Calcium 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:

Manganese

(Mn)

4 atoms

The binding sites of Calcium 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 Calcium atom.
In total 4 binding sites of Calcium where determined in the Structure of Fril, A Legume Lectin That Delays Hematopoietic Progenitor Maturation, PDB code: 1qmo:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium 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 Calcium with other atoms in the Ca 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:Ca300 b:40.7 occ:1.00 OD2 E:ASP149 2.3 57.1 1.0 OD2 E:ASP140 2.5 48.2 1.0 O E:TYR142 2.6 56.5 1.0 OD1 E:ASP140 2.9 51.2 1.0 OD1 E:ASN144 2.9 73.0 1.0 CG E:ASP140 3.1 48.0 1.0 CG E:ASP149 3.5 60.2 1.0 CG E:ASN144 3.6 68.5 1.0 C E:TYR142 3.9 63.5 1.0 CA A:GLY104 3.9 43.8 1.0 O A:GLY104 4.0 38.8 1.0 OD1 A:ASP86 4.1 63.9 1.0 OD1 E:ASP149 4.1 62.4 1.0 CB E:ASN144 4.2 65.1 1.0 MN A:MN301 4.2 74.4 1.0 N E:ASN144 4.3 62.6 1.0 ND2 E:ASN144 4.4 70.3 1.0 C A:GLY104 4.4 42.5 1.0 CB E:ASP140 4.5 44.0 1.0 CB E:ASP149 4.6 57.2 1.0 CA E:LEU143 4.7 59.5 1.0 C E:LEU143 4.7 61.2 1.0 N E:LEU143 4.7 61.3 1.0 CA E:TYR142 4.8 67.1 1.0 CA E:ASN144 4.9 65.7 1.0 N E:TYR142 4.9 65.9 1.0 CB E:TYR142 4.9 76.6 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca300 b:40.7 occ:1.00 OD2 F:ASP149 2.3 57.1 1.0 OD2 F:ASP140 2.5 48.2 1.0 O F:TYR142 2.6 56.5 1.0 OD1 F:ASP140 2.9 51.2 1.0 OD1 F:ASN144 2.9 73.0 1.0 CG F:ASP140 3.1 48.0 1.0 CG F:ASP149 3.5 60.2 1.0 CG F:ASN144 3.6 68.5 1.0 C F:TYR142 3.9 63.5 1.0 CA B:GLY104 3.9 43.8 1.0 O B:GLY104 4.0 38.8 1.0 OD1 B:ASP86 4.0 63.9 1.0 OD1 F:ASP149 4.1 62.4 1.0 CB F:ASN144 4.2 65.1 1.0 MN B:MN301 4.2 74.4 1.0 N F:ASN144 4.3 62.6 1.0 ND2 F:ASN144 4.4 70.3 1.0 C B:GLY104 4.4 42.5 1.0 CB F:ASP140 4.5 44.0 1.0 CB F:ASP149 4.6 57.2 1.0 CA F:LEU143 4.7 59.5 1.0 C F:LEU143 4.7 61.2 1.0 N F:LEU143 4.7 61.3 1.0 CA F:TYR142 4.8 67.1 1.0 CA F:ASN144 4.9 65.7 1.0 N F:TYR142 4.9 65.9 1.0 CB F:TYR142 4.9 76.6 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca300 b:40.7 occ:1.00 OD2 G:ASP149 2.3 57.1 1.0 OD2 G:ASP140 2.5 48.2 1.0 O G:TYR142 2.6 56.5 1.0 OD1 G:ASP140 2.9 51.2 1.0 OD1 G:ASN144 2.9 73.0 1.0 CG G:ASP140 3.1 48.0 1.0 CG G:ASP149 3.5 60.2 1.0 CG G:ASN144 3.6 68.5 1.0 C G:TYR142 3.9 63.5 1.0 CA C:GLY104 3.9 43.8 1.0 O C:GLY104 4.0 38.8 1.0 OD1 C:ASP86 4.1 63.9 1.0 OD1 G:ASP149 4.1 62.4 1.0 CB G:ASN144 4.2 65.1 1.0 MN C:MN301 4.2 74.4 1.0 N G:ASN144 4.3 62.6 1.0 ND2 G:ASN144 4.4 70.3 1.0 C C:GLY104 4.4 42.5 1.0 CB G:ASP140 4.5 44.0 1.0 CB G:ASP149 4.6 57.2 1.0 CA G:LEU143 4.7 59.5 1.0 C G:LEU143 4.7 61.2 1.0 N G:LEU143 4.7 61.3 1.0 CA G:TYR142 4.8 67.1 1.0 CA G:ASN144 4.9 65.7 1.0 N G:TYR142 4.9 65.9 1.0 CB G:TYR142 4.9 76.6 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca300 b:40.7 occ:1.00 OD2 H:ASP149 2.3 57.1 1.0 OD2 H:ASP140 2.5 48.2 1.0 O H:TYR142 2.6 56.5 1.0 OD1 H:ASP140 2.9 51.2 1.0 OD1 H:ASN144 2.9 73.0 1.0 CG H:ASP140 3.1 48.0 1.0 CG H:ASP149 3.5 60.2 1.0 CG H:ASN144 3.6 68.5 1.0 C H:TYR142 3.9 63.5 1.0 CA D:GLY104 3.9 43.8 1.0 O D:GLY104 4.0 38.8 1.0 OD1 D:ASP86 4.1 63.9 1.0 OD1 H:ASP149 4.1 62.4 1.0 CB H:ASN144 4.2 65.1 1.0 MN D:MN301 4.2 74.4 1.0 N H:ASN144 4.3 62.6 1.0 ND2 H:ASN144 4.4 70.3 1.0 C D:GLY104 4.4 42.5 1.0 CB H:ASP140 4.5 44.0 1.0 CB H:ASP149 4.6 57.2 1.0 CA H:LEU143 4.7 59.5 1.0 C H:LEU143 4.7 61.2 1.0 N H:LEU143 4.7 61.3 1.0 CA H:TYR142 4.8 67.1 1.0 CA H:ASN144 4.9 65.7 1.0 N H:TYR142 4.9 65.9 1.0 CB H:TYR142 4.9 76.6 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