Manganese in PDB 1qmo: Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation

The structure of Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation, PDB code: 1qmo was solved by T.W.Hamelryck, J.G.Moore, M.Chrispeels, R.Loris, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.50
Space group	P 65 2 2
Cell size a, b, c (Å), α, β, γ (°)	151.360, 151.360, 309.880, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 25.2

The structure of Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Manganese atom in the Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation (pdb code 1qmo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation, PDB code: 1qmo:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:74.4 occ:1.00 OD1 E:ASP149 2.0 62.4 1.0 OD2 E:ASP140 2.5 48.2 1.0 OE2 E:GLU138 2.7 53.9 1.0 NE2 E:HIS154 2.8 41.0 1.0 CG E:ASP149 3.0 60.2 1.0 OD2 E:ASP149 3.3 57.1 1.0 CD E:GLU138 3.4 49.2 1.0 CG E:ASP140 3.6 48.0 1.0 CE1 E:HIS154 3.7 42.8 1.0 OG E:SER164 3.7 53.2 1.0 OE1 E:GLU138 3.8 51.0 1.0 CD2 E:HIS154 3.8 46.1 1.0 CB E:ASP140 4.0 44.0 1.0 CA A:CA300 4.2 40.7 1.0 O E:ILE162 4.3 52.8 1.0 CD1 E:ILE162 4.3 58.8 1.0 CB E:ASP149 4.3 57.2 1.0 CG E:GLU138 4.5 45.0 1.0 CA E:ASP149 4.7 58.1 1.0 OD1 E:ASP140 4.7 51.2 1.0 ND1 E:HIS154 4.8 40.3 1.0 CG E:HIS154 4.9 45.0 1.0 CG1 E:ILE162 5.0 57.2 1.0

Manganese binding site 2 out of 4 in the Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:74.4 occ:1.00 OD1 F:ASP149 2.0 62.4 1.0 OD2 F:ASP140 2.5 48.2 1.0 OE2 F:GLU138 2.7 53.9 1.0 NE2 F:HIS154 2.8 41.0 1.0 CG F:ASP149 3.0 60.2 1.0 OD2 F:ASP149 3.3 57.1 1.0 CD F:GLU138 3.4 49.2 1.0 CG F:ASP140 3.6 48.0 1.0 CE1 F:HIS154 3.7 42.8 1.0 OG F:SER164 3.7 53.2 1.0 OE1 F:GLU138 3.8 51.0 1.0 CD2 F:HIS154 3.8 46.1 1.0 CB F:ASP140 4.0 44.0 1.0 CA B:CA300 4.2 40.7 1.0 O F:ILE162 4.3 52.8 1.0 CD1 F:ILE162 4.3 58.8 1.0 CB F:ASP149 4.3 57.2 1.0 CG F:GLU138 4.5 45.0 1.0 CA F:ASP149 4.7 58.1 1.0 OD1 F:ASP140 4.7 51.2 1.0 ND1 F:HIS154 4.8 40.3 1.0 CG F:HIS154 4.9 45.0 1.0 CG1 F:ILE162 5.0 57.2 1.0

Manganese binding site 3 out of 4 in the Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:74.4 occ:1.00 OD1 G:ASP149 2.0 62.4 1.0 OD2 G:ASP140 2.5 48.2 1.0 OE2 G:GLU138 2.7 53.9 1.0 NE2 G:HIS154 2.8 41.0 1.0 CG G:ASP149 3.0 60.2 1.0 OD2 G:ASP149 3.3 57.1 1.0 CD G:GLU138 3.4 49.2 1.0 CG G:ASP140 3.6 48.0 1.0 CE1 G:HIS154 3.7 42.8 1.0 OG G:SER164 3.7 53.2 1.0 OE1 G:GLU138 3.8 51.0 1.0 CD2 G:HIS154 3.8 46.1 1.0 CB G:ASP140 4.0 44.0 1.0 CA C:CA300 4.2 40.7 1.0 O G:ILE162 4.3 52.8 1.0 CD1 G:ILE162 4.3 58.8 1.0 CB G:ASP149 4.3 57.2 1.0 CG G:GLU138 4.5 45.0 1.0 CA G:ASP149 4.6 58.1 1.0 OD1 G:ASP140 4.7 51.2 1.0 ND1 G:HIS154 4.8 40.3 1.0 CG G:HIS154 4.9 45.0 1.0 CG1 G:ILE162 5.0 57.2 1.0

Manganese binding site 4 out of 4 in the Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:74.4 occ:1.00 OD1 H:ASP149 2.0 62.4 1.0 OD2 H:ASP140 2.5 48.2 1.0 OE2 H:GLU138 2.7 53.9 1.0 NE2 H:HIS154 2.8 41.0 1.0 CG H:ASP149 3.0 60.2 1.0 OD2 H:ASP149 3.3 57.1 1.0 CD H:GLU138 3.4 49.2 1.0 CG H:ASP140 3.6 48.0 1.0 CE1 H:HIS154 3.7 42.8 1.0 OG H:SER164 3.7 53.2 1.0 OE1 H:GLU138 3.8 51.0 1.0 CD2 H:HIS154 3.8 46.1 1.0 CB H:ASP140 4.0 44.0 1.0 CA D:CA300 4.2 40.7 1.0 O H:ILE162 4.3 52.8 1.0 CD1 H:ILE162 4.3 58.8 1.0 CB H:ASP149 4.3 57.2 1.0 CG H:GLU138 4.5 45.0 1.0 CA H:ASP149 4.7 58.1 1.0 OD1 H:ASP140 4.7 51.2 1.0 ND1 H:HIS154 4.8 40.3 1.0 CG H:HIS154 4.9 45.0 1.0 CG1 H:ILE162 5.0 57.2 1.0

T.W.Hamelryck, J.G.Moore, M.J.Chrispeels, R.Loris, L.Wyns. The Role of Weak Protein-Protein Interactions in Multivalent Lectin-Carbohydrate Binding: Crystal Structure of Cross-Linked Fril J.Mol.Biol. V. 299 875 2000.
ISSN: ISSN 0022-2836
PubMed: 10843844
DOI: 10.1006/JMBI.2000.3785