Manganese in PDB 5kxc: Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5.

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5., PDB code: 5kxc 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 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.745, 103.383, 148.922, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 21.9

The structure of Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5. 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 8.5. (pdb code 5kxc). 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 8.5., PDB code: 5kxc:
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 8.5.


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 8.5. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn305 b:28.2 occ:1.00 O A:HOH433 2.0 19.8 1.0 OD2 A:ASP157 2.1 19.9 1.0 OE2 A:GLU155 2.2 22.9 1.0 OD1 A:ASP164 2.2 24.2 1.0 NE2 A:HIS169 2.3 25.3 1.0 O A:HOH414 2.3 22.8 1.0 CD A:GLU155 3.2 24.7 1.0 CG A:ASP157 3.2 22.9 1.0 CG A:ASP164 3.2 24.5 1.0 CE1 A:HIS169 3.2 23.7 1.0 CD2 A:HIS169 3.3 25.5 1.0 OE1 A:GLU155 3.5 22.2 1.0 CB A:ASP157 3.6 24.1 1.0 OD2 A:ASP164 3.7 25.3 1.0 O A:HOH471 3.9 26.8 1.0 OG A:SER179 4.1 23.9 1.0 CA A:CA304 4.2 26.4 1.0 OD1 A:ASP157 4.2 21.1 1.0 CB A:ASP164 4.4 26.1 1.0 ND1 A:HIS169 4.4 26.4 1.0 CG A:HIS169 4.4 22.3 1.0 CG A:GLU155 4.5 22.2 1.0 O A:HOH470 4.5 26.3 1.0 O A:ILE177 4.5 25.6 1.0 NE1 A:TRP163 4.5 30.6 1.0 CD A:PRO165 4.7 29.2 1.0 CD1 A:TRP163 4.7 29.9 1.0 CA A:ASP164 4.8 26.1 1.0

Manganese binding site 2 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5.


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 8.5. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn304 b:27.6 occ:1.00 OD2 B:ASP157 2.1 21.0 1.0 O B:HOH474 2.1 21.5 1.0 OE2 B:GLU155 2.2 21.5 1.0 OD1 B:ASP164 2.2 23.4 1.0 O B:HOH416 2.2 22.0 1.0 NE2 B:HIS169 2.3 21.6 1.0 CG B:ASP157 3.1 23.2 1.0 CG B:ASP164 3.2 25.4 1.0 CD B:GLU155 3.2 24.2 1.0 CE1 B:HIS169 3.3 20.6 1.0 CD2 B:HIS169 3.3 21.2 1.0 OE1 B:GLU155 3.5 23.4 1.0 CB B:ASP157 3.6 22.4 1.0 OD2 B:ASP164 3.6 23.4 1.0 O B:HOH475 3.9 22.0 1.0 OG B:SER179 4.1 24.1 1.0 CA B:CA303 4.2 22.5 1.0 OD1 B:ASP157 4.2 22.0 1.0 CB B:ASP164 4.3 25.0 1.0 ND1 B:HIS169 4.4 22.1 1.0 O B:ILE177 4.4 23.9 1.0 CG B:HIS169 4.5 21.3 1.0 CG B:GLU155 4.5 20.9 1.0 NE1 B:TRP163 4.6 27.5 1.0 O B:HOH500 4.6 26.2 1.0 CD B:PRO165 4.7 28.4 1.0 CD1 B:TRP163 4.8 28.1 1.0 CA B:ASP164 4.8 26.9 1.0

Manganese binding site 3 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5.


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 8.5. within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn307 b:30.2 occ:1.00 O C:HOH480 2.0 23.8 1.0 OD2 C:ASP157 2.1 24.6 1.0 OE2 C:GLU155 2.2 26.5 1.0 OD1 C:ASP164 2.2 25.4 1.0 O C:HOH422 2.2 25.3 1.0 NE2 C:HIS169 2.3 30.3 1.0 CG C:ASP157 3.1 28.3 1.0 CD C:GLU155 3.2 28.3 1.0 CG C:ASP164 3.2 29.8 1.0 CE1 C:HIS169 3.3 28.8 1.0 CD2 C:HIS169 3.3 28.3 1.0 OE1 C:GLU155 3.5 27.0 1.0 CB C:ASP157 3.6 27.2 1.0 OD2 C:ASP164 3.6 30.2 1.0 O C:HOH482 3.8 26.4 1.0 OG C:SER179 4.1 25.6 1.0 CA C:CA306 4.2 27.7 1.0 OD1 C:ASP157 4.2 28.3 1.0 CB C:ASP164 4.3 30.7 1.0 O C:HOH488 4.4 27.5 1.0 ND1 C:HIS169 4.4 29.5 1.0 CG C:HIS169 4.5 28.1 1.0 O C:ILE177 4.5 25.0 1.0 CG C:GLU155 4.5 27.4 1.0 NE1 C:TRP163 4.5 31.5 1.0 CD C:PRO165 4.7 35.7 1.0 CD1 C:TRP163 4.7 31.8 1.0 CA C:ASP164 4.8 32.2 1.0

Manganese binding site 4 out of 4 in the Wisteria Floribunda Lectin in Complex with Galnac(BETA1-4)Glcnac (Lacdinac) at pH 8.5.


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 8.5. within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn304 b:27.4 occ:1.00 OD2 D:ASP157 2.1 20.5 1.0 OE2 D:GLU155 2.2 22.6 1.0 O D:HOH412 2.2 22.9 1.0 OD1 D:ASP164 2.2 24.9 1.0 O D:HOH407 2.2 23.0 1.0 NE2 D:HIS169 2.3 25.8 1.0 CG D:ASP157 3.1 21.9 1.0 CD D:GLU155 3.1 25.3 1.0 CG D:ASP164 3.1 26.3 1.0 CE1 D:HIS169 3.2 24.3 1.0 CD2 D:HIS169 3.3 23.8 1.0 OE1 D:GLU155 3.5 25.2 1.0 CB D:ASP157 3.6 22.1 1.0 OD2 D:ASP164 3.6 26.3 1.0 O D:HOH465 3.9 24.1 1.0 OG D:SER179 4.1 22.6 1.0 CA D:CA303 4.1 23.6 1.0 OD1 D:ASP157 4.2 20.6 1.0 CB D:ASP164 4.3 25.4 1.0 ND1 D:HIS169 4.4 24.3 1.0 O D:HOH492 4.4 24.3 1.0 CG D:HIS169 4.4 23.1 1.0 CG D:GLU155 4.5 23.4 1.0 O D:ILE177 4.5 24.2 1.0 NE1 D:TRP163 4.5 30.3 1.0 CD D:PRO165 4.7 28.8 1.0 CD1 D:TRP163 4.7 28.4 1.0 CA D:ASP164 4.8 25.9 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