Calcium 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:

Manganese

(Mn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Galactose-Specific Seed Lectin From Dolichos Lablab in Complex with Adenine and Galactose, PDB code: 3ujo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca304 b:49.6 occ:1.00 OD2 A:ASP148 2.8 66.6 1.0 OD2 A:ASP156 3.1 66.2 1.0 OD1 A:ASP148 3.2 66.8 1.0 CG A:ASP148 3.4 66.7 1.0 OD1 A:ASN152 3.4 66.8 1.0 CG A:ASP156 3.8 66.2 1.0 O A:PHE150 3.9 67.0 1.0 OD1 A:ASP156 3.9 66.2 1.0 CG A:ASN152 4.0 66.8 1.0 NE1 A:TRP155 4.2 66.8 1.0 MN A:MN303 4.2 57.2 1.0 O A:GLY126 4.3 65.3 1.0 O A:HOH404 4.5 48.4 1.0 ND2 A:ASN152 4.7 66.7 1.0 CB A:ASN152 4.7 66.8 1.0 CA A:GLY126 4.8 65.1 1.0 OD1 A:ASP108 4.8 54.8 1.0 C A:PHE150 4.8 66.9 1.0 CB A:ASP148 4.9 66.7 1.0 CD1 A:TRP155 4.9 66.8 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca304 b:24.4 occ:1.00 O B:HOH403 2.2 24.9 1.0 O B:HOH401 2.3 16.9 1.0 OD1 B:ASN152 2.3 23.0 1.0 OD2 B:ASP156 2.4 23.1 1.0 OD2 B:ASP148 2.5 19.2 1.0 O B:PHE150 2.5 22.3 1.0 OD1 B:ASP148 2.6 21.1 1.0 CG B:ASP148 2.9 20.0 1.0 CG B:ASN152 3.4 23.8 1.0 CG B:ASP156 3.5 24.3 1.0 C B:PHE150 3.7 22.1 1.0 OD1 B:ASP156 3.9 24.2 1.0 CB B:ASN152 4.0 23.9 1.0 N B:ASN152 4.2 23.6 1.0 MN B:MN303 4.2 35.2 1.0 O B:GLY126 4.3 21.4 1.0 OD1 B:ASP108 4.3 22.9 1.0 CB B:PHE150 4.3 21.4 1.0 CA B:PHE150 4.4 21.5 1.0 CA B:GLY126 4.4 21.7 1.0 CB B:ASP148 4.4 19.6 1.0 NE1 B:TRP155 4.4 26.0 1.0 O B:HOH404 4.5 13.9 1.0 N B:PHE150 4.5 20.8 1.0 O B:ASP108 4.5 23.0 1.0 CD1 B:PHE150 4.5 21.7 1.0 ND2 B:ASN152 4.6 23.5 1.0 CA B:ASN152 4.7 24.0 1.0 N B:TYR151 4.8 22.5 1.0 CB B:ASP156 4.8 24.7 1.0 C B:GLY126 4.8 21.6 1.0 CE1 B:HIS161 4.9 21.1 1.0 C B:TYR151 4.9 23.3 1.0 CG B:PHE150 5.0 21.4 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca304 b:31.7 occ:1.00 O C:HOH403 2.1 16.1 1.0 OD1 C:ASN152 2.4 30.9 1.0 OD2 C:ASP148 2.4 28.4 1.0 O C:HOH404 2.4 23.4 1.0 OD2 C:ASP156 2.4 31.8 1.0 OD1 C:ASP148 2.6 27.8 1.0 CG C:ASP148 2.9 28.7 1.0 O C:PHE150 2.9 31.9 1.0 CG C:ASN152 3.4 32.0 1.0 CG C:ASP156 3.5 32.8 1.0 OD1 C:ASP156 3.9 32.4 1.0 CB C:ASN152 3.9 32.2 1.0 C C:PHE150 3.9 31.7 1.0 MN C:MN303 4.0 36.2 1.0 N C:ASN152 4.1 32.2 1.0 O C:HOH401 4.2 22.6 1.0 O C:GLY126 4.2 33.9 1.0 CB C:ASP148 4.4 28.9 1.0 CB C:PHE150 4.5 31.4 1.0 NE1 C:TRP155 4.5 34.0 1.0 CA C:PHE150 4.5 31.4 1.0 ND2 C:ASN152 4.5 31.3 1.0 CD2 C:PHE150 4.6 31.7 1.0 N C:PHE150 4.6 31.0 1.0 CA C:ASN152 4.6 32.3 1.0 CA C:GLY126 4.6 33.8 1.0 OD2 C:ASP108 4.7 29.9 1.0 CB C:ASP156 4.8 33.3 1.0 O C:ASP108 4.9 29.9 1.0 N C:TYR151 4.9 31.9 1.0 CZ2 C:TRP155 4.9 34.2 1.0 C C:GLY126 4.9 34.0 1.0 CE1 C:HIS161 4.9 31.5 1.0 CE2 C:TRP155 5.0 34.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca304 b:31.8 occ:1.00 OD2 D:ASP156 2.3 26.9 1.0 O D:PHE150 2.4 27.6 1.0 OD2 D:ASP148 2.4 26.1 1.0 OD1 D:ASN152 2.5 27.7 1.0 OD1 D:ASP148 2.6 25.5 1.0 CG D:ASP148 2.8 25.4 1.0 CG D:ASN152 3.3 28.6 1.0 CG D:ASP156 3.4 27.9 1.0 C D:PHE150 3.5 27.7 1.0 CB D:ASN152 3.6 28.6 1.0 N D:ASN152 3.8 28.5 1.0 OD1 D:ASP156 3.8 27.6 1.0 MN D:MN303 4.2 47.5 1.0 CA D:PHE150 4.3 27.4 1.0 NE1 D:TRP155 4.3 27.9 1.0 CA D:ASN152 4.3 28.7 1.0 CB D:ASP148 4.3 25.1 1.0 N D:PHE150 4.4 27.1 1.0 CB D:PHE150 4.4 27.4 1.0 N D:TYR151 4.6 28.0 1.0 ND2 D:ASN152 4.6 28.0 1.0 O D:GLY126 4.6 29.0 1.0 CB D:ASP156 4.6 28.4 1.0 CD2 D:PHE150 4.6 27.6 1.0 OD1 D:ASP108 4.7 28.7 1.0 C D:TYR151 4.7 28.4 1.0 CA D:TYR151 4.8 28.4 1.0 CD1 D:TRP155 4.9 28.3 1.0 O D:ASP108 5.0 28.2 1.0 CE1 D:HIS161 5.0 26.7 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