Calcium in PDB 3ul2: Galactose-Specific Lectin From Dolichos Lablab in P6522 Space Group

The structure of Galactose-Specific Lectin From Dolichos Lablab in P6522 Space Group, PDB code: 3ul2 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)	50.00 / 2.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	90.496, 90.496, 514.240, 90.00, 90.00, 120.00
R / Rfree (%)	27.3 / 29.6

The structure of Galactose-Specific Lectin From Dolichos Lablab in P6522 Space Group 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 P6522 Space Group (pdb code 3ul2). 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 P6522 Space Group, PDB code: 3ul2:
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 P6522 Space Group


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 P6522 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:34.0 occ:1.00 O A:HOH406 2.2 34.3 1.0 OD2 A:ASP156 2.2 42.6 1.0 OD1 A:ASN152 2.3 43.7 1.0 O A:PHE150 2.4 42.5 1.0 O A:HOH407 2.4 27.5 1.0 OD1 A:ASP148 2.5 35.0 1.0 OD2 A:ASP148 2.6 35.0 1.0 CG A:ASP148 2.9 35.3 1.0 CG A:ASN152 3.3 44.1 1.0 CG A:ASP156 3.4 43.8 1.0 C A:PHE150 3.5 42.4 1.0 CB A:ASN152 3.7 44.6 1.0 OD1 A:ASP156 3.9 43.3 1.0 N A:ASN152 3.9 44.6 1.0 MN A:MN302 4.3 44.3 1.0 CA A:PHE150 4.3 41.6 1.0 NE1 A:TRP155 4.3 44.0 1.0 CA A:ASN152 4.4 44.9 1.0 O A:HOH401 4.4 21.6 1.0 CB A:PHE150 4.4 41.7 1.0 CB A:ASP148 4.4 35.3 1.0 O A:GLY126 4.4 38.7 1.0 N A:PHE150 4.5 40.5 1.0 ND2 A:ASN152 4.5 43.7 1.0 OD1 A:ASP108 4.5 35.8 1.0 N A:TYR151 4.6 43.4 1.0 CB A:ASP156 4.6 44.4 1.0 CD1 A:PHE150 4.6 42.5 1.0 CA A:GLY126 4.7 39.3 1.0 C A:TYR151 4.7 44.4 1.0 O A:ASP108 4.8 35.0 1.0 CA A:TYR151 4.8 44.3 1.0 CE1 A:HIS161 4.8 33.1 1.0 CE2 A:TRP155 5.0 43.5 1.0

Calcium binding site 2 out of 4 in the Galactose-Specific Lectin From Dolichos Lablab in P6522 Space Group


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 P6522 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:39.1 occ:1.00 O B:HOH403 2.2 30.1 1.0 OD2 B:ASP156 2.2 42.5 1.0 OD1 B:ASN152 2.3 43.7 1.0 O B:PHE150 2.4 42.4 1.0 OD1 B:ASP148 2.5 35.0 1.0 O B:HOH404 2.5 27.8 1.0 OD2 B:ASP148 2.6 35.0 1.0 CG B:ASP148 2.9 35.2 1.0 CG B:ASN152 3.3 44.1 1.0 CG B:ASP156 3.4 43.8 1.0 C B:PHE150 3.6 42.3 1.0 CB B:ASN152 3.7 44.6 1.0 OD1 B:ASP156 3.8 43.3 1.0 N B:ASN152 3.9 44.5 1.0 MN B:MN302 4.1 52.3 1.0 CA B:PHE150 4.3 41.6 1.0 NE1 B:TRP155 4.3 44.1 1.0 CB B:ASP148 4.4 35.3 1.0 CB B:PHE150 4.4 41.7 1.0 CA B:ASN152 4.4 44.8 1.0 N B:PHE150 4.4 40.5 1.0 O B:GLY126 4.5 38.8 1.0 ND2 B:ASN152 4.5 43.7 1.0 OD1 B:ASP108 4.5 35.9 1.0 N B:TYR151 4.6 43.3 1.0 CB B:ASP156 4.6 44.5 1.0 CD1 B:PHE150 4.6 42.5 1.0 O B:HOH401 4.7 21.4 1.0 CA B:GLY126 4.7 39.3 1.0 C B:TYR151 4.7 44.4 1.0 O B:ASP108 4.7 35.1 1.0 CE1 B:HIS161 4.8 33.1 1.0 CA B:TYR151 4.9 44.3 1.0 CE2 B:TRP155 5.0 43.6 1.0

Calcium binding site 3 out of 4 in the Galactose-Specific Lectin From Dolichos Lablab in P6522 Space Group


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 P6522 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:36.3 occ:1.00 OD1 C:ASN152 2.3 43.7 1.0 O C:PHE150 2.3 42.5 1.0 O C:HOH403 2.3 27.0 1.0 O C:HOH404 2.3 26.5 1.0 OD2 C:ASP156 2.3 42.5 1.0 OD1 C:ASP148 2.4 34.9 1.0 OD2 C:ASP148 2.7 34.9 1.0 CG C:ASP148 2.9 35.2 1.0 CG C:ASN152 3.3 44.1 1.0 C C:PHE150 3.4 42.3 1.0 CG C:ASP156 3.5 43.7 1.0 CB C:ASN152 3.7 44.6 1.0 N C:ASN152 3.9 44.6 1.0 OD1 C:ASP156 4.0 43.2 1.0 CA C:PHE150 4.1 41.6 1.0 CB C:PHE150 4.3 41.6 1.0 N C:PHE150 4.3 40.5 1.0 OD1 C:ASP108 4.4 35.9 1.0 CA C:ASN152 4.4 44.9 1.0 CB C:ASP148 4.4 35.4 1.0 N C:TYR151 4.5 43.3 1.0 MN C:MN302 4.5 46.1 1.0 CD1 C:PHE150 4.5 42.5 1.0 ND2 C:ASN152 4.5 43.6 1.0 NE1 C:TRP155 4.5 44.0 1.0 O C:GLY126 4.5 38.7 1.0 O C:HOH402 4.6 18.8 1.0 O C:ASP108 4.6 35.1 1.0 C C:TYR151 4.7 44.4 1.0 CA C:GLY126 4.7 39.2 1.0 CB C:ASP156 4.7 44.4 1.0 CA C:TYR151 4.8 44.3 1.0 CG C:PHE150 4.9 42.4 1.0 CE1 C:HIS161 4.9 33.1 1.0

Calcium binding site 4 out of 4 in the Galactose-Specific Lectin From Dolichos Lablab in P6522 Space Group


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 P6522 Space Group within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca301 b:36.1 occ:1.00 O D:HOH402 2.3 29.0 1.0 OD1 D:ASN152 2.3 43.7 1.0 O D:HOH401 2.4 30.9 1.0 OD2 D:ASP156 2.4 42.5 1.0 O D:PHE150 2.4 42.6 1.0 OD1 D:ASP148 2.4 35.0 1.0 OD2 D:ASP148 2.6 34.9 1.0 CG D:ASP148 2.8 35.3 1.0 CG D:ASN152 3.4 44.1 1.0 CG D:ASP156 3.5 43.8 1.0 C D:PHE150 3.5 42.4 1.0 CB D:ASN152 3.8 44.6 1.0 OD1 D:ASP156 4.0 43.3 1.0 N D:ASN152 4.0 44.6 1.0 CA D:PHE150 4.2 41.7 1.0 O D:HOH403 4.3 27.0 1.0 CB D:PHE150 4.3 41.7 1.0 N D:PHE150 4.3 40.5 1.0 CB D:ASP148 4.4 35.3 1.0 OD1 D:ASP108 4.4 35.9 1.0 O D:GLY126 4.4 38.8 1.0 MN D:MN302 4.5 51.5 1.0 NE1 D:TRP155 4.5 44.0 1.0 CA D:ASN152 4.5 44.8 1.0 ND2 D:ASN152 4.6 43.7 1.0 CD1 D:PHE150 4.6 42.5 1.0 N D:TYR151 4.6 43.3 1.0 O D:ASP108 4.6 35.1 1.0 CA D:GLY126 4.6 39.3 1.0 CB D:ASP156 4.7 44.5 1.0 C D:TYR151 4.8 44.5 1.0 CE1 D:HIS161 4.9 33.1 1.0 CA D:TYR151 4.9 44.3 1.0 CG D:PHE150 5.0 42.3 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