Manganese in PDB 3zvx: Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside

The structure of Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside, PDB code: 3zvx was solved by R.G.Benevides, G.Ganne, C.Unverzagt, B.S.Cavada, C.Breton, A.Varrot, A.Imberty, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.25 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	42.620, 80.680, 148.760, 90.00, 90.00, 90.00
R / Rfree (%)	19.497 / 25.18

The structure of Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Manganese atom in the Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside (pdb code 3zvx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside, PDB code: 3zvx:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn300 b:20.9 occ:1.00 NE2 A:HIS155 2.2 18.8 1.0 OD1 A:ASP150 2.3 17.6 1.0 O A:HOH2115 2.3 17.5 1.0 OD2 A:ASP139 2.3 16.1 1.0 O A:HOH2114 2.4 15.1 1.0 OE2 A:GLU137 2.5 17.8 1.0 CE1 A:HIS155 3.0 20.4 1.0 CG A:ASP150 3.2 19.7 1.0 OE1 A:GLU137 3.2 13.2 1.0 CD A:GLU137 3.2 17.7 1.0 CD2 A:HIS155 3.3 20.2 1.0 CG A:ASP139 3.4 19.1 1.0 OD2 A:ASP150 3.5 17.0 1.0 O A:HOH2101 3.7 16.0 1.0 CB A:ASP139 3.7 19.0 1.0 CA A:CA301 4.2 19.7 1.0 ND1 A:HIS155 4.2 20.1 1.0 OG A:SER165 4.3 21.3 1.0 O A:ILE163 4.4 22.0 1.0 CG A:HIS155 4.4 19.6 1.0 CB A:ASP150 4.4 20.9 1.0 OD1 A:ASP139 4.4 16.6 1.0 CD1 A:TRP149 4.6 23.1 1.0 CG A:GLU137 4.7 17.8 1.0 NE1 A:TRP149 4.7 22.5 1.0 O A:HOH2118 4.7 25.6 1.0 CA A:ASP150 4.8 20.9 1.0 CD A:PRO151 4.8 21.6 1.0

Manganese binding site 2 out of 2 in the Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of the Lectin From Platypodium Elegans in Complex with A Trimannoside within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn300 b:21.9 occ:1.00 OD2 B:ASP139 2.2 20.2 1.0 O B:HOH2097 2.2 26.1 1.0 NE2 B:HIS155 2.2 18.6 1.0 O B:HOH2096 2.3 17.3 1.0 OE2 B:GLU137 2.3 21.8 1.0 OD1 B:ASP150 2.4 22.5 1.0 CE1 B:HIS155 3.0 19.5 1.0 CD B:GLU137 3.2 21.5 1.0 CG B:ASP139 3.2 20.5 1.0 OE1 B:GLU137 3.3 19.3 1.0 CG B:ASP150 3.3 24.8 1.0 CD2 B:HIS155 3.3 19.7 1.0 CB B:ASP139 3.6 21.1 1.0 OD2 B:ASP150 3.7 24.2 1.0 O B:HOH2082 3.8 15.2 1.0 ND1 B:HIS155 4.2 21.1 1.0 CA B:CA301 4.3 21.8 1.0 OD1 B:ASP139 4.3 22.1 1.0 CG B:HIS155 4.4 21.6 1.0 OG B:SER165 4.4 22.2 1.0 O B:ILE163 4.5 20.6 1.0 CD1 B:TRP149 4.5 23.1 1.0 CB B:ASP150 4.6 25.1 1.0 NE1 B:TRP149 4.6 25.8 1.0 CG B:GLU137 4.6 20.8 1.0 CA B:ASP150 4.8 25.6 1.0 CD B:PRO151 4.8 27.3 1.0

R.G.Benevides, G.Ganne, R.D.C.Simoes, V.Schubert, M.Niemietz, C.Unverzagt, V.Chazalet, C.Breton, A.Varrot, B.S.Cavada, A.Imberty. A Lectin From Platypodium Elegans with Unusual Specificity and Affinity For Asymmetric Complex N-Glycans. J.Biol.Chem. V. 287 26352 2012.
ISSN: ISSN 0021-9258
PubMed: 22692206
DOI: 10.1074/JBC.M112.375816