:VAL145 4.3 24.7 1.0 CG D:GLU121 4.3 21.4 1.0 O D:HOH417 4.4 21.8 1.0 CB D:ASP132 4.5 24.9 1.0 CD D:PRO133 4.8 27.2 1.0 CA D:ASP132 4.9 23.4 1.0 CA D:ASP123 5.0 18.2 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