Calcium in PDB 1dzq: Lectin Uea-II Complexed with Galactose

The structure of Lectin Uea-II Complexed with Galactose, PDB code: 1dzq was solved by R.Loris, H.De Greve, M.-H.Dao-Thi, J.Messens, A.Imberty, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.00 / 2.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.870, 104.870, 175.300, 90.00, 90.00, 120.00
R / Rfree (%)	18.6 / 20.9

The structure of Lectin Uea-II Complexed with Galactose also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Lectin Uea-II Complexed with Galactose (pdb code 1dzq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Lectin Uea-II Complexed with Galactose, PDB code: 1dzq:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Lectin Uea-II Complexed with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lectin Uea-II Complexed with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:29.5 occ:1.00 OD1 A:ASP128 2.3 29.3 1.0 OD1 A:ASN136 2.3 41.1 1.0 O A:TYR130 2.5 36.2 1.0 OD2 A:ASP139 2.5 37.1 1.0 OD2 A:ASP128 2.7 22.8 1.0 CG A:ASP128 2.8 25.0 1.0 CG A:ASN136 3.5 39.5 1.0 CG A:ASP139 3.6 35.4 1.0 C A:TYR130 3.7 34.9 1.0 OD1 A:ASP139 4.0 38.0 1.0 CB A:ASN136 4.1 40.4 1.0 OD2 A:ASP86 4.2 35.4 1.0 CB A:ASP128 4.3 22.8 1.0 O A:GLY106 4.3 23.7 1.0 O A:ASP86 4.4 29.6 1.0 MN A:MN301 4.4 21.6 1.0 CA A:TYR130 4.4 32.5 1.0 CD2 A:TYR130 4.4 36.2 1.0 CB A:TYR130 4.5 34.1 1.0 NE1 A:TRP138 4.5 30.1 1.0 ND2 A:ASN136 4.5 40.3 1.0 N A:TYR130 4.5 29.6 1.0 CZ A:PHE108 4.6 21.4 1.0 N A:PHE131 4.7 36.8 1.0 CB A:ASP139 4.8 32.9 1.0 CA A:PHE131 4.8 39.0 1.0 CA A:GLY106 4.9 27.1 1.0 CG A:TYR130 5.0 35.2 1.0

Calcium binding site 2 out of 4 in the Lectin Uea-II Complexed with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lectin Uea-II Complexed with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:19.4 occ:1.00 OD1 B:ASP128 2.2 28.2 1.0 OD1 B:ASN136 2.3 40.0 1.0 O B:TYR130 2.4 35.5 1.0 OD2 B:ASP139 2.4 34.7 1.0 OD2 B:ASP128 2.7 21.1 1.0 CG B:ASP128 2.8 24.4 1.0 CG B:ASP139 3.5 33.4 1.0 CG B:ASN136 3.5 37.3 1.0 C B:TYR130 3.5 34.3 1.0 OD1 B:ASP139 3.9 38.0 1.0 CB B:ASN136 4.1 38.4 1.0 CB B:ASP128 4.2 23.9 1.0 OD2 B:ASP86 4.3 32.7 1.0 CA B:TYR130 4.4 31.4 1.0 CD2 B:TYR130 4.4 36.3 1.0 CB B:TYR130 4.4 32.1 1.0 N B:TYR130 4.4 28.4 1.0 O B:ASP86 4.5 28.7 1.0 MN B:MN301 4.5 14.3 1.0 NE1 B:TRP138 4.5 28.1 1.0 N B:PHE131 4.5 36.6 1.0 O B:GLY106 4.5 22.6 1.0 ND2 B:ASN136 4.6 39.0 1.0 CB B:ASP139 4.6 31.9 1.0 CA B:PHE131 4.7 38.0 1.0 CZ B:PHE108 4.7 17.0 1.0 CE1 B:HIS144 4.9 21.3 1.0 CG B:TYR130 4.9 34.6 1.0 CA B:ASP128 5.0 20.1 1.0

Calcium binding site 3 out of 4 in the Lectin Uea-II Complexed with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lectin Uea-II Complexed with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:33.3 occ:1.00 OD1 C:ASP128 2.3 30.7 1.0 OD1 C:ASN136 2.3 42.1 1.0 O C:TYR130 2.3 35.8 1.0 OD2 C:ASP139 2.5 35.8 1.0 OD2 C:ASP128 2.8 24.9 1.0 CG C:ASP128 2.9 27.1 1.0 CG C:ASN136 3.4 36.7 1.0 C C:TYR130 3.5 35.3 1.0 CG C:ASP139 3.6 35.0 1.0 OD1 C:ASP139 4.1 39.9 1.0 CB C:ASN136 4.1 38.0 1.0 OD2 C:ASP86 4.2 33.6 1.0 CA C:TYR130 4.3 32.5 1.0 CD2 C:TYR130 4.3 36.6 1.0 CB C:TYR130 4.3 33.8 1.0 CB C:ASP128 4.3 25.3 1.0 N C:TYR130 4.4 30.1 1.0 O C:ASP86 4.4 29.4 1.0 O C:GLY106 4.5 23.5 1.0 ND2 C:ASN136 4.5 36.9 1.0 N C:PHE131 4.5 36.2 1.0 NE1 C:TRP138 4.6 33.8 1.0 MN C:MN301 4.6 18.1 1.0 CA C:PHE131 4.7 38.1 1.0 CZ C:PHE108 4.7 21.6 1.0 CB C:ASP139 4.7 32.9 1.0 CG C:TYR130 4.8 34.9 1.0 CE1 C:HIS144 5.0 23.5 1.0 CA C:GLY106 5.0 26.0 1.0

Calcium binding site 4 out of 4 in the Lectin Uea-II Complexed with Galactose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lectin Uea-II Complexed with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:24.2 occ:1.00 OD1 D:ASP128 2.2 28.5 1.0 OD1 D:ASN136 2.3 41.8 1.0 O D:TYR130 2.4 37.0 1.0 OD2 D:ASP139 2.6 35.6 1.0 OD2 D:ASP128 2.8 24.4 1.0 CG D:ASP128 2.8 26.0 1.0 CG D:ASN136 3.5 38.6 1.0 C D:TYR130 3.6 34.6 1.0 CG D:ASP139 3.6 34.3 1.0 OD1 D:ASP139 4.1 36.3 1.0 OD2 D:ASP86 4.1 35.0 1.0 CB D:ASN136 4.2 39.2 1.0 CB D:ASP128 4.3 24.7 1.0 O D:ASP86 4.4 27.4 1.0 CA D:TYR130 4.4 32.5 1.0 CB D:TYR130 4.4 33.8 1.0 CD2 D:TYR130 4.4 37.5 1.0 O D:GLY106 4.4 27.3 1.0 N D:TYR130 4.4 30.9 1.0 ND2 D:ASN136 4.5 37.8 1.0 NE1 D:TRP138 4.6 30.1 1.0 N D:PHE131 4.6 36.1 1.0 CZ D:PHE108 4.6 22.5 1.0 MN D:MN301 4.6 17.9 1.0 CA D:PHE131 4.8 38.7 1.0 CB D:ASP139 4.8 33.0 1.0 CG D:TYR130 4.9 36.1 1.0 CA D:GLY106 4.9 26.6 1.0

R.Loris, H.De Greve, M.-H.Dao-Thi, J.Messens, A.Imberty, L.Wyns. Structural Basis of Carbohydrate Recognition By Lectin II From Ulex Europaeus, A Protein with A Promiscuous Carbohydrate Binding Site J.Mol.Biol. V. 301 987 2000.
ISSN: ISSN 0022-2836
PubMed: 10966800
DOI: 10.1006/JMBI.2000.4016