Manganese in PDB 3ujo: Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose

The structure of Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose, PDB code: 3ujo was solved by K.N.Shetty, V.L.Latha, R.N.Rao, S.K.Nadimpalli, K.Suguna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.20 / 2.00
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	89.780, 89.780, 123.890, 90.00, 90.00, 120.00
R / Rfree (%)	20.7 / 24.9

The structure of Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose (pdb code 3ujo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose, PDB code: 3ujo:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:57.2 occ:1.00 OD1 A:ASP156 2.0 66.2 1.0 O A:HOH405 2.3 15.2 1.0 O A:HOH404 2.4 48.4 1.0 NE2 A:HIS161 2.5 64.7 1.0 OE1 A:GLU146 2.7 66.5 1.0 OD2 A:ASP148 2.8 66.6 1.0 OE2 A:GLU146 2.9 66.5 1.0 CD A:GLU146 3.1 66.6 1.0 CG A:ASP156 3.1 66.2 1.0 CE1 A:HIS161 3.4 64.7 1.0 CD2 A:HIS161 3.5 64.8 1.0 OD2 A:ASP156 3.9 66.2 1.0 CG A:ASP148 4.0 66.7 1.0 CB A:ASP156 4.1 66.2 1.0 CA A:CA304 4.2 49.6 1.0 CG A:GLU146 4.5 66.7 1.0 CA A:ASP156 4.5 66.2 1.0 ND1 A:HIS161 4.6 64.6 1.0 CB A:ASP148 4.6 66.7 1.0 CG A:HIS161 4.6 64.5 1.0 O A:ILE169 4.6 57.8 1.0 O A:TRP155 4.7 66.4 1.0 CD1 A:TRP155 4.7 66.8 1.0 CD A:PRO157 4.7 66.0 1.0 OG A:SER171 4.7 56.5 1.0 OD1 A:ASP165 4.9 61.1 1.0

Manganese binding site 2 out of 4 in the Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:35.2 occ:1.00 O B:HOH404 1.9 13.9 1.0 OD1 B:ASP156 2.0 24.2 1.0 OE2 B:GLU146 2.1 16.5 1.0 O B:HOH405 2.2 13.6 1.0 NE2 B:HIS161 2.3 21.2 1.0 OD2 B:ASP148 2.4 19.2 1.0 CD B:GLU146 3.0 16.9 1.0 CG B:ASP156 3.1 24.3 1.0 OE1 B:GLU146 3.2 18.6 1.0 CE1 B:HIS161 3.3 21.1 1.0 CD2 B:HIS161 3.3 21.4 1.0 CG B:ASP148 3.4 20.0 1.0 OD2 B:ASP156 3.6 23.1 1.0 CB B:ASP148 3.8 19.6 1.0 O B:HOH401 3.8 16.9 1.0 CD1 B:TRP155 4.2 26.0 1.0 OG B:SER171 4.2 21.6 1.0 CA B:CA304 4.2 24.4 1.0 CB B:ASP156 4.3 24.7 1.0 NE1 B:TRP155 4.3 26.0 1.0 O B:HOH424 4.4 21.4 1.0 CG B:GLU146 4.4 17.8 1.0 ND1 B:HIS161 4.4 21.2 1.0 CG B:HIS161 4.4 21.7 1.0 OD1 B:ASP148 4.5 21.1 1.0 O B:ILE169 4.5 21.4 1.0 CA B:ASP156 4.6 24.9 1.0 CD B:PRO157 4.8 24.8 1.0

Manganese binding site 3 out of 4 in the Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn303 b:36.2 occ:1.00 OE2 C:GLU146 2.0 25.9 1.0 O C:HOH402 2.2 10.9 1.0 OD2 C:ASP148 2.2 28.4 1.0 OD1 C:ASP156 2.3 32.4 1.0 NE2 C:HIS161 2.3 31.6 1.0 O C:HOH401 2.4 22.6 1.0 CD C:GLU146 3.0 27.3 1.0 CG C:ASP148 3.2 28.7 1.0 CG C:ASP156 3.2 32.8 1.0 CE1 C:HIS161 3.3 31.5 1.0 CD2 C:HIS161 3.3 31.5 1.0 OE1 C:GLU146 3.4 28.1 1.0 CB C:ASP148 3.5 28.9 1.0 OD2 C:ASP156 3.6 31.8 1.0 O C:HOH403 3.8 16.1 1.0 CA C:CA304 4.0 31.7 1.0 NE1 C:TRP155 4.2 34.0 1.0 OG C:SER171 4.2 31.3 1.0 OD1 C:ASP148 4.3 27.8 1.0 CG C:GLU146 4.4 27.9 1.0 CD1 C:TRP155 4.4 34.1 1.0 ND1 C:HIS161 4.4 31.7 1.0 CB C:ASP156 4.4 33.3 1.0 CG C:HIS161 4.4 31.6 1.0 O C:ILE169 4.6 31.0 1.0 O C:HOH425 4.7 42.2 1.0 CA C:ASP156 4.7 33.3 1.0

Manganese binding site 4 out of 4 in the Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn303 b:47.5 occ:1.00 OE2 D:GLU146 2.1 21.4 1.0 OD1 D:ASP156 2.2 27.6 1.0 NE2 D:HIS161 2.2 26.4 1.0 OD2 D:ASP148 2.3 26.1 1.0 CE1 D:HIS161 3.1 26.7 1.0 CD D:GLU146 3.1 21.8 1.0 CG D:ASP156 3.2 27.9 1.0 CD2 D:HIS161 3.3 26.6 1.0 CG D:ASP148 3.3 25.4 1.0 OE1 D:GLU146 3.6 21.9 1.0 OD2 D:ASP156 3.6 26.9 1.0 CB D:ASP148 3.6 25.1 1.0 OG D:SER171 4.1 23.4 1.0 O D:HOH425 4.1 17.4 1.0 CA D:CA304 4.2 31.8 1.0 ND1 D:HIS161 4.3 26.7 1.0 CG D:GLU146 4.4 23.4 1.0 CG D:HIS161 4.4 26.9 1.0 CB D:ASP156 4.4 28.4 1.0 OD1 D:ASP148 4.5 25.5 1.0 O D:ILE169 4.5 22.7 1.0 CD D:PRO157 4.5 28.1 1.0 CD1 D:TRP155 4.6 28.3 1.0 CA D:ASP156 4.7 28.4 1.0

K.N.Shetty, V.L.Latha, R.N.Rao, S.K.Nadimpalli, K.Suguna. Affinity of A Galactose-Specific Legume Lectin From Dolichos Lablab to Adenine Revealed By X-Ray Cystallography. Iubmb Life V. 65 633 2013.
ISSN: ISSN 1521-6543
PubMed: 23794513
DOI: 10.1002/IUB.1177