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Calcium in PDB 1lul: DB58, A Legume Lectin From Dolichos Biflorus

Protein crystallography data

The structure of DB58, A Legume Lectin From Dolichos Biflorus, PDB code: 1lul was solved by T.W.Hamelryck, J.Bouckaert, M.H.Dao-Thi, L.Wyns, M.Etzler, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 101.390, 130.950, 138.230, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 26.6

Other elements in 1lul:

The structure of DB58, A Legume Lectin From Dolichos Biflorus also contains other interesting chemical elements:

Manganese (Mn) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the DB58, A Legume Lectin From Dolichos Biflorus (pdb code 1lul). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the DB58, A Legume Lectin From Dolichos Biflorus, PDB code: 1lul:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1lul

Go back to Calcium Binding Sites List in 1lul
Calcium binding site 1 out of 6 in the DB58, A Legume Lectin From Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:50.4
occ:1.00
 OD1 A:ASN129 2.0 71.8 1.0
OD1 A:ASP125 2.2 65.8 1.0
O A:PHE127 2.3 57.8 1.0
OD2 A:ASP133 2.5 51.4 1.0
CG A:ASP125 2.9 57.1 1.0
OD2 A:ASP125 2.9 51.2 1.0
CG A:ASN129 3.1 62.5 1.0
C A:PHE127 3.5 52.9 1.0
CG A:ASP133 3.8 65.9 1.0
ND2 A:ASN129 3.8 60.1 1.0
OD1 A:ASP85 3.9 81.7 1.0
N A:ASN129 3.9 61.8 1.0
O A:ASP85 4.1 52.9 1.0
CB A:ASN129 4.2 62.0 1.0
CA A:PHE127 4.3 44.2 1.0
CB A:ASP125 4.3 47.1 1.0
N A:PHE127 4.3 48.5 1.0
CB A:PHE127 4.3 35.2 1.0
N A:SER128 4.4 57.4 1.0
OD1 A:ASP133 4.4 81.2 1.0
CA A:SER128 4.6 64.4 1.0
C A:SER128 4.7 67.3 1.0
CA A:ASN129 4.7 63.1 1.0
NE1 A:TRP132 4.7 78.8 1.0
CB A:ASP133 4.8 54.5 1.0
CG A:ASP85 4.9 76.1 1.0
CA A:ASP125 5.0 48.1 1.0
MN A:MN301 5.0 57.0 1.0

Calcium binding site 2 out of 6 in 1lul

Go back to Calcium Binding Sites List in 1lul
Calcium binding site 2 out of 6 in the DB58, A Legume Lectin From Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:45.2
occ:1.00
 OD1 B:ASN129 1.8 73.8 1.0
OD1 B:ASP125 2.4 64.7 1.0
O B:PHE127 2.4 47.8 1.0
OD2 B:ASP133 2.6 43.5 1.0
OD2 B:ASP125 3.0 56.2 1.0
CG B:ASP125 3.0 57.3 1.0
CG B:ASN129 3.0 65.0 1.0
C B:PHE127 3.6 48.8 1.0
ND2 B:ASN129 3.7 62.4 1.0
OD1 B:ASP85 3.8 82.5 1.0
CG B:ASP133 3.8 60.8 1.0
N B:ASN129 4.0 63.6 1.0
CB B:ASN129 4.1 62.0 1.0
O B:ASP85 4.2 46.6 1.0
CB B:PHE127 4.4 34.4 1.0
CA B:PHE127 4.4 42.1 1.0
CB B:ASP125 4.5 45.6 1.0
OD1 B:ASP133 4.5 77.9 1.0
N B:PHE127 4.5 48.4 1.0
N B:SER128 4.6 63.2 1.0
NE1 B:TRP132 4.7 78.0 1.0
CA B:ASN129 4.7 63.1 1.0
CA B:SER128 4.7 67.1 1.0
C B:SER128 4.8 66.4 1.0
CZ2 B:TRP132 4.8 74.5 1.0
CG B:ASP85 4.8 76.3 1.0
CB B:ASP133 4.9 55.1 1.0

Calcium binding site 3 out of 6 in 1lul

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Calcium binding site 3 out of 6 in the DB58, A Legume Lectin From Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:45.8
occ:1.00
 OD1 C:ASN129 1.8 76.3 1.0
OD2 C:ASP133 2.3 46.9 1.0
OD1 C:ASP125 2.4 67.0 1.0
OD2 C:ASP125 2.7 58.9 1.0
O C:PHE127 2.7 53.9 1.0
CG C:ASP125 2.8 59.8 1.0
CG C:ASN129 3.0 65.5 1.0
CG C:ASP133 3.5 60.8 1.0
ND2 C:ASN129 3.8 62.4 1.0
C C:PHE127 3.9 53.3 1.0
N C:ASN129 4.0 62.9 1.0
CB C:ASN129 4.1 62.2 1.0
OD1 C:ASP133 4.1 78.2 1.0
OD1 C:ASP85 4.2 84.5 1.0
NE1 C:TRP132 4.3 75.2 1.0
CB C:ASP125 4.4 46.0 1.0
O C:ASP85 4.4 50.8 1.0
CZ2 C:TRP132 4.6 75.2 1.0
CB C:ASP133 4.7 53.4 1.0
CA C:ASN129 4.7 64.3 1.0
MN C:MN301 4.7 57.9 1.0
CE2 C:TRP132 4.8 72.3 1.0
CA C:PHE127 4.8 44.5 1.0
N C:SER128 4.8 60.5 1.0
CA C:SER128 4.8 63.9 1.0
N C:PHE127 4.8 45.4 1.0
CB C:PHE127 4.9 33.8 1.0
C C:SER128 4.9 67.1 1.0

Calcium binding site 4 out of 6 in 1lul

Go back to Calcium Binding Sites List in 1lul
Calcium binding site 4 out of 6 in the DB58, A Legume Lectin From Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca302

b:50.1
occ:1.00
 OD1 D:ASN129 2.0 74.8 1.0
OD1 D:ASP125 2.2 63.3 1.0
O D:PHE127 2.4 55.9 1.0
OD2 D:ASP133 2.4 43.3 1.0
OD2 D:ASP125 2.7 54.1 1.0
CG D:ASP125 2.7 55.4 1.0
CG D:ASN129 3.2 63.4 1.0
C D:PHE127 3.6 52.7 1.0
CG D:ASP133 3.6 58.6 1.0
ND2 D:ASN129 3.9 60.2 1.0
N D:ASN129 4.0 62.2 1.0
OD1 D:ASP85 4.1 87.8 1.0
O D:ASP85 4.2 49.6 1.0
CB D:ASP125 4.2 45.0 1.0
CB D:ASN129 4.2 62.0 1.0
OD1 D:ASP133 4.3 74.8 1.0
CA D:PHE127 4.4 42.6 1.0
N D:PHE127 4.5 44.7 1.0
CB D:PHE127 4.5 35.4 1.0
N D:SER128 4.5 61.6 1.0
NE1 D:TRP132 4.6 75.2 1.0
CA D:SER128 4.6 64.4 1.0
CB D:ASP133 4.7 53.7 1.0
MN D:MN301 4.7 49.1 1.0
CA D:ASN129 4.8 64.5 1.0
C D:SER128 4.8 65.5 1.0
CA D:ASP125 4.9 44.3 1.0
CZ2 D:TRP132 4.9 77.2 1.0

Calcium binding site 5 out of 6 in 1lul

Go back to Calcium Binding Sites List in 1lul
Calcium binding site 5 out of 6 in the DB58, A Legume Lectin From Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca302

b:47.1
occ:1.00
 OD1 E:ASP125 1.9 61.0 1.0
OD2 E:ASP133 2.2 41.3 1.0
OD1 E:ASN129 2.3 74.7 1.0
OD2 E:ASP125 2.3 54.2 1.0
O E:PHE127 2.4 53.1 1.0
CG E:ASP125 2.4 51.7 1.0
CG E:ASP133 3.4 60.3 1.0
CG E:ASN129 3.4 63.9 1.0
C E:PHE127 3.6 48.5 1.0
CB E:ASP125 3.9 40.5 1.0
OD1 E:ASP133 4.0 79.2 1.0
N E:ASN129 4.0 61.9 1.0
O E:ASP85 4.2 49.2 1.0
ND2 E:ASN129 4.3 63.0 1.0
OD1 E:ASP85 4.4 83.1 1.0
CB E:ASN129 4.4 63.1 1.0
N E:PHE127 4.4 45.8 1.0
CA E:PHE127 4.5 41.0 1.0
N E:SER128 4.5 57.9 1.0
CB E:ASP133 4.5 52.8 1.0
NE1 E:TRP132 4.6 77.2 1.0
CA E:SER128 4.6 65.2 1.0
CA E:ASP125 4.6 44.8 1.0
MN E:MN301 4.6 49.0 1.0
CB E:PHE127 4.7 33.4 1.0
CE1 E:HIS138 4.8 37.2 1.0
C E:SER128 4.8 67.5 1.0
CA E:ASN129 4.9 64.1 1.0
N E:THR126 5.0 33.1 1.0

Calcium binding site 6 out of 6 in 1lul

Go back to Calcium Binding Sites List in 1lul
Calcium binding site 6 out of 6 in the DB58, A Legume Lectin From Dolichos Biflorus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca302

b:56.6
occ:1.00
 OD1 F:ASP125 1.9 63.9 1.0
O F:PHE127 2.1 51.0 1.0
OD1 F:ASN129 2.2 76.0 1.0
OD2 F:ASP133 2.6 49.5 1.0
CG F:ASP125 2.6 55.0 1.0
OD2 F:ASP125 2.8 57.3 1.0
C F:PHE127 3.3 49.2 1.0
CG F:ASN129 3.4 65.8 1.0
CG F:ASP133 3.8 63.5 1.0
O F:ASP85 4.0 53.7 1.0
OD1 F:ASP85 4.0 84.8 1.0
N F:ASN129 4.0 61.1 1.0
ND2 F:ASN129 4.1 65.3 1.0
CB F:ASP125 4.1 41.3 1.0
N F:PHE127 4.1 52.9 1.0
CA F:PHE127 4.1 41.9 1.0
CB F:PHE127 4.2 33.5 1.0
N F:SER128 4.3 60.7 1.0
OD1 F:ASP133 4.4 80.4 1.0
CB F:ASN129 4.4 61.1 1.0
CA F:SER128 4.5 67.0 1.0
C F:SER128 4.7 68.2 1.0
CA F:ASP125 4.7 44.4 1.0
CB F:ASP133 4.8 56.1 1.0
CA F:ASN129 4.9 62.3 1.0
N F:THR126 4.9 38.6 1.0
NE1 F:TRP132 4.9 74.4 1.0

Reference:

T.W.Hamelryck, R.Loris, J.Bouckaert, M.H.Dao-Thi, G.Strecker, A.Imberty, E.Fernandez, L.Wyns, M.E.Etzler. Carbohydrate Binding, Quaternary Structure and A Novel Hydrophobic Binding Site in Two Legume Lectin Oligomers From Dolichos Biflorus. J.Mol.Biol. V. 286 1161 1999.
ISSN: ISSN 0022-2836
PubMed: 10047489
DOI: 10.1006/JMBI.1998.2534
Page generated: Mon Jul 7 17:00:27 2025

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