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