Atomistry » Manganese » PDB 1lu1-1n0j » 1lul
Atomistry »
  Manganese »
    PDB 1lu1-1n0j »
      1lul »

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

Go back to Manganese Binding Sites List in 1lul
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

Go back to Manganese Binding Sites List in 1lul
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy