Manganese in PDB 2dvf: Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal

The structure of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal, PDB code: 2dvf was solved by S.K.Natchiar, O.Srinivas, N.Mitra, A.Surolia, N.Jayaraman, M.Vijayan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.94 / 2.74
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.810, 124.060, 75.400, 90.00, 90.00, 90.00
R / Rfree (%)	20 / 26.3

The structure of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal (pdb code 2dvf). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal, PDB code: 2dvf:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:58.5 occ:1.00 OE2 A:GLU121 2.1 38.2 1.0 OD1 A:ASP132 2.2 47.5 1.0 NE2 A:HIS137 2.4 39.4 1.0 OD2 A:ASP123 2.5 42.1 1.0 CD A:GLU121 3.0 37.2 1.0 OE1 A:GLU121 3.3 39.4 1.0 CD2 A:HIS137 3.3 33.8 1.0 CG A:ASP132 3.3 47.1 1.0 CG A:ASP123 3.4 40.6 1.0 CE1 A:HIS137 3.4 36.1 1.0 OG A:SER147 3.6 38.3 1.0 O A:VAL145 3.7 34.5 1.0 CB A:ASP123 3.8 38.5 1.0 OD2 A:ASP132 4.0 42.2 1.0 CG A:GLU121 4.4 33.3 1.0 CB A:ASP132 4.5 45.3 1.0 CD A:PRO133 4.5 44.9 1.0 OD1 A:ASP123 4.5 39.3 1.0 CG A:HIS137 4.5 39.3 1.0 ND1 A:HIS137 4.5 37.2 1.0 CA A:ASP132 4.6 46.8 1.0 CB A:SER147 4.8 38.4 1.0 CA A:CA237 4.9 37.6 1.0 C A:VAL145 4.9 34.5 1.0 CG2 A:THR150 4.9 22.3 1.0 N A:SER147 5.0 47.4 1.0

Manganese binding site 2 out of 4 in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:53.9 occ:1.00 OE2 B:GLU121 2.0 36.6 1.0 OD1 B:ASP132 2.1 46.4 1.0 OD2 B:ASP123 2.3 25.4 1.0 NE2 B:HIS137 2.5 29.4 1.0 CD B:GLU121 3.0 36.3 1.0 CG B:ASP132 3.2 46.0 1.0 OE1 B:GLU121 3.4 33.9 1.0 CG B:ASP123 3.4 26.0 1.0 CE1 B:HIS137 3.4 23.8 1.0 OG B:SER147 3.4 28.5 1.0 CD2 B:HIS137 3.6 25.2 1.0 OD2 B:ASP132 3.7 43.3 1.0 O B:VAL145 3.8 25.8 1.0 CB B:ASP123 3.8 26.2 1.0 O B:HOH312 3.8 26.7 1.0 CG B:GLU121 4.3 31.0 1.0 CB B:ASP132 4.4 43.6 1.0 OD1 B:ASP123 4.5 25.2 1.0 ND1 B:HIS137 4.6 25.2 1.0 CG B:HIS137 4.7 26.8 1.0 CD B:PRO133 4.7 42.7 1.0 CA B:ASP132 4.7 34.7 1.0 CA B:CA237 4.8 38.9 1.0 CB B:SER147 4.8 26.7 1.0 CG2 B:THR150 5.0 25.9 1.0 C B:VAL145 5.0 21.5 1.0

Manganese binding site 3 out of 4 in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:59.0 occ:1.00 OD1 C:ASP132 2.1 53.7 1.0 OE2 C:GLU121 2.3 30.1 1.0 OD2 C:ASP123 2.5 45.5 1.0 NE2 C:HIS137 2.5 36.4 1.0 CG C:ASP132 3.1 57.2 1.0 CD C:GLU121 3.3 30.1 1.0 CD2 C:HIS137 3.4 31.3 1.0 CE1 C:HIS137 3.4 32.8 1.0 CG C:ASP123 3.5 41.2 1.0 OE1 C:GLU121 3.5 27.9 1.0 OG C:SER147 3.6 39.5 1.0 OD2 C:ASP132 3.7 53.1 1.0 O C:VAL145 3.8 30.5 1.0 CB C:ASP123 3.9 38.2 1.0 CB C:ASP132 4.3 54.7 1.0 CD C:PRO133 4.3 34.6 1.0 CA C:ASP132 4.4 31.8 1.0 OD1 C:ASP123 4.5 43.7 1.0 ND1 C:HIS137 4.6 35.0 1.0 CB C:SER147 4.6 37.1 1.0 CG C:GLU121 4.6 27.8 1.0 CG C:HIS137 4.6 33.0 1.0 CA C:CA237 4.8 41.7 1.0 CG2 C:THR150 4.9 19.4 1.0 N C:SER147 5.0 34.9 1.0

Manganese binding site 4 out of 4 in the Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystals of Peanut Lectin Grown in the Presence of Gal- Alpha-1,3-Gal-Beta-1,4-Gal within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:59.2 occ:1.00 OD1 D:ASP132 2.2 43.6 1.0 OE2 D:GLU121 2.3 32.0 1.0 OD2 D:ASP123 2.6 32.8 1.0 NE2 D:HIS137 2.7 46.5 1.0 CD D:GLU121 3.0 31.0 1.0 OE1 D:GLU121 3.1 32.0 1.0 OG D:SER147 3.3 24.7 1.0 CG D:ASP132 3.3 46.8 1.0 CD2 D:HIS137 3.5 43.5 1.0 O D:VAL145 3.6 23.5 1.0 CG D:ASP123 3.6 31.1 1.0 CE1 D:HIS137 3.7 41.7 1.0 OD2 D:ASP132 3.9 48.2 1.0 CB D:ASP123 3.9 30.9 1.0 O D:HOH420 4.0 27.8 1.0 CG D:GLU121 4.4 28.9 1.0 CB D:ASP132 4.5 47.0 1.0 CB D:SER147 4.7 28.4 1.0 OD1 D:ASP123 4.7 28.8 1.0 CD D:PRO133 4.7 39.0 1.0 CA D:ASP132 4.7 34.3 1.0 CA D:CA237 4.7 38.9 1.0 CG D:HIS137 4.7 44.2 1.0 ND1 D:HIS137 4.8 44.8 1.0 C D:VAL145 4.8 24.8 1.0 N D:SER147 4.9 33.1 1.0

S.K.Natchiar, O.Srinivas, N.Mitra, A.Surolia, N.Jayaraman, M.Vijayan. Structural Studies on Peanut Lectin Complexed with Disaccharides Involving Different Linkages: Further Insights Into the Structure and Interactions of the Lectin Acta Crystallogr.,Sect.D V. 62 1413 2006.
ISSN: ISSN 0907-4449
PubMed: 17057347
DOI: 10.1107/S0907444906035712