Calcium in PDB 1qoo: Lectin Uea-II Complexed with Nag

The structure of Lectin Uea-II Complexed with Nag, PDB code: 1qoo 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)	20.00 / 2.75
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	104.480, 104.480, 175.350, 90.00, 90.00, 120.00
R / Rfree (%)	17.4 / 20.8

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

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Lectin Uea-II Complexed with Nag (pdb code 1qoo). 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 Nag, PDB code: 1qoo:
Jump to Calcium binding site number: 1; 2; 3; 4;

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


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 Nag within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:26.8 occ:1.00 OD1 A:ASP128 2.3 29.3 1.0 OD1 A:ASN136 2.5 33.6 1.0 O A:TYR130 2.5 18.5 1.0 OD2 A:ASP139 2.6 20.4 1.0 OD2 A:ASP128 2.8 15.4 1.0 CG A:ASP128 2.9 17.6 1.0 CG A:ASN136 3.4 20.9 1.0 C A:TYR130 3.7 16.9 1.0 CG A:ASP139 3.7 22.6 1.0 CB A:ASN136 4.1 20.2 1.0 OD1 A:ASP139 4.2 29.1 1.0 OD2 A:ASP86 4.2 35.0 1.0 O A:GLY106 4.2 16.0 1.0 ND2 A:ASN136 4.3 15.6 1.0 O A:ASP86 4.4 22.3 1.0 CB A:ASP128 4.4 16.9 1.0 CD2 A:TYR130 4.4 29.7 1.0 CA A:TYR130 4.4 16.7 1.0 CB A:TYR130 4.4 18.4 1.0 CZ A:PHE108 4.5 10.2 1.0 N A:TYR130 4.5 17.1 1.0 MN A:MN301 4.6 18.2 1.0 NE1 A:TRP138 4.6 27.6 1.0 N A:PHE131 4.7 16.8 1.0 CA A:GLY106 4.8 11.8 1.0 CA A:PHE131 4.9 19.3 1.0 CG A:TYR130 4.9 25.7 1.0 CB A:ASP139 4.9 17.4 1.0 C A:GLY106 5.0 11.4 1.0

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


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 Nag within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca304 b:21.9 occ:1.00 OD1 B:ASN136 2.3 22.8 1.0 O B:TYR130 2.3 22.8 1.0 OD1 B:ASP128 2.3 21.1 1.0 OD2 B:ASP139 2.3 22.1 1.0 OD2 B:ASP128 2.7 13.0 1.0 CG B:ASP128 2.8 15.4 1.0 CG B:ASN136 3.4 14.3 1.0 CG B:ASP139 3.5 24.3 1.0 C B:TYR130 3.5 19.9 1.0 OD1 B:ASP139 4.0 33.0 1.0 CB B:ASN136 4.1 15.2 1.0 CA B:TYR130 4.3 17.0 1.0 CB B:ASP128 4.3 17.2 1.0 ND2 B:ASN136 4.4 17.9 1.0 CD2 B:TYR130 4.4 23.2 1.0 CB B:TYR130 4.4 16.1 1.0 OD2 B:ASP86 4.4 25.5 1.0 MN B:MN303 4.4 15.7 1.0 N B:TYR130 4.4 13.7 1.0 N B:PHE131 4.5 20.4 1.0 O B:GLY106 4.5 19.1 1.0 O B:ASP86 4.5 22.9 1.0 CA B:PHE131 4.6 19.0 1.0 NE1 B:TRP138 4.6 22.2 1.0 CB B:ASP139 4.7 19.7 1.0 CZ B:PHE108 4.7 8.3 1.0 CE1 B:HIS144 4.9 10.2 1.0 CG B:TYR130 4.9 20.4 1.0

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


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 Nag within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca306 b:28.9 occ:1.00 O C:TYR130 2.3 23.2 1.0 OD1 C:ASP128 2.3 25.5 1.0 OD2 C:ASP139 2.4 24.1 1.0 OD1 C:ASN136 2.5 31.9 1.0 OD2 C:ASP128 2.8 17.4 1.0 CG C:ASP128 2.9 15.9 1.0 CG C:ASN136 3.5 28.2 1.0 C C:TYR130 3.5 23.3 1.0 CG C:ASP139 3.6 23.1 1.0 CB C:ASN136 4.0 25.9 1.0 OD1 C:ASP139 4.1 31.6 1.0 OD2 C:ASP86 4.3 31.1 1.0 CA C:TYR130 4.3 18.5 1.0 CD2 C:TYR130 4.4 24.1 1.0 CB C:TYR130 4.4 22.0 1.0 O C:GLY106 4.4 15.8 1.0 CB C:ASP128 4.4 17.9 1.0 N C:TYR130 4.5 16.4 1.0 MN C:MN305 4.5 15.5 1.0 O C:ASP86 4.5 22.6 1.0 N C:PHE131 4.5 21.9 1.0 ND2 C:ASN136 4.6 29.2 1.0 NE1 C:TRP138 4.6 27.9 1.0 CA C:PHE131 4.7 18.4 1.0 CZ C:PHE108 4.7 16.5 1.0 CB C:ASP139 4.8 20.8 1.0 CG C:TYR130 4.9 24.1 1.0 CA C:GLY106 5.0 14.7 1.0 CE1 C:HIS144 5.0 18.6 1.0

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


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 Nag within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca308 b:26.0 occ:1.00 OD2 D:ASP139 2.3 19.4 1.0 OD1 D:ASP128 2.4 20.5 1.0 O D:TYR130 2.4 21.1 1.0 OD1 D:ASN136 2.4 34.3 1.0 OD2 D:ASP128 2.7 10.1 1.0 CG D:ASP128 2.9 17.8 1.0 CG D:ASN136 3.5 24.4 1.0 CG D:ASP139 3.5 20.0 1.0 C D:TYR130 3.6 17.6 1.0 OD1 D:ASP139 4.0 30.9 1.0 CB D:ASN136 4.1 22.1 1.0 CB D:ASP128 4.4 20.2 1.0 O D:GLY106 4.4 21.8 1.0 CA D:TYR130 4.4 15.6 1.0 OD2 D:ASP86 4.4 32.4 1.0 MN D:MN307 4.4 22.5 1.0 CD2 D:TYR130 4.4 26.3 1.0 CB D:TYR130 4.5 18.7 1.0 NE1 D:TRP138 4.5 18.3 1.0 N D:TYR130 4.5 22.1 1.0 ND2 D:ASN136 4.6 23.2 1.0 N D:PHE131 4.6 20.8 1.0 O D:ASP86 4.6 24.6 1.0 CZ D:PHE108 4.7 16.8 1.0 CA D:PHE131 4.7 22.8 1.0 CB D:ASP139 4.7 17.8 1.0 CE1 D:HIS144 4.9 14.1 1.0 CG D:TYR130 4.9 28.4 1.0 CA D:GLY106 5.0 13.6 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