Calcium in PDB 1qnw: Lectin II From Ulex Europaeus

The structure of Lectin II From Ulex Europaeus, PDB code: 1qnw 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)	50.0 / 2.35
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.910, 104.910, 175.450, 90.00, 90.00, 120.00
R / Rfree (%)	17.8 / 21.8

The structure of Lectin II From Ulex Europaeus also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Lectin II From Ulex Europaeus (pdb code 1qnw). 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 II From Ulex Europaeus, PDB code: 1qnw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Lectin II From Ulex Europaeus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Lectin II From Ulex Europaeus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:25.5 occ:1.00 O A:TYR130 2.2 25.7 1.0 OD1 A:ASN136 2.3 35.5 1.0 O A:HOH2023 2.4 25.1 1.0 OD1 A:ASP128 2.4 29.8 1.0 O A:HOH2020 2.4 21.3 1.0 OD2 A:ASP139 2.4 20.8 1.0 OD2 A:ASP128 2.6 24.7 1.0 CG A:ASP128 2.8 20.8 1.0 CG A:ASN136 3.4 31.9 1.0 C A:TYR130 3.4 27.4 1.0 CG A:ASP139 3.6 25.4 1.0 CB A:ASN136 4.0 33.6 1.0 OD1 A:ASP139 4.1 31.9 1.0 MN A:MN301 4.2 38.0 1.0 CA A:TYR130 4.3 26.1 1.0 CB A:ASP128 4.3 22.7 1.0 CD2 A:TYR130 4.4 35.3 1.0 N A:TYR130 4.4 23.5 1.0 CB A:TYR130 4.4 30.6 1.0 ND2 A:ASN136 4.4 30.3 1.0 O A:HOH2049 4.4 32.1 1.0 N A:PHE131 4.4 28.2 1.0 O A:GLY106 4.5 22.2 1.0 O A:ASP86 4.6 23.7 1.0 CA A:PHE131 4.6 32.8 1.0 NE1 A:TRP138 4.6 27.7 1.0 OD2 A:ASP86 4.6 31.6 1.0 CZ A:PHE108 4.7 20.9 1.0 CB A:ASP139 4.8 27.1 1.0 CG A:TYR130 4.9 35.2 1.0

Calcium binding site 2 out of 4 in the Lectin II From Ulex Europaeus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Lectin II From Ulex Europaeus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:17.9 occ:1.00 O B:HOH2010 2.2 19.7 1.0 O B:TYR130 2.3 22.4 1.0 OD2 B:ASP139 2.3 20.4 1.0 OD1 B:ASN136 2.4 18.3 1.0 OD1 B:ASP128 2.4 20.6 1.0 O B:HOH2019 2.5 9.3 1.0 OD2 B:ASP128 2.5 15.2 1.0 CG B:ASP128 2.8 18.5 1.0 CG B:ASP139 3.4 23.6 1.0 CG B:ASN136 3.4 21.3 1.0 C B:TYR130 3.5 25.7 1.0 OD1 B:ASP139 3.9 29.3 1.0 CB B:ASN136 4.0 15.1 1.0 MN B:MN303 4.2 20.0 1.0 CB B:ASP128 4.3 22.9 1.0 CA B:TYR130 4.3 24.1 1.0 O B:HOH2050 4.4 22.0 1.0 N B:PHE131 4.4 23.2 1.0 CB B:TYR130 4.5 21.9 1.0 CD2 B:TYR130 4.5 31.6 1.0 N B:TYR130 4.5 20.4 1.0 NE1 B:TRP138 4.5 22.3 1.0 ND2 B:ASN136 4.5 16.5 1.0 O B:GLY106 4.5 20.5 1.0 CA B:PHE131 4.5 27.9 1.0 CB B:ASP139 4.6 21.1 1.0 O B:ASP86 4.7 20.0 1.0 CZ B:PHE108 4.7 13.6 1.0 OD2 B:ASP86 4.8 17.6 1.0 CG B:TYR130 4.9 29.3 1.0 CE1 B:HIS144 5.0 11.4 1.0

Calcium binding site 3 out of 4 in the Lectin II From Ulex Europaeus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Lectin II From Ulex Europaeus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca306 b:30.4 occ:1.00 O C:TYR130 2.3 31.2 1.0 O C:HOH2018 2.3 24.1 1.0 OD2 C:ASP139 2.3 23.9 1.0 OD1 C:ASP128 2.4 28.9 1.0 O C:HOH2016 2.4 17.8 1.0 OD1 C:ASN136 2.4 36.5 1.0 OD2 C:ASP128 2.5 26.0 1.0 CG C:ASP128 2.8 26.4 1.0 CG C:ASP139 3.5 28.1 1.0 CG C:ASN136 3.5 34.4 1.0 C C:TYR130 3.5 30.0 1.0 OD1 C:ASP139 3.9 34.1 1.0 CB C:ASN136 4.0 38.0 1.0 O C:HOH2051 4.3 24.5 1.0 MN C:MN305 4.3 30.2 1.0 CB C:ASP128 4.3 22.9 1.0 CA C:TYR130 4.4 28.3 1.0 N C:PHE131 4.5 30.2 1.0 N C:TYR130 4.5 26.1 1.0 CB C:TYR130 4.5 28.0 1.0 O C:GLY106 4.5 22.0 1.0 CD2 C:TYR130 4.5 36.9 1.0 NE1 C:TRP138 4.5 26.4 1.0 ND2 C:ASN136 4.6 42.3 1.0 CA C:PHE131 4.6 32.3 1.0 CZ C:PHE108 4.7 19.5 1.0 O C:ASP86 4.7 22.7 1.0 CB C:ASP139 4.7 27.2 1.0 OD2 C:ASP86 4.7 21.2 1.0 CE1 C:HIS144 5.0 21.7 1.0 CG C:TYR130 5.0 34.1 1.0

Calcium binding site 4 out of 4 in the Lectin II From Ulex Europaeus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Lectin II From Ulex Europaeus within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca308 b:25.9 occ:1.00 O D:HOH2022 2.2 24.0 1.0 OD2 D:ASP139 2.2 21.5 1.0 O D:HOH2019 2.2 21.3 1.0 O D:TYR130 2.3 31.5 1.0 OD1 D:ASP128 2.4 22.3 1.0 OD2 D:ASP128 2.4 20.6 1.0 OD1 D:ASN136 2.5 36.7 1.0 CG D:ASP128 2.8 22.6 1.0 CG D:ASP139 3.3 27.4 1.0 C D:TYR130 3.5 30.3 1.0 CG D:ASN136 3.5 25.8 1.0 OD1 D:ASP139 3.8 33.2 1.0 CB D:ASN136 4.0 31.9 1.0 MN D:MN307 4.0 28.7 1.0 CB D:ASP128 4.3 23.6 1.0 O D:HOH2048 4.3 15.2 1.0 CA D:TYR130 4.4 26.1 1.0 N D:PHE131 4.4 28.6 1.0 NE1 D:TRP138 4.4 23.1 1.0 CA D:PHE131 4.5 33.4 1.0 N D:TYR130 4.5 28.2 1.0 CB D:TYR130 4.5 29.3 1.0 CB D:ASP139 4.5 25.8 1.0 CD2 D:TYR130 4.6 36.3 1.0 ND2 D:ASN136 4.6 27.3 1.0 O D:GLY106 4.6 24.3 1.0 CZ D:PHE108 4.8 24.6 1.0 O D:ASP86 4.8 28.5 1.0 CE1 D:HIS144 4.8 18.6 1.0 OD2 D:ASP86 4.8 29.6 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