Manganese in PDB 2dv9: Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal Complex

The structure of Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal Complex, PDB code: 2dv9 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)	19.89 / 2.48
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	127.770, 124.910, 76.280, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.7

The structure of Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal 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-Beta-1,3-Gal Complex (pdb code 2dv9). 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-Beta-1,3-Gal Complex, PDB code: 2dv9:
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-Beta-1,3-Gal 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-Beta-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:46.0 occ:1.00 O A:HOH438 2.1 26.5 1.0 OE2 A:GLU121 2.1 19.4 1.0 OD1 A:ASP132 2.1 39.7 1.0 OD2 A:ASP123 2.2 32.8 1.0 O A:HOH437 2.3 28.1 1.0 NE2 A:HIS137 2.4 23.9 1.0 CG A:ASP123 3.1 32.7 1.0 CG A:ASP132 3.2 38.5 1.0 CD A:GLU121 3.2 21.4 1.0 CE1 A:HIS137 3.3 23.0 1.0 CD2 A:HIS137 3.3 25.1 1.0 CB A:ASP123 3.4 31.6 1.0 OE1 A:GLU121 3.7 23.7 1.0 OD2 A:ASP132 3.7 39.0 1.0 O A:HOH338 3.9 26.2 1.0 OD1 A:ASP123 4.2 35.2 1.0 OG A:SER147 4.2 26.2 1.0 O A:VAL145 4.3 26.0 1.0 CA A:CA237 4.3 36.9 1.0 CB A:ASP132 4.3 36.7 1.0 ND1 A:HIS137 4.5 24.6 1.0 CG A:GLU121 4.5 23.1 1.0 CG A:HIS137 4.5 25.1 1.0 O A:HOH348 4.7 29.1 1.0 CD A:PRO133 4.8 38.4 1.0 CA A:ASP132 4.9 36.4 1.0 CA A:ASP123 4.9 31.5 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal 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-Beta-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:39.1 occ:1.00 OD1 B:ASP132 2.1 28.9 1.0 OD2 B:ASP123 2.2 25.8 1.0 OE2 B:GLU121 2.2 24.1 1.0 O B:HOH1386 2.4 21.0 1.0 NE2 B:HIS137 2.4 26.1 1.0 O B:HOH1393 2.4 25.8 1.0 CG B:ASP132 3.0 27.5 1.0 CE1 B:HIS137 3.1 21.6 1.0 CG B:ASP123 3.1 25.2 1.0 CD B:GLU121 3.3 24.4 1.0 OD2 B:ASP132 3.3 26.1 1.0 CB B:ASP123 3.5 27.1 1.0 CD2 B:HIS137 3.5 25.2 1.0 OE1 B:GLU121 3.6 23.2 1.0 O B:HOH1494 3.8 36.5 1.0 CA B:CA237 4.1 25.8 1.0 OD1 B:ASP123 4.2 28.0 1.0 OG B:SER147 4.3 22.4 1.0 O B:VAL145 4.3 25.2 1.0 CB B:ASP132 4.3 27.6 1.0 ND1 B:HIS137 4.3 24.4 1.0 O B:HOH1479 4.3 19.0 1.0 CG B:HIS137 4.5 25.9 1.0 CG B:GLU121 4.6 24.0 1.0 CD B:PRO133 4.8 29.8 1.0 CA B:ASP132 4.8 28.6 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal 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-Beta-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:56.4 occ:1.00 OE2 C:GLU121 2.0 35.4 1.0 O C:HOH2395 2.1 27.6 1.0 OD2 C:ASP123 2.2 42.9 1.0 OD1 C:ASP132 2.3 45.1 1.0 O C:HOH2396 2.4 34.7 1.0 NE2 C:HIS137 2.4 37.2 1.0 CG C:ASP123 3.1 42.6 1.0 CD C:GLU121 3.2 32.5 1.0 CE1 C:HIS137 3.3 36.6 1.0 CG C:ASP132 3.3 41.7 1.0 CD2 C:HIS137 3.4 36.2 1.0 CB C:ASP123 3.5 41.4 1.0 OE1 C:GLU121 3.8 34.5 1.0 OD2 C:ASP132 3.8 43.5 1.0 CA C:CA237 3.9 40.2 1.0 OD1 C:ASP123 4.2 44.7 1.0 OG C:SER147 4.2 34.5 1.0 O C:HOH2397 4.2 40.9 1.0 CG C:GLU121 4.4 30.4 1.0 O C:VAL145 4.4 39.6 1.0 ND1 C:HIS137 4.4 37.0 1.0 CG C:HIS137 4.5 35.4 1.0 CB C:ASP132 4.5 40.5 1.0 CD C:PRO133 4.8 37.4 1.0 CA C:ASP123 5.0 38.9 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,3-Gal 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-Beta-1,3-Gal Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:49.6 occ:1.00 OD1 D:ASP132 2.2 39.4 1.0 OD2 D:ASP123 2.2 33.7 1.0 OE2 D:GLU121 2.2 29.2 1.0 NE2 D:HIS137 2.3 27.6 1.0 O D:HOH355 2.4 36.2 1.0 O D:HOH354 2.5 18.2 1.0 CG D:ASP123 3.1 32.2 1.0 CE1 D:HIS137 3.2 27.3 1.0 CG D:ASP132 3.2 37.8 1.0 CD D:GLU121 3.2 27.7 1.0 CB D:ASP123 3.4 29.7 1.0 CD2 D:HIS137 3.4 25.7 1.0 OE1 D:GLU121 3.6 25.2 1.0 OD2 D:ASP132 3.7 35.4 1.0 O D:HOH352 3.8 24.3 1.0 OD1 D:ASP123 4.1 32.9 1.0 OG D:SER147 4.2 33.0 1.0 CA D:CA237 4.3 31.7 1.0 CB D:ASP132 4.3 36.2 1.0 ND1 D:HIS137 4.4 27.6 1.0 O D:VAL145 4.4 32.2 1.0 CG D:HIS137 4.5 24.9 1.0 O D:HOH276 4.5 22.7 1.0 CG D:GLU121 4.5 28.4 1.0 CD D:PRO133 4.7 35.6 1.0 CA D:ASP132 4.8 35.0 1.0 CA D:ASP123 4.8 29.1 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