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

Protein crystallography data

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

Other elements in 1qmo:

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

Calcium (Ca) 4 atoms

Manganese Binding Sites:

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 1qmo

Go back to Manganese Binding Sites List in 1qmo
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 1qmo

Go back to Manganese Binding Sites List in 1qmo
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 1qmo

Go back to Manganese Binding Sites List in 1qmo
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 1qmo

Go back to Manganese Binding Sites List in 1qmo
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

Reference:

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
Page generated: Sat Oct 5 12:13:38 2024

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