Calcium in PDB 5kxb: Wisteria Floribunda Lectin in Complex with Galnac

The structure of Wisteria Floribunda Lectin in Complex with Galnac, PDB code: 5kxb was solved by S.V.Evans, O.Haji-Ghassemi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.33
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	121.191, 157.269, 55.730, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22.4

The structure of Wisteria Floribunda Lectin in Complex with Galnac also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Calcium atom in the Wisteria Floribunda Lectin in Complex with Galnac (pdb code 5kxb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Wisteria Floribunda Lectin in Complex with Galnac, PDB code: 5kxb:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Wisteria Floribunda Lectin in Complex with Galnac within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca308 b:31.4 occ:1.00 O A:HOH437 2.2 27.8 1.0 O A:HOH426 2.3 31.8 1.0 O A:PHE159 2.4 32.7 1.0 OD1 A:ASN161 2.4 42.7 1.0 OD2 A:ASP164 2.4 34.4 1.0 OD1 A:ASP157 2.4 39.2 1.0 OD2 A:ASP157 2.6 33.7 1.0 CG A:ASP157 2.9 34.6 1.0 CG A:ASP164 3.5 36.2 1.0 CG A:ASN161 3.5 41.3 1.0 C A:PHE159 3.6 37.5 1.0 OD1 A:ASP164 4.0 35.7 1.0 N A:ASN161 4.0 40.0 1.0 O A:HOH421 4.1 17.5 1.0 CB A:ASN161 4.1 40.6 1.0 MN A:MN309 4.3 37.7 1.0 CB A:ASP157 4.4 31.5 1.0 CA A:PHE159 4.4 37.9 1.0 N A:PHE159 4.5 35.5 1.0 NE1 A:TRP163 4.5 45.9 1.0 O A:GLY135 4.6 36.1 1.0 O A:ASP117 4.6 32.5 1.0 OD1 A:ASP117 4.6 31.6 1.0 N A:LYS160 4.6 38.9 1.0 CB A:PHE159 4.6 39.8 1.0 ND2 A:ASN161 4.6 40.7 1.0 CA A:GLY135 4.7 37.1 1.0 CB A:ASP164 4.7 36.2 1.0 CA A:LYS160 4.7 42.6 1.0 CA A:ASN161 4.8 40.5 1.0 C A:LYS160 4.8 42.1 1.0 CD2 A:PHE159 4.8 44.5 1.0 CZ2 A:TRP163 4.9 44.7 1.0 CE1 A:HIS169 4.9 25.2 1.0 CE2 A:TRP163 5.0 43.6 1.0

Calcium binding site 2 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Wisteria Floribunda Lectin in Complex with Galnac within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca306 b:38.6 occ:1.00 OD2 B:ASP164 2.3 34.3 1.0 O B:PHE159 2.4 37.0 1.0 OD1 B:ASN161 2.4 53.4 1.0 O B:HOH411 2.4 29.8 1.0 OD1 B:ASP157 2.5 37.2 1.0 O B:HOH413 2.5 30.6 1.0 OD2 B:ASP157 2.6 33.2 1.0 CG B:ASP157 2.9 35.0 1.0 CG B:ASP164 3.4 39.9 1.0 CG B:ASN161 3.5 51.9 1.0 C B:PHE159 3.6 43.3 1.0 OD1 B:ASP164 3.9 43.2 1.0 N B:ASN161 4.0 50.8 1.0 MN B:MN307 4.1 43.6 1.0 CB B:ASN161 4.1 50.5 1.0 O B:HOH409 4.4 35.7 1.0 NE1 B:TRP163 4.4 49.9 1.0 CB B:ASP157 4.4 36.8 1.0 CA B:PHE159 4.5 45.6 1.0 O B:GLY135 4.5 41.6 1.0 N B:PHE159 4.5 47.2 1.0 N B:LYS160 4.6 43.8 1.0 ND2 B:ASN161 4.6 54.3 1.0 CB B:ASP164 4.6 40.8 1.0 OD1 B:ASP117 4.6 46.3 1.0 O B:ASP117 4.6 36.5 1.0 CA B:GLY135 4.7 42.5 1.0 CA B:LYS160 4.7 46.6 1.0 CA B:ASN161 4.7 51.4 1.0 CB B:PHE159 4.7 52.7 1.0 C B:LYS160 4.7 49.9 1.0 CZ2 B:TRP163 4.8 52.4 1.0 CD1 B:PHE159 4.9 59.3 1.0 CE1 B:HIS169 4.9 39.5 1.0 CE2 B:TRP163 4.9 50.4 1.0

Calcium binding site 3 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Wisteria Floribunda Lectin in Complex with Galnac within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca306 b:26.3 occ:1.00 O C:HOH441 2.2 32.3 1.0 O C:PHE159 2.3 29.1 1.0 OD1 C:ASP157 2.4 23.9 1.0 O C:HOH417 2.4 23.2 1.0 OD2 C:ASP164 2.4 30.9 1.0 OD1 C:ASN161 2.4 33.3 1.0 OD2 C:ASP157 2.6 22.9 1.0 CG C:ASP157 2.8 23.7 1.0 C C:PHE159 3.5 34.1 1.0 CG C:ASP164 3.5 30.2 1.0 CG C:ASN161 3.6 30.5 1.0 N C:ASN161 4.1 33.9 1.0 OD1 C:ASP164 4.1 32.7 1.0 MN C:MN307 4.2 32.8 1.0 CB C:ASN161 4.2 30.5 1.0 O C:HOH405 4.3 25.1 1.0 CA C:PHE159 4.3 33.4 1.0 CB C:ASP157 4.4 23.6 1.0 N C:PHE159 4.4 34.4 1.0 O C:ASP117 4.5 27.7 1.0 N C:LYS160 4.5 35.7 1.0 CB C:PHE159 4.5 34.0 1.0 NE1 C:TRP163 4.5 27.2 1.0 OD1 C:ASP117 4.6 25.5 1.0 O C:GLY135 4.6 24.4 1.0 ND2 C:ASN161 4.7 28.9 1.0 CA C:LYS160 4.7 36.2 1.0 CA C:GLY135 4.7 27.7 1.0 CB C:ASP164 4.7 28.8 1.0 CD2 C:PHE159 4.8 35.3 1.0 C C:LYS160 4.8 37.0 1.0 CA C:ASN161 4.8 31.3 1.0 CE1 C:HIS169 4.9 28.4 1.0 CZ2 C:TRP163 4.9 26.5 1.0

Calcium binding site 4 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Wisteria Floribunda Lectin in Complex with Galnac within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca302 b:40.2 occ:1.00 O D:HOH427 2.2 31.4 1.0 O D:PHE159 2.3 43.1 1.0 OD1 D:ASN161 2.3 47.8 1.0 OD2 D:ASP164 2.3 44.7 1.0 O D:HOH409 2.4 32.3 1.0 OD1 D:ASP157 2.4 36.8 1.0 OD2 D:ASP157 2.7 36.0 1.0 CG D:ASP157 2.9 36.7 1.0 CG D:ASN161 3.5 48.0 1.0 CG D:ASP164 3.5 47.2 1.0 C D:PHE159 3.5 43.9 1.0 N D:ASN161 4.0 44.0 1.0 OD1 D:ASP164 4.0 45.9 1.0 CB D:ASN161 4.1 47.7 1.0 MN D:MN303 4.3 40.8 1.0 CA D:PHE159 4.4 42.9 1.0 CB D:ASP157 4.4 35.3 1.0 N D:PHE159 4.4 40.3 1.0 O D:HOH413 4.5 24.0 1.0 NE1 D:TRP163 4.5 56.2 1.0 N D:LYS160 4.5 44.0 1.0 CB D:PHE159 4.6 43.6 1.0 ND2 D:ASN161 4.6 49.3 1.0 O D:ASP117 4.6 37.2 1.0 O D:GLY135 4.6 44.5 1.0 OD1 D:ASP117 4.6 42.2 1.0 CA D:LYS160 4.6 45.7 1.0 CB D:ASP164 4.7 45.8 1.0 C D:LYS160 4.7 43.7 1.0 CA D:ASN161 4.7 46.0 1.0 CA D:GLY135 4.7 42.8 1.0 CD2 D:PHE159 4.7 41.7 1.0 CZ2 D:TRP163 4.9 52.7 1.0 CE1 D:HIS169 4.9 41.3 1.0 CE2 D:TRP163 5.0 51.9 1.0

O.Haji-Ghassemi, M.Gilbert, J.Spence, M.J.Schur, M.J.Parker, M.L.Jenkins, J.E.Burke, H.Van Faassen, N.M.Young, S.V.Evans. Molecular Basis For Recognition of the Cancer Glycobiomarker, Lacdinac (Galnac[ Beta 14]Glcnac), By Wisteria Floribunda Agglutinin. J.Biol.Chem. V. 291 24085 2016.
ISSN: ESSN 1083-351X
PubMed: 27601469
DOI: 10.1074/JBC.M116.750463