Manganese in PDB 2dvb: Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac Complex

The structure of Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac Complex, PDB code: 2dvb 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)	19.98 / 2.25
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.740, 124.330, 75.500, 90.00, 90.00, 90.00
R / Rfree (%)	21.4 / 26.6

The structure of Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac 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-1,6-Galnac Complex (pdb code 2dvb). 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-1,6-Galnac Complex, PDB code: 2dvb:
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-1,6-Galnac 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-1,6-Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:57.7 occ:1.00 OD1 A:ASP132 2.2 33.2 1.0 OD2 A:ASP123 2.2 30.4 1.0 OE2 A:GLU121 2.2 25.1 1.0 O A:HOH1347 2.3 26.1 1.0 O A:HOH1346 2.4 23.4 1.0 NE2 A:HIS137 2.4 29.2 1.0 CG A:ASP132 3.1 34.8 1.0 CG A:ASP123 3.1 29.1 1.0 CE1 A:HIS137 3.2 27.0 1.0 CD A:GLU121 3.2 24.3 1.0 CB A:ASP123 3.5 30.2 1.0 CD2 A:HIS137 3.5 28.1 1.0 OE1 A:GLU121 3.6 21.8 1.0 OD2 A:ASP132 3.6 34.7 1.0 O A:HOH1295 3.9 28.8 1.0 O A:HOH1348 4.0 31.0 1.0 CA A:CA237 4.1 36.3 1.0 OD1 A:ASP123 4.1 35.1 1.0 O A:VAL145 4.1 29.6 1.0 CB A:ASP132 4.2 34.9 1.0 OG A:SER147 4.3 30.4 1.0 ND1 A:HIS137 4.4 28.1 1.0 CG A:GLU121 4.5 24.3 1.0 CG A:HIS137 4.6 29.8 1.0 CA A:ASP132 4.7 36.0 1.0 CD A:PRO133 4.9 36.6 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac 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-1,6-Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:47.8 occ:1.00 OE2 B:GLU121 2.1 22.5 1.0 OD2 B:ASP123 2.2 33.0 1.0 O B:HOH2385 2.2 26.9 1.0 OD1 B:ASP132 2.3 32.8 1.0 NE2 B:HIS137 2.4 25.8 1.0 O B:HOH2386 2.5 42.4 1.0 CD B:GLU121 3.1 21.2 1.0 CE1 B:HIS137 3.2 23.5 1.0 CG B:ASP123 3.2 29.7 1.0 CG B:ASP132 3.3 33.4 1.0 OE1 B:GLU121 3.4 19.7 1.0 CD2 B:HIS137 3.5 24.8 1.0 CB B:ASP123 3.6 30.7 1.0 OD2 B:ASP132 3.9 32.3 1.0 OG B:SER147 4.0 28.0 1.0 O B:VAL145 4.2 25.4 1.0 OD1 B:ASP123 4.3 31.4 1.0 CA B:CA237 4.3 31.5 1.0 O B:HOH2269 4.3 27.1 1.0 ND1 B:HIS137 4.4 24.0 1.0 O B:HOH2383 4.4 24.4 1.0 CB B:ASP132 4.5 31.5 1.0 CG B:GLU121 4.5 22.4 1.0 CG B:HIS137 4.5 26.3 1.0 CD B:PRO133 4.8 33.3 1.0 CA B:ASP132 4.9 32.3 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac 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-1,6-Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:42.3 occ:1.00 OD1 C:ASP132 2.1 33.7 1.0 OD2 C:ASP123 2.2 32.0 1.0 O C:HOH3389 2.2 28.0 1.0 OE2 C:GLU121 2.3 23.8 1.0 O C:HOH3390 2.3 27.4 1.0 NE2 C:HIS137 2.4 25.5 1.0 CG C:ASP132 3.1 33.4 1.0 CD C:GLU121 3.2 23.1 1.0 CG C:ASP123 3.2 31.6 1.0 CD2 C:HIS137 3.3 26.1 1.0 CE1 C:HIS137 3.3 25.9 1.0 OE1 C:GLU121 3.4 25.2 1.0 OD2 C:ASP132 3.6 34.4 1.0 CB C:ASP123 3.7 32.2 1.0 O C:HOH3396 3.9 43.2 1.0 O C:HOH3391 4.0 24.1 1.0 O C:VAL145 4.1 31.0 1.0 OG C:SER147 4.1 28.5 1.0 CA C:CA237 4.2 36.1 1.0 CB C:ASP132 4.3 33.7 1.0 OD1 C:ASP123 4.3 32.5 1.0 ND1 C:HIS137 4.4 24.8 1.0 CG C:HIS137 4.5 25.4 1.0 CG C:GLU121 4.6 23.6 1.0 CD C:PRO133 4.7 35.3 1.0 CA C:ASP132 4.8 34.6 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,6-Galnac 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-1,6-Galnac Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:44.4 occ:1.00 OD1 D:ASP132 2.2 34.2 1.0 OD2 D:ASP123 2.2 31.5 1.0 OE2 D:GLU121 2.2 24.2 1.0 O D:HOH4373 2.2 22.4 1.0 O D:HOH4374 2.3 19.5 1.0 NE2 D:HIS137 2.4 20.2 1.0 CG D:ASP123 3.1 30.0 1.0 CG D:ASP132 3.1 31.7 1.0 CD D:GLU121 3.2 23.5 1.0 CE1 D:HIS137 3.3 18.9 1.0 CD2 D:HIS137 3.3 19.8 1.0 OE1 D:GLU121 3.5 23.8 1.0 CB D:ASP123 3.5 29.1 1.0 OD2 D:ASP132 3.5 35.6 1.0 O D:HOH4372 4.0 28.4 1.0 CA D:CA237 4.1 32.4 1.0 OD1 D:ASP123 4.1 29.7 1.0 OG D:SER147 4.1 26.1 1.0 O D:VAL145 4.2 30.6 1.0 CB D:ASP132 4.3 31.6 1.0 O D:HOH4298 4.3 21.4 1.0 ND1 D:HIS137 4.4 20.2 1.0 CG D:HIS137 4.5 20.6 1.0 CG D:GLU121 4.5 22.8 1.0 CD D:PRO133 4.8 33.0 1.0 CA D:ASP132 4.8 30.5 1.0 CA D:ASP123 5.0 28.2 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