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Manganese in PDB 1qoo: Lectin Uea-II Complexed with Nag

Protein crystallography data

The structure of Lectin Uea-II Complexed with Nag, PDB code: 1qoo was solved by R.Loris, H.De Greve, M.-H.Dao-Thi, J.Messens, A.Imberty, L.Wyns, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.75
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 104.480, 104.480, 175.350, 90.00, 90.00, 120.00
R / Rfree (%) 17.4 / 20.8

Other elements in 1qoo:

The structure of Lectin Uea-II Complexed with Nag also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Lectin Uea-II Complexed with Nag (pdb code 1qoo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Lectin Uea-II Complexed with Nag, PDB code: 1qoo:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1qoo

Go back to Manganese Binding Sites List in 1qoo
Manganese binding site 1 out of 4 in the Lectin Uea-II Complexed with Nag


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Lectin Uea-II Complexed with Nag within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:18.2
occ:1.00
OD1 A:ASP139 2.0 29.1 1.0
OE2 A:GLU126 2.1 25.2 1.0
NE2 A:HIS144 2.1 11.3 1.0
OD2 A:ASP128 2.2 15.4 1.0
CD A:GLU126 3.0 19.9 1.0
CD2 A:HIS144 3.1 21.3 1.0
CG A:ASP139 3.1 22.6 1.0
CE1 A:HIS144 3.2 19.5 1.0
OE1 A:GLU126 3.3 24.4 1.0
CG A:ASP128 3.3 17.6 1.0
OD2 A:ASP139 3.6 20.4 1.0
CB A:ASP128 3.7 16.9 1.0
OG A:SER154 3.9 15.2 1.0
ND1 A:HIS144 4.3 16.3 1.0
CG A:HIS144 4.3 14.9 1.0
CB A:ASP139 4.3 17.4 1.0
OD1 A:ASP128 4.4 29.3 1.0
O A:ILE152 4.4 14.8 1.0
CG A:GLU126 4.4 16.3 1.0
CD1 A:TRP138 4.6 19.1 1.0
CA A:CA302 4.6 26.8 1.0
NE1 A:TRP138 4.6 27.6 1.0
CA A:ASP139 4.7 19.8 1.0
CD A:PRO140 4.8 21.8 1.0

Manganese binding site 2 out of 4 in 1qoo

Go back to Manganese Binding Sites List in 1qoo
Manganese binding site 2 out of 4 in the Lectin Uea-II Complexed with Nag


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Lectin Uea-II Complexed with Nag within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn303

b:15.7
occ:1.00
OD1 B:ASP139 2.0 33.0 1.0
OE2 B:GLU126 2.1 24.7 1.0
OD2 B:ASP128 2.2 13.0 1.0
NE2 B:HIS144 2.2 2.0 1.0
CD B:GLU126 3.0 19.8 1.0
CG B:ASP139 3.1 24.3 1.0
CD2 B:HIS144 3.2 14.8 1.0
OE1 B:GLU126 3.2 19.4 1.0
CE1 B:HIS144 3.2 10.2 1.0
CG B:ASP128 3.3 15.4 1.0
OD2 B:ASP139 3.6 22.1 1.0
CB B:ASP128 3.7 17.2 1.0
OG B:SER154 3.9 23.9 1.0
O B:ILE152 4.3 21.2 1.0
ND1 B:HIS144 4.3 14.3 1.0
CG B:HIS144 4.3 14.2 1.0
CB B:ASP139 4.4 19.7 1.0
CG B:GLU126 4.4 19.2 1.0
OD1 B:ASP128 4.4 21.1 1.0
CA B:CA304 4.4 21.9 1.0
CD1 B:TRP138 4.5 11.2 1.0
NE1 B:TRP138 4.6 22.2 1.0
CA B:ASP139 4.7 20.7 1.0
CD B:PRO140 4.8 22.2 1.0

Manganese binding site 3 out of 4 in 1qoo

Go back to Manganese Binding Sites List in 1qoo
Manganese binding site 3 out of 4 in the Lectin Uea-II Complexed with Nag


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Lectin Uea-II Complexed with Nag within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn305

b:15.5
occ:1.00
OD1 C:ASP139 2.0 31.6 1.0
OE2 C:GLU126 2.1 19.8 1.0
OD2 C:ASP128 2.2 17.4 1.0
NE2 C:HIS144 2.3 10.2 1.0
CD C:GLU126 3.0 15.8 1.0
CG C:ASP139 3.1 23.1 1.0
OE1 C:GLU126 3.2 21.6 1.0
CD2 C:HIS144 3.2 24.3 1.0
CE1 C:HIS144 3.3 18.6 1.0
CG C:ASP128 3.3 15.9 1.0
OD2 C:ASP139 3.6 24.1 1.0
CB C:ASP128 3.7 17.9 1.0
OG C:SER154 4.0 22.9 1.0
O C:ILE152 4.3 19.2 1.0
CB C:ASP139 4.4 20.8 1.0
OD1 C:ASP128 4.4 25.5 1.0
ND1 C:HIS144 4.4 23.6 1.0
CG C:HIS144 4.4 17.8 1.0
CG C:GLU126 4.4 15.1 1.0
CD1 C:TRP138 4.5 19.4 1.0
CA C:CA306 4.5 28.9 1.0
NE1 C:TRP138 4.5 27.9 1.0
CA C:ASP139 4.7 21.3 1.0
CD C:PRO140 4.9 22.8 1.0

Manganese binding site 4 out of 4 in 1qoo

Go back to Manganese Binding Sites List in 1qoo
Manganese binding site 4 out of 4 in the Lectin Uea-II Complexed with Nag


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Lectin Uea-II Complexed with Nag within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn307

b:22.5
occ:1.00
OD1 D:ASP139 2.1 30.9 1.0
OE2 D:GLU126 2.1 21.4 1.0
OD2 D:ASP128 2.2 10.1 1.0
NE2 D:HIS144 2.3 11.3 1.0
CD D:GLU126 3.0 18.1 1.0
CG D:ASP139 3.2 20.0 1.0
OE1 D:GLU126 3.2 16.1 1.0
CD2 D:HIS144 3.2 22.7 1.0
CE1 D:HIS144 3.3 14.1 1.0
CG D:ASP128 3.3 17.8 1.0
OD2 D:ASP139 3.6 19.4 1.0
CB D:ASP128 3.8 20.2 1.0
OG D:SER154 3.9 15.0 1.0
O D:ILE152 4.2 22.8 1.0
CG D:GLU126 4.4 17.7 1.0
CB D:ASP139 4.4 17.8 1.0
ND1 D:HIS144 4.4 17.0 1.0
CG D:HIS144 4.4 20.6 1.0
OD1 D:ASP128 4.4 20.5 1.0
CA D:CA308 4.4 26.0 1.0
CD1 D:TRP138 4.5 19.7 1.0
NE1 D:TRP138 4.5 18.3 1.0
CA D:ASP139 4.7 19.1 1.0
CD D:PRO140 4.9 23.5 1.0

Reference:

R.Loris, H.De Greve, M.-H.Dao-Thi, J.Messens, A.Imberty, L.Wyns. Structural Basis of Carbohydrate Recognition By Lectin II From Ulex Europaeus, A Protein with A Promiscuous Carbohydrate Binding Site J.Mol.Biol. V. 301 987 2000.
ISSN: ISSN 0022-2836
PubMed: 10966800
DOI: 10.1006/JMBI.2000.4016
Page generated: Tue Dec 15 03:54:51 2020

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