Manganese in PDB 2dva: Crystal Structure of Peanut Lectin Gal-Beta-1,3-Galnac- Alpha-O-Me (Methyl-T-Antigen) Complex

The structure of Crystal Structure of Peanut Lectin Gal-Beta-1,3-Galnac- Alpha-O-Me (Methyl-T-Antigen) Complex, PDB code: 2dva 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 / 2.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	126.590, 124.620, 75.780, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 25

The structure of Crystal Structure of Peanut Lectin Gal-Beta-1,3-Galnac- Alpha-O-Me (Methyl-T-Antigen) 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-Galnac- Alpha-O-Me (Methyl-T-Antigen) Complex (pdb code 2dva). 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-Galnac- Alpha-O-Me (Methyl-T-Antigen) Complex, PDB code: 2dva:
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-Galnac- Alpha-O-Me (Methyl-T-Antigen) 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-Galnac- Alpha-O-Me (Methyl-T-Antigen) Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn238 b:42.1 occ:1.00 OD2 A:ASP123 2.2 32.7 1.0 OE2 A:GLU121 2.2 25.5 1.0 OD1 A:ASP132 2.2 29.5 1.0 O A:HOH381 2.3 25.3 1.0 O A:HOH380 2.3 27.2 1.0 NE2 A:HIS137 2.4 26.3 1.0 CD A:GLU121 3.1 25.0 1.0 CG A:ASP123 3.2 32.2 1.0 CG A:ASP132 3.2 32.4 1.0 CE1 A:HIS137 3.3 24.4 1.0 CD2 A:HIS137 3.4 26.1 1.0 OE1 A:GLU121 3.4 24.8 1.0 CB A:ASP123 3.6 30.9 1.0 OD2 A:ASP132 3.8 31.3 1.0 O A:HOH379 4.0 28.0 1.0 O A:VAL145 4.1 30.3 1.0 OG A:SER147 4.2 25.2 1.0 CA A:CA237 4.2 32.6 1.0 O A:HOH382 4.2 26.7 1.0 OD1 A:ASP123 4.3 35.7 1.0 CB A:ASP132 4.3 33.7 1.0 ND1 A:HIS137 4.4 25.1 1.0 CG A:GLU121 4.5 25.9 1.0 CG A:HIS137 4.5 25.9 1.0 CA A:ASP132 4.8 35.8 1.0 CD A:PRO133 4.8 35.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,3-Galnac- Alpha-O-Me (Methyl-T-Antigen) 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-Galnac- Alpha-O-Me (Methyl-T-Antigen) Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn238 b:39.4 occ:1.00 OD1 B:ASP132 2.1 27.0 1.0 OD2 B:ASP123 2.2 28.2 1.0 OE2 B:GLU121 2.2 21.1 1.0 O B:HOH2407 2.3 19.1 1.0 O B:HOH2406 2.4 26.8 1.0 NE2 B:HIS137 2.4 27.5 1.0 CG B:ASP132 3.1 28.5 1.0 CG B:ASP123 3.1 30.2 1.0 CD B:GLU121 3.2 22.4 1.0 CE1 B:HIS137 3.3 24.9 1.0 CD2 B:HIS137 3.4 25.4 1.0 OE1 B:GLU121 3.5 20.6 1.0 CB B:ASP123 3.5 29.8 1.0 OD2 B:ASP132 3.6 28.4 1.0 O B:HOH2405 3.9 28.6 1.0 OG B:SER147 4.1 23.2 1.0 O B:VAL145 4.1 25.8 1.0 OD1 B:ASP123 4.2 30.7 1.0 CA B:CA237 4.3 29.3 1.0 CB B:ASP132 4.3 28.1 1.0 O B:HOH2279 4.3 28.1 1.0 ND1 B:HIS137 4.4 26.1 1.0 CG B:HIS137 4.5 28.0 1.0 CG B:GLU121 4.5 21.7 1.0 CD B:PRO133 4.8 31.8 1.0 CA B:ASP132 4.8 30.2 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,3-Galnac- Alpha-O-Me (Methyl-T-Antigen) 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-Galnac- Alpha-O-Me (Methyl-T-Antigen) Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn238 b:46.8 occ:1.00 OD2 C:ASP123 2.2 35.0 1.0 OE2 C:GLU121 2.2 27.8 1.0 O C:HOH1341 2.3 27.9 1.0 OD1 C:ASP132 2.3 33.7 1.0 NE2 C:HIS137 2.4 36.5 1.0 O C:HOH1340 2.5 34.5 1.0 CG C:ASP132 3.2 34.1 1.0 CG C:ASP123 3.2 34.8 1.0 CE1 C:HIS137 3.3 33.3 1.0 CD C:GLU121 3.3 30.9 1.0 CD2 C:HIS137 3.4 34.1 1.0 OD2 C:ASP132 3.6 31.9 1.0 CB C:ASP123 3.6 35.5 1.0 OE1 C:GLU121 3.7 29.5 1.0 O C:HOH1339 4.1 35.5 1.0 OG C:SER147 4.1 33.8 1.0 O C:VAL145 4.2 40.3 1.0 O C:HOH1342 4.2 36.9 1.0 CA C:CA237 4.2 38.9 1.0 OD1 C:ASP123 4.3 35.7 1.0 CB C:ASP132 4.4 36.3 1.0 ND1 C:HIS137 4.4 33.5 1.0 CG C:HIS137 4.5 33.8 1.0 CG C:GLU121 4.6 28.5 1.0 CD C:PRO133 4.6 40.7 1.0 CA C:ASP132 4.8 38.5 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of Peanut Lectin Gal-Beta-1,3-Galnac- Alpha-O-Me (Methyl-T-Antigen) 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-Galnac- Alpha-O-Me (Methyl-T-Antigen) Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn238 b:44.5 occ:1.00 OE2 D:GLU121 2.2 27.2 1.0 OD1 D:ASP132 2.2 38.7 1.0 OD2 D:ASP123 2.2 28.8 1.0 O D:HOH311 2.3 34.0 1.0 O D:HOH312 2.3 29.2 1.0 NE2 D:HIS137 2.3 26.8 1.0 CE1 D:HIS137 3.1 24.8 1.0 CD D:GLU121 3.2 25.2 1.0 CG D:ASP132 3.2 38.8 1.0 CG D:ASP123 3.2 28.4 1.0 CD2 D:HIS137 3.4 24.2 1.0 OE1 D:GLU121 3.5 23.6 1.0 CB D:ASP123 3.6 30.2 1.0 OD2 D:ASP132 3.8 40.7 1.0 OG D:SER147 4.1 28.6 1.0 O D:VAL145 4.2 32.7 1.0 CA D:CA237 4.2 35.0 1.0 O D:HOH313 4.2 33.6 1.0 CB D:ASP132 4.2 37.4 1.0 OD1 D:ASP123 4.3 28.0 1.0 ND1 D:HIS137 4.3 25.9 1.0 O D:HOH305 4.4 28.4 1.0 CG D:HIS137 4.5 24.1 1.0 CG D:GLU121 4.5 24.0 1.0 CD D:PRO133 4.6 35.6 1.0 CA D:ASP132 4.6 35.7 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