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Calcium 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:

Manganese (Mn) 4 atoms

Calcium Binding Sites:

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 1qmo

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

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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 1qmo

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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 1qmo

Go back to Calcium Binding Sites List in 1qmo
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

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: Thu Jul 11 21:54:57 2024

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