Manganese in PDB 5kxd: Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5, PDB code: 5kxd 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 / 1.95
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.096, 104.271, 148.739, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 19.8

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 (pdb code 5kxd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5, PDB code: 5kxd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn304 b:19.2 occ:1.00 O A:HOH432 2.1 11.1 1.0 OE2 A:GLU155 2.1 14.8 1.0 OD2 A:ASP157 2.2 11.2 1.0 OD1 A:ASP164 2.2 15.3 1.0 NE2 A:HIS169 2.3 13.3 1.0 O A:HOH415 2.3 14.9 1.0 CD A:GLU155 3.1 16.8 1.0 CG A:ASP164 3.2 15.0 1.0 CG A:ASP157 3.2 13.2 1.0 CE1 A:HIS169 3.3 13.5 1.0 CD2 A:HIS169 3.3 13.5 1.0 OE1 A:GLU155 3.5 18.2 1.0 CB A:ASP157 3.6 13.5 1.0 OD2 A:ASP164 3.7 14.0 1.0 O A:HOH440 4.0 13.2 1.0 OG A:SER179 4.1 14.9 1.0 CA A:CA303 4.2 15.6 1.0 OD1 A:ASP157 4.3 13.9 1.0 CB A:ASP164 4.3 15.9 1.0 O A:HOH511 4.3 15.9 1.0 ND1 A:HIS169 4.4 14.2 1.0 O A:ILE177 4.4 14.8 1.0 CG A:HIS169 4.5 13.5 1.0 CG A:GLU155 4.5 15.9 1.0 NE1 A:TRP163 4.6 19.1 1.0 CD A:PRO165 4.7 18.4 1.0 CD1 A:TRP163 4.7 18.1 1.0 CA A:ASP164 4.8 16.0 1.0

Manganese binding site 2 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:19.3 occ:1.00 O B:HOH465 2.1 11.0 1.0 OD2 B:ASP157 2.1 12.5 1.0 OD1 B:ASP164 2.2 14.5 1.0 OE2 B:GLU155 2.2 14.9 1.0 O B:HOH448 2.3 14.2 1.0 NE2 B:HIS169 2.3 14.2 1.0 CG B:ASP164 3.2 15.1 1.0 CG B:ASP157 3.2 13.5 1.0 CE1 B:HIS169 3.2 13.3 1.0 CD B:GLU155 3.2 16.2 1.0 CD2 B:HIS169 3.3 13.8 1.0 OE1 B:GLU155 3.5 15.3 1.0 CB B:ASP157 3.6 14.3 1.0 OD2 B:ASP164 3.7 16.0 1.0 O B:HOH478 3.8 15.9 1.0 OG B:SER179 4.2 15.7 1.0 CA B:CA302 4.2 14.7 1.0 OD1 B:ASP157 4.3 12.4 1.0 CB B:ASP164 4.3 15.7 1.0 O B:HOH492 4.3 19.1 1.0 ND1 B:HIS169 4.3 13.5 1.0 CG B:HIS169 4.4 13.4 1.0 O B:ILE177 4.4 18.7 1.0 CG B:GLU155 4.6 15.1 1.0 NE1 B:TRP163 4.6 20.2 1.0 CD B:PRO165 4.7 18.5 1.0 CD1 B:TRP163 4.7 20.4 1.0 CA B:ASP164 4.8 17.3 1.0

Manganese binding site 3 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn309 b:20.0 occ:1.00 OD2 C:ASP157 2.1 14.2 1.0 O C:HOH451 2.1 15.9 1.0 OD1 C:ASP164 2.2 15.6 1.0 OE2 C:GLU155 2.2 16.0 1.0 O C:HOH448 2.3 13.2 1.0 NE2 C:HIS169 2.4 15.4 1.0 CG C:ASP164 3.2 15.9 1.0 CD C:GLU155 3.2 17.2 1.0 CG C:ASP157 3.2 15.2 1.0 CE1 C:HIS169 3.3 15.5 1.0 CD2 C:HIS169 3.4 15.2 1.0 OE1 C:GLU155 3.5 17.0 1.0 CB C:ASP157 3.6 15.7 1.0 OD2 C:ASP164 3.7 15.4 1.0 O C:HOH453 3.9 13.7 1.0 CA C:CA308 4.2 15.6 1.0 OG C:SER179 4.2 15.7 1.0 OD1 C:ASP157 4.3 15.2 1.0 CB C:ASP164 4.3 17.2 1.0 O C:HOH503 4.4 17.6 1.0 O C:ILE177 4.4 15.7 1.0 ND1 C:HIS169 4.4 15.4 1.0 CG C:HIS169 4.5 15.0 1.0 CG C:GLU155 4.5 16.2 1.0 NE1 C:TRP163 4.5 15.8 1.0 CD1 C:TRP163 4.7 16.3 1.0 CD C:PRO165 4.7 21.0 1.0 CA C:ASP164 4.8 18.2 1.0

Manganese binding site 4 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 6.5 within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn304 b:19.7 occ:1.00 OD2 D:ASP157 2.1 12.1 1.0 O D:HOH426 2.1 12.3 1.0 OD1 D:ASP164 2.2 15.1 1.0 OE2 D:GLU155 2.2 16.1 1.0 O D:HOH410 2.3 13.3 1.0 NE2 D:HIS169 2.3 13.9 1.0 CG D:ASP164 3.1 14.8 1.0 CG D:ASP157 3.2 12.8 1.0 CE1 D:HIS169 3.2 14.4 1.0 CD D:GLU155 3.2 17.4 1.0 CD2 D:HIS169 3.3 14.6 1.0 OE1 D:GLU155 3.6 18.3 1.0 CB D:ASP157 3.6 13.1 1.0 OD2 D:ASP164 3.6 15.3 1.0 O D:HOH433 3.9 15.1 1.0 CA D:CA303 4.2 15.3 1.0 OG D:SER179 4.2 16.1 1.0 OD1 D:ASP157 4.2 12.8 1.0 CB D:ASP164 4.3 16.7 1.0 ND1 D:HIS169 4.4 14.3 1.0 CG D:HIS169 4.4 14.8 1.0 O D:HOH489 4.5 17.7 1.0 O D:ILE177 4.5 16.0 1.0 CG D:GLU155 4.6 17.0 1.0 NE1 D:TRP163 4.6 20.3 1.0 CD D:PRO165 4.6 21.0 1.0 CD1 D:TRP163 4.7 20.0 1.0 CA D:ASP164 4.8 17.8 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