Manganese in PDB 2dvg: Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex

The structure of Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex, PDB code: 2dvg 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)	19.93 / 2.78
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.190, 124.660, 75.740, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 27.4

The structure of Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex (pdb code 2dvg). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex, PDB code: 2dvg:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:43.1 occ:1.00 OD1 A:ASP132 2.3 47.7 1.0 OE2 A:GLU121 2.3 29.4 1.0 O A:HOH470 2.4 21.6 1.0 NE2 A:HIS137 2.5 24.2 1.0 OD2 A:ASP123 2.9 28.2 1.0 CD A:GLU121 3.2 28.4 1.0 O A:HOH420 3.2 25.1 1.0 CG A:ASP132 3.3 47.2 1.0 OG A:SER147 3.4 16.3 1.0 CE1 A:HIS137 3.4 20.9 1.0 OE1 A:GLU121 3.5 30.5 1.0 CD2 A:HIS137 3.5 18.6 1.0 CG A:ASP123 3.7 26.8 1.0 OD2 A:ASP132 3.7 42.4 1.0 O A:VAL145 3.8 35.3 1.0 CB A:ASP123 4.0 24.7 1.0 CD A:PRO133 4.3 27.8 1.0 CG A:GLU121 4.4 24.5 1.0 CB A:ASP132 4.5 45.4 1.0 ND1 A:HIS137 4.6 22.0 1.0 CA A:CA237 4.6 23.6 1.0 CG A:HIS137 4.6 24.1 1.0 OD1 A:ASP123 4.7 25.4 1.0 CB A:SER147 4.7 16.4 1.0 CA A:ASP132 4.8 28.6 1.0 N A:SER147 5.0 19.2 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:42.3 occ:1.00 OE2 B:GLU121 2.3 20.1 1.0 OD1 B:ASP132 2.3 29.9 1.0 OD2 B:ASP123 2.4 22.3 1.0 NE2 B:HIS137 2.5 30.5 1.0 CG B:ASP132 3.1 29.4 1.0 CD B:GLU121 3.1 19.9 1.0 OD2 B:ASP132 3.2 26.8 1.0 OE1 B:GLU121 3.3 17.5 1.0 CD2 B:HIS137 3.4 26.3 1.0 CG B:ASP123 3.4 22.9 1.0 CE1 B:HIS137 3.5 24.9 1.0 OG B:SER147 3.7 29.2 1.0 O B:HOH352 3.8 28.0 1.0 CB B:ASP123 3.9 23.2 1.0 O B:VAL145 4.0 27.5 1.0 CA B:CA237 4.4 24.3 1.0 CB B:ASP132 4.4 27.1 1.0 OD1 B:ASP123 4.4 22.1 1.0 CG B:GLU121 4.5 14.5 1.0 CD B:PRO133 4.6 23.1 1.0 CG B:HIS137 4.6 27.9 1.0 ND1 B:HIS137 4.6 26.4 1.0 CA B:ASP132 4.8 27.4 1.0 CG2 B:THR150 4.9 13.3 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:45.2 occ:1.00 OD2 C:ASP123 2.2 47.0 1.0 OE2 C:GLU121 2.3 22.0 1.0 OD1 C:ASP132 2.3 28.4 1.0 NE2 C:HIS137 2.6 37.7 1.0 CD C:GLU121 3.0 22.0 1.0 OE1 C:GLU121 3.1 19.7 1.0 CG C:ASP123 3.4 42.8 1.0 CG C:ASP132 3.4 32.0 1.0 CE1 C:HIS137 3.5 34.1 1.0 CD2 C:HIS137 3.6 32.7 1.0 OG C:SER147 3.7 32.5 1.0 O C:VAL145 3.8 39.3 1.0 OD2 C:ASP132 3.9 27.9 1.0 CB C:ASP123 4.1 39.8 1.0 CA C:CA237 4.3 26.2 1.0 OD1 C:ASP123 4.4 45.3 1.0 CG C:GLU121 4.5 19.6 1.0 ND1 C:HIS137 4.6 36.4 1.0 CB C:ASP132 4.7 29.5 1.0 CG C:HIS137 4.7 34.4 1.0 CD C:PRO133 4.8 32.3 1.0 CB C:SER147 4.9 30.1 1.0 C C:VAL145 5.0 37.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Peanut Lectin Gal-Alpha-1,6-Glc Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:42.8 occ:1.00 OE2 D:GLU121 2.3 24.6 1.0 OD1 D:ASP132 2.3 45.2 1.0 O D:HOH495 2.5 20.7 1.0 NE2 D:HIS137 2.6 40.4 1.0 OD2 D:ASP123 2.7 34.9 1.0 CD D:GLU121 3.1 23.6 1.0 CD2 D:HIS137 3.3 37.5 1.0 OE1 D:GLU121 3.4 24.6 1.0 CG D:ASP132 3.4 48.4 1.0 OG D:SER147 3.5 18.9 1.0 O D:HOH400 3.6 20.0 1.0 O D:HOH493 3.6 37.8 1.0 CG D:ASP123 3.6 33.2 1.0 CE1 D:HIS137 3.7 35.6 1.0 O D:VAL145 3.9 21.8 1.0 CB D:ASP123 3.9 33.0 1.0 OD2 D:ASP132 4.1 49.8 1.0 CG D:GLU121 4.5 21.5 1.0 CB D:ASP132 4.5 48.6 1.0 CG D:HIS137 4.6 38.1 1.0 CD D:PRO133 4.6 64.5 1.0 ND1 D:HIS137 4.7 38.8 1.0 CB D:SER147 4.7 22.7 1.0 CA D:ASP132 4.7 30.9 1.0 OD1 D:ASP123 4.8 30.9 1.0 CA D:CA237 4.8 25.2 1.0 CG2 D:THR150 5.0 26.1 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