Calcium in PDB 3ujq: Galactose-Specific Lectin From Dolichos Lablab in Complex with Galactose

The structure of Galactose-Specific Lectin From Dolichos Lablab in Complex with Galactose, PDB code: 3ujq 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)	42.34 / 2.06
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	89.990, 89.990, 125.080, 90.00, 90.00, 120.00
R / Rfree (%)	19.7 / 24.6

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

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Galactose-Specific Lectin From Dolichos Lablab in Complex with Galactose (pdb code 3ujq). 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 Lectin From Dolichos Lablab in Complex with Galactose, PDB code: 3ujq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Galactose-Specific Lectin From Dolichos Lablab in Complex with 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 Lectin From Dolichos Lablab in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:78.5 occ:1.00 OD2 A:ASP156 2.6 60.8 1.0 OD2 A:ASP148 2.6 62.6 1.0 O A:HOH416 2.8 25.0 1.0 OD1 A:ASN152 3.2 62.0 1.0 NE1 A:TRP155 3.5 61.1 1.0 O A:GLY126 3.6 56.8 1.0 CG A:ASN152 3.6 61.9 1.0 CG A:ASP148 3.6 62.6 1.0 CG A:ASP156 3.6 60.8 1.0 CA A:GLY126 3.8 56.6 1.0 OD1 A:ASP148 3.8 62.6 1.0 O A:HOH415 3.8 17.2 1.0 OD1 A:ASP156 4.0 60.8 1.0 CB A:ASN152 4.0 61.9 1.0 C A:GLY126 4.1 56.7 1.0 CD1 A:TRP155 4.3 61.1 1.0 MN A:MN304 4.3 41.0 1.0 ND2 A:ASN152 4.3 61.9 1.0 CE2 A:TRP155 4.4 61.1 1.0 O A:PHE150 4.5 62.2 1.0 CZ2 A:TRP155 4.8 61.1 1.0 CB A:ASP156 4.9 60.7 1.0 CB A:ASP148 5.0 62.5 1.0 N A:ASN152 5.0 62.0 1.0

Calcium binding site 2 out of 4 in the Galactose-Specific Lectin From Dolichos Lablab in Complex with 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 Lectin From Dolichos Lablab in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca306 b:27.7 occ:1.00 O B:HOH413 2.3 13.7 1.0 O B:HOH405 2.3 2.3 1.0 OD1 B:ASN152 2.3 17.9 1.0 OD2 B:ASP156 2.4 17.9 1.0 OD2 B:ASP148 2.5 16.9 1.0 O B:PHE150 2.6 17.3 1.0 OD1 B:ASP148 2.9 16.8 1.0 CG B:ASP148 3.1 16.9 1.0 CG B:ASN152 3.4 18.1 1.0 CG B:ASP156 3.5 18.1 1.0 C B:PHE150 3.7 17.3 1.0 CB B:ASN152 3.9 18.1 1.0 OD1 B:ASP156 4.0 18.4 1.0 N B:ASN152 4.2 17.9 1.0 OD1 B:ASP108 4.2 16.8 1.0 O B:GLY126 4.3 16.6 1.0 NE1 B:TRP155 4.3 19.1 1.0 CB B:PHE150 4.3 17.1 1.0 CA B:GLY126 4.4 16.6 1.0 CA B:PHE150 4.4 17.2 1.0 CD1 B:PHE150 4.4 17.6 1.0 ND2 B:ASN152 4.5 18.1 1.0 MN B:MN307 4.5 38.1 1.0 O B:HOH414 4.5 11.4 1.0 CB B:ASP148 4.6 16.8 1.0 N B:PHE150 4.6 16.9 1.0 CA B:ASN152 4.7 18.1 1.0 O B:ASP108 4.7 16.7 1.0 N B:TYR151 4.7 17.4 1.0 CB B:ASP156 4.8 18.2 1.0 C B:GLY126 4.8 16.6 1.0 C B:TYR151 4.9 17.7 1.0 CG B:PHE150 4.9 17.3 1.0 CA B:TYR151 5.0 17.7 1.0

Calcium binding site 3 out of 4 in the Galactose-Specific Lectin From Dolichos Lablab in Complex with 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 Lectin From Dolichos Lablab in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:24.8 occ:1.00 O C:HOH403 2.2 5.5 1.0 O C:HOH418 2.3 19.1 1.0 OD1 C:ASN152 2.4 25.2 1.0 OD2 C:ASP156 2.5 25.5 1.0 OD2 C:ASP148 2.6 24.1 1.0 OD1 C:ASP148 2.7 24.0 1.0 O C:PHE150 2.8 25.8 1.0 CG C:ASP148 3.0 24.4 1.0 CG C:ASN152 3.4 25.7 1.0 CG C:ASP156 3.6 25.9 1.0 C C:PHE150 3.7 25.8 1.0 CB C:ASN152 3.9 25.7 1.0 N C:ASN152 4.0 25.8 1.0 OD1 C:ASP156 4.1 25.6 1.0 CB C:PHE150 4.2 25.8 1.0 O C:HOH420 4.3 17.0 1.0 O C:GLY126 4.3 28.5 1.0 CD2 C:PHE150 4.3 26.4 1.0 CA C:PHE150 4.3 25.7 1.0 N C:PHE150 4.5 25.5 1.0 ND2 C:ASN152 4.5 25.3 1.0 CB C:ASP148 4.5 24.6 1.0 CA C:ASN152 4.5 25.8 1.0 OD2 C:ASP108 4.6 24.6 1.0 CA C:GLY126 4.6 28.4 1.0 MN C:MN303 4.6 65.5 1.0 N C:TYR151 4.6 25.8 1.0 NE1 C:TRP155 4.8 26.0 1.0 C C:TYR151 4.8 25.9 1.0 CG C:PHE150 4.8 26.1 1.0 CB C:ASP156 4.9 26.0 1.0 O C:ASP108 4.9 24.5 1.0 CA C:TYR151 4.9 25.9 1.0 C C:GLY126 5.0 28.5 1.0 CZ2 C:TRP155 5.0 26.1 1.0

Calcium binding site 4 out of 4 in the Galactose-Specific Lectin From Dolichos Lablab in Complex with 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 Lectin From Dolichos Lablab in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca305 b:22.4 occ:1.00 OD2 D:ASP148 2.3 20.2 1.0 O D:HOH407 2.4 17.8 1.0 OD2 D:ASP156 2.4 21.2 1.0 OD1 D:ASN152 2.5 22.4 1.0 O D:PHE150 2.6 22.0 1.0 OD1 D:ASP148 2.8 20.0 1.0 CG D:ASP148 2.9 20.3 1.0 CG D:ASN152 3.4 22.7 1.0 CG D:ASP156 3.6 21.8 1.0 CB D:ASN152 3.6 22.7 1.0 C D:PHE150 3.7 22.1 1.0 N D:ASN152 3.9 22.8 1.0 OD1 D:ASP156 4.0 21.5 1.0 MN D:MN306 4.0 45.9 1.0 NE1 D:TRP155 4.3 22.3 1.0 CA D:ASN152 4.4 22.8 1.0 CB D:ASP148 4.4 20.5 1.0 CA D:PHE150 4.4 21.9 1.0 O D:GLY126 4.5 22.3 1.0 CB D:PHE150 4.5 21.9 1.0 N D:PHE150 4.6 21.6 1.0 CA D:GLY126 4.6 22.4 1.0 N D:TYR151 4.7 22.3 1.0 CD2 D:PHE150 4.7 22.3 1.0 ND2 D:ASN152 4.7 22.4 1.0 O D:ASP108 4.7 22.1 1.0 OD1 D:ASP108 4.8 22.6 1.0 C D:TYR151 4.8 22.6 1.0 CB D:ASP156 4.8 22.1 1.0 CA D:TYR151 4.9 22.6 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