Manganese in PDB 6vaw: Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs)

The structure of Peanut Lectin Complexed with N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs), PDB code: 6vaw 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)	45.42 / 1.75
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.222, 125.052, 126.844, 90.00, 90.00, 90.00
R / Rfree (%)	21.2 / 23.2

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

Calcium

(Ca)

4 atoms

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

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


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 N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:37.3 occ:1.00 OD2 A:ASP123 2.1 19.9 1.0 NE2 A:HIS137 2.1 27.7 1.0 OE2 A:GLU121 2.1 18.8 1.0 OD1 A:ASP132 2.2 30.1 1.0 O A:HOH452 2.3 24.3 1.0 O A:HOH401 2.5 21.5 1.0 CE1 A:HIS137 3.0 27.2 1.0 CG A:ASP123 3.1 22.2 1.0 CD2 A:HIS137 3.1 28.1 1.0 CG A:ASP132 3.2 31.5 1.0 CD A:GLU121 3.2 32.3 1.0 CB A:ASP123 3.5 21.9 1.0 OE1 A:GLU121 3.6 22.7 1.0 OD2 A:ASP132 3.7 28.3 1.0 O A:HOH426 4.1 21.2 1.0 CA A:CA303 4.2 23.6 1.0 ND1 A:HIS137 4.2 27.8 1.0 OD1 A:ASP123 4.2 23.4 1.0 CG A:HIS137 4.2 26.1 1.0 OG A:SER147 4.3 27.7 1.0 CB A:ASP132 4.3 26.6 1.0 O A:VAL145 4.4 26.7 1.0 O A:HOH504 4.4 27.3 1.0 CG A:GLU121 4.5 25.1 1.0 CD A:PRO133 4.6 28.7 1.0 CA A:ASP132 4.7 27.1 1.0

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


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 N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:34.7 occ:1.00 O B:HOH423 2.1 25.8 1.0 OD2 B:ASP123 2.2 17.8 1.0 NE2 B:HIS137 2.2 22.1 1.0 OE2 B:GLU121 2.2 18.8 1.0 OD1 B:ASP132 2.2 21.5 1.0 O B:HOH422 2.2 23.0 1.0 CE1 B:HIS137 3.1 20.8 1.0 CG B:ASP123 3.2 20.4 1.0 CD B:GLU121 3.2 37.0 1.0 CD2 B:HIS137 3.2 22.2 1.0 CG B:ASP132 3.2 26.3 1.0 OE1 B:GLU121 3.5 23.3 1.0 CB B:ASP123 3.6 18.8 1.0 OD2 B:ASP132 3.7 24.8 1.0 O B:HOH403 4.1 17.7 1.0 OG B:SER147 4.1 23.8 1.0 O B:VAL145 4.2 26.0 1.0 CA B:CA303 4.2 21.3 1.0 OD1 B:ASP123 4.3 20.0 1.0 ND1 B:HIS137 4.3 21.8 1.0 CG B:HIS137 4.3 20.6 1.0 O B:HOH517 4.4 22.6 1.0 CB B:ASP132 4.4 24.6 1.0 CG B:GLU121 4.6 22.0 1.0 CD B:PRO133 4.7 27.1 1.0 CA B:ASP132 4.7 24.2 1.0

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


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 N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:55.1 occ:1.00 O C:HOH418 2.0 36.1 1.0 OE2 C:GLU121 2.1 30.0 1.0 OD1 C:ASP132 2.2 48.5 1.0 OD2 C:ASP123 2.3 43.4 1.0 NE2 C:HIS137 2.3 38.7 1.0 O C:HOH404 2.4 34.9 1.0 CD C:GLU121 3.1 46.5 1.0 CG C:ASP132 3.2 49.1 1.0 CE1 C:HIS137 3.2 38.4 1.0 CG C:ASP123 3.3 43.5 1.0 CD2 C:HIS137 3.4 39.3 1.0 OE1 C:GLU121 3.5 35.6 1.0 CB C:ASP123 3.5 34.8 1.0 OD2 C:ASP132 3.6 52.0 1.0 O C:HOH409 4.1 43.2 1.0 OG C:SER147 4.2 46.2 1.0 O C:VAL145 4.2 45.3 1.0 CA C:CA303 4.2 42.7 1.0 CB C:ASP132 4.4 48.0 1.0 O C:HOH437 4.4 43.1 1.0 ND1 C:HIS137 4.4 38.9 1.0 OD1 C:ASP123 4.4 44.3 1.0 CG C:GLU121 4.4 30.7 1.0 CG C:HIS137 4.5 37.3 1.0 CA C:ASP132 4.8 46.9 1.0 CD C:PRO133 4.8 46.8 1.0

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


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 N-Beta-D-Galactopyranosyl-L-Succinamoyl Derivative (Ngs) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn302 b:36.6 occ:1.00 O D:HOH430 2.1 27.1 1.0 OD2 D:ASP123 2.1 22.6 1.0 OE2 D:GLU121 2.2 21.5 1.0 OD1 D:ASP132 2.2 31.3 1.0 NE2 D:HIS137 2.2 24.9 1.0 O D:HOH402 2.3 21.9 1.0 CG D:ASP123 3.1 21.1 1.0 CE1 D:HIS137 3.1 25.3 1.0 CD D:GLU121 3.2 32.7 1.0 CG D:ASP132 3.2 28.8 1.0 CD2 D:HIS137 3.2 24.8 1.0 CB D:ASP123 3.5 21.4 1.0 OE1 D:GLU121 3.5 26.9 1.0 OD2 D:ASP132 3.7 29.1 1.0 O D:HOH418 4.0 30.6 1.0 CA D:CA303 4.1 25.8 1.0 OG D:SER147 4.2 27.4 1.0 OD1 D:ASP123 4.2 21.8 1.0 O D:VAL145 4.3 26.5 1.0 ND1 D:HIS137 4.3 26.2 1.0 CG D:HIS137 4.3 24.2 1.0 O D:HOH422 4.4 31.4 1.0 CB D:ASP132 4.4 27.3 1.0 CG D:GLU121 4.5 23.5 1.0 CD D:PRO133 4.7 34.7 1.0 CA D:ASP132 4.7 26.4 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