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Manganese 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:

Calcium (Ca) 6 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 6 in 1lul

Go back to Manganese Binding Sites List in 1lul
Manganese 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 Manganese with other atoms in the Mn binding site number 1 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:57.0
occ:1.00
 OD1 A:ASP133 1.6 81.2 1.0
OE2 A:GLU123 2.0 60.8 1.0
NE2 A:HIS138 2.3 37.1 1.0
OD2 A:ASP125 2.4 51.2 1.0
CG A:ASP133 2.8 65.9 1.0
CD A:GLU123 3.0 50.5 1.0
CE1 A:HIS138 3.2 38.1 1.0
OE1 A:GLU123 3.3 53.7 1.0
CD2 A:HIS138 3.4 46.7 1.0
OD2 A:ASP133 3.4 51.4 1.0
CG A:ASP125 3.5 57.1 1.0
OG A:SER148 3.8 45.9 1.0
CB A:ASP125 3.8 47.1 1.0
CB A:ASP133 4.0 54.5 1.0
NE1 A:TRP132 4.1 78.8 1.0
O A:ILE146 4.2 48.6 1.0
CD1 A:TRP132 4.2 75.3 1.0
CG A:GLU123 4.3 31.9 1.0
CA A:ASP133 4.4 51.6 1.0
ND1 A:HIS138 4.4 34.8 1.0
CD A:PRO134 4.5 62.0 1.0
CG A:HIS138 4.5 40.6 1.0
OD1 A:ASP125 4.6 65.8 1.0
CA A:CA302 5.0 50.4 1.0

Manganese binding site 2 out of 6 in 1lul

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Manganese 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 Manganese with other atoms in the Mn binding site number 2 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:49.4
occ:1.00
 OE2 B:GLU123 1.9 60.0 1.0
OD1 B:ASP133 1.9 77.9 1.0
NE2 B:HIS138 2.4 35.3 1.0
OD2 B:ASP125 2.7 56.2 1.0
CD B:GLU123 2.8 49.7 1.0
CG B:ASP133 3.1 60.8 1.0
OE1 B:GLU123 3.1 52.3 1.0
CD2 B:HIS138 3.4 45.0 1.0
CE1 B:HIS138 3.4 34.9 1.0
OG B:SER148 3.5 54.4 1.0
OD2 B:ASP133 3.7 43.5 1.0
CG B:ASP125 3.7 57.3 1.0
O B:ILE146 4.0 46.9 1.0
CB B:ASP125 4.0 45.6 1.0
CG B:GLU123 4.1 29.8 1.0
NE1 B:TRP132 4.2 78.0 1.0
CD1 B:TRP132 4.3 77.1 1.0
CB B:ASP133 4.3 55.1 1.0
CA B:ASP133 4.5 51.1 1.0
ND1 B:HIS138 4.6 34.4 1.0
CD B:PRO134 4.6 59.9 1.0
CG B:HIS138 4.6 41.1 1.0
CB B:SER148 4.7 56.2 1.0
OD1 B:ASP125 4.9 64.7 1.0
N B:SER148 5.0 62.6 1.0

Manganese binding site 3 out of 6 in 1lul

Go back to Manganese Binding Sites List in 1lul
Manganese 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 Manganese with other atoms in the Mn binding site number 3 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:57.9
occ:1.00
 OE2 C:GLU123 1.6 59.9 1.0
OD1 C:ASP133 1.9 78.2 1.0
NE2 C:HIS138 2.1 34.7 1.0
OD2 C:ASP125 2.4 58.9 1.0
CD C:GLU123 2.7 47.8 1.0
CG C:ASP133 3.1 60.8 1.0
CE1 C:HIS138 3.1 35.6 1.0
CD2 C:HIS138 3.1 43.6 1.0
OE1 C:GLU123 3.2 56.1 1.0
CG C:ASP125 3.3 59.8 1.0
CB C:ASP125 3.6 46.0 1.0
OD2 C:ASP133 3.6 46.9 1.0
OG C:SER148 3.7 49.6 1.0
CG C:GLU123 4.0 26.9 1.0
ND1 C:HIS138 4.2 37.5 1.0
CG C:HIS138 4.3 39.7 1.0
CB C:ASP133 4.3 53.4 1.0
O C:ILE146 4.4 44.0 1.0
NE1 C:TRP132 4.5 75.2 1.0
OD1 C:ASP125 4.5 67.0 1.0
CD C:PRO134 4.6 62.0 1.0
CD1 C:TRP132 4.6 76.9 1.0
CA C:ASP133 4.6 48.9 1.0
CA C:CA302 4.7 45.8 1.0

Manganese binding site 4 out of 6 in 1lul

Go back to Manganese Binding Sites List in 1lul
Manganese 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 Manganese with other atoms in the Mn binding site number 4 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:49.1
occ:1.00
 OD1 D:ASP133 1.8 74.8 1.0
OE2 D:GLU123 1.8 54.3 1.0
OD2 D:ASP125 2.4 54.1 1.0
NE2 D:HIS138 2.5 34.4 1.0
CD D:GLU123 2.7 46.5 1.0
CG D:ASP133 2.9 58.6 1.0
OE1 D:GLU123 3.0 55.1 1.0
CE1 D:HIS138 3.4 34.7 1.0
OD2 D:ASP133 3.4 43.3 1.0
CG D:ASP125 3.4 55.4 1.0
CD2 D:HIS138 3.5 41.1 1.0
OG D:SER148 3.8 47.8 1.0
CB D:ASP125 3.8 45.0 1.0
O D:ILE146 4.0 44.1 1.0
NE1 D:TRP132 4.0 75.2 1.0
CG D:GLU123 4.1 25.9 1.0
CD1 D:TRP132 4.2 74.6 1.0
CB D:ASP133 4.2 53.7 1.0
CA D:ASP133 4.6 48.2 1.0
OD1 D:ASP125 4.6 63.3 1.0
ND1 D:HIS138 4.6 34.0 1.0
CG D:HIS138 4.7 38.3 1.0
CA D:CA302 4.7 50.1 1.0
CD D:PRO134 4.8 61.9 1.0

Manganese binding site 5 out of 6 in 1lul

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Manganese 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 Manganese with other atoms in the Mn binding site number 5 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn301

b:49.0
occ:1.00
 OE2 E:GLU123 1.7 60.4 1.0
OD1 E:ASP133 2.0 79.2 1.0
NE2 E:HIS138 2.3 35.1 1.0
OD2 E:ASP125 2.5 54.2 1.0
CD E:GLU123 2.7 50.1 1.0
OE1 E:GLU123 3.0 57.4 1.0
CG E:ASP133 3.1 60.3 1.0
CD2 E:HIS138 3.3 44.4 1.0
CE1 E:HIS138 3.3 37.2 1.0
CG E:ASP125 3.5 51.7 1.0
OG E:SER148 3.6 48.5 1.0
OD2 E:ASP133 3.7 41.3 1.0
CB E:ASP125 3.8 40.5 1.0
CG E:GLU123 4.0 27.6 1.0
O E:ILE146 4.2 48.0 1.0
NE1 E:TRP132 4.3 77.2 1.0
CB E:ASP133 4.4 52.8 1.0
CD1 E:TRP132 4.4 74.9 1.0
ND1 E:HIS138 4.5 38.4 1.0
CG E:HIS138 4.5 42.5 1.0
CA E:CA302 4.6 47.1 1.0
CA E:ASP133 4.6 48.5 1.0
CD E:PRO134 4.7 60.7 1.0
OD1 E:ASP125 4.7 61.0 1.0
CB E:SER148 4.9 45.1 1.0

Manganese binding site 6 out of 6 in 1lul

Go back to Manganese Binding Sites List in 1lul
Manganese 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 Manganese with other atoms in the Mn binding site number 6 of DB58, A Legume Lectin From Dolichos Biflorus within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn301

b:61.0
occ:1.00
 OE2 F:GLU123 1.8 60.7 1.0
OD1 F:ASP133 1.8 80.4 1.0
NE2 F:HIS138 2.3 37.0 1.0
OD2 F:ASP125 2.5 57.3 1.0
CD F:GLU123 2.8 53.0 1.0
CG F:ASP133 3.0 63.5 1.0
OE1 F:GLU123 3.2 56.7 1.0
CE1 F:HIS138 3.2 37.9 1.0
CD2 F:HIS138 3.3 45.8 1.0
CG F:ASP125 3.5 55.0 1.0
OD2 F:ASP133 3.6 49.5 1.0
OG F:SER148 3.7 54.3 1.0
CB F:ASP125 3.8 41.3 1.0
CG F:GLU123 4.1 34.2 1.0
O F:ILE146 4.2 45.9 1.0
CB F:ASP133 4.2 56.1 1.0
NE1 F:TRP132 4.2 74.4 1.0
CD1 F:TRP132 4.3 75.2 1.0
ND1 F:HIS138 4.4 37.1 1.0
CG F:HIS138 4.5 41.7 1.0
CA F:ASP133 4.5 52.0 1.0
CD F:PRO134 4.5 64.8 1.0
OD1 F:ASP125 4.7 63.9 1.0
CB F:SER148 4.9 53.3 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: Sat Oct 5 11:37:09 2024

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