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Calcium in PDB 2auy: Pterocarpus Angolensis Lectin in Complex with the Trisaccharide Glcnac(B1-2)Man(A1-3)Man

Protein crystallography data

The structure of Pterocarpus Angolensis Lectin in Complex with the Trisaccharide Glcnac(B1-2)Man(A1-3)Man, PDB code: 2auy was solved by L.Buts, A.Garcia-Pino, A.Imberty, N.Amiot, G.-J.Boons, S.Beeckmans, W.Versees, L.Wyns, R.Loris, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.800, 83.140, 123.020, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.3

Other elements in 2auy:

The structure of Pterocarpus Angolensis Lectin in Complex with the Trisaccharide Glcnac(B1-2)Man(A1-3)Man also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Pterocarpus Angolensis Lectin in Complex with the Trisaccharide Glcnac(B1-2)Man(A1-3)Man (pdb code 2auy). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Pterocarpus Angolensis Lectin in Complex with the Trisaccharide Glcnac(B1-2)Man(A1-3)Man, PDB code: 2auy:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2auy

Go back to Calcium Binding Sites List in 2auy
Calcium binding site 1 out of 2 in the Pterocarpus Angolensis Lectin in Complex with the Trisaccharide Glcnac(B1-2)Man(A1-3)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pterocarpus Angolensis Lectin in Complex with the Trisaccharide Glcnac(B1-2)Man(A1-3)Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca273

b:20.3
occ:1.00
OD2 A:ASP141 2.2 23.8 1.0
O A:PHE132 2.4 19.4 1.0
OD1 A:ASN138 2.4 25.6 1.0
O A:HOH303 2.4 21.1 1.0
OD1 A:ASP130 2.4 22.4 1.0
OD2 A:ASP130 2.5 24.2 1.0
O A:HOH304 2.5 20.8 1.0
CG A:ASP130 2.8 20.5 1.0
CG A:ASP141 3.4 18.8 1.0
CG A:ASN138 3.5 29.6 1.0
C A:PHE132 3.6 22.3 1.0
OD1 A:ASP141 3.9 19.1 1.0
CB A:ASN138 4.0 20.8 1.0
MN A:MN271 4.2 20.0 1.0
CB A:ASP130 4.3 20.9 1.0
NE1 A:TRP140 4.4 26.6 1.0
CA A:PHE132 4.5 23.3 1.0
N A:PHE132 4.5 23.1 1.0
N A:TYR133 4.5 23.4 1.0
O A:HOH306 4.5 19.5 1.0
CA A:TYR133 4.5 23.4 1.0
CB A:ASP141 4.6 22.4 1.0
O A:GLY106 4.6 23.2 1.0
ND2 A:ASN138 4.6 26.1 1.0
CA A:GLY106 4.6 25.9 1.0
CB A:PHE132 4.7 22.1 1.0
O A:ASP86 4.8 19.4 1.0
OD1 A:ASP86 4.8 23.8 1.0
CE1 A:HIS146 4.9 20.0 1.0

Calcium binding site 2 out of 2 in 2auy

Go back to Calcium Binding Sites List in 2auy
Calcium binding site 2 out of 2 in the Pterocarpus Angolensis Lectin in Complex with the Trisaccharide Glcnac(B1-2)Man(A1-3)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pterocarpus Angolensis Lectin in Complex with the Trisaccharide Glcnac(B1-2)Man(A1-3)Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca274

b:22.3
occ:1.00
OD2 B:ASP141 2.3 22.1 1.0
O B:PHE132 2.3 24.4 1.0
O B:HOH303 2.4 22.1 1.0
OD1 B:ASN138 2.4 25.6 1.0
O B:HOH304 2.4 22.1 1.0
OD2 B:ASP130 2.5 20.9 1.0
OD1 B:ASP130 2.5 21.9 1.0
CG B:ASP130 2.8 19.9 1.0
CG B:ASP141 3.4 20.2 1.0
CG B:ASN138 3.5 31.9 1.0
C B:PHE132 3.5 26.5 1.0
OD1 B:ASP141 3.9 23.4 1.0
CB B:ASN138 4.0 26.9 1.0
MN B:MN272 4.2 20.2 1.0
CB B:ASP130 4.3 21.3 1.0
CA B:PHE132 4.4 23.5 1.0
NE1 B:TRP140 4.4 27.2 1.0
N B:PHE132 4.4 21.1 1.0
N B:TYR133 4.5 24.2 1.0
CB B:PHE132 4.5 21.9 1.0
O B:HOH305 4.5 20.6 1.0
CA B:TYR133 4.6 26.7 1.0
CB B:ASP141 4.6 23.3 1.0
O B:GLY106 4.6 26.0 1.0
CA B:GLY106 4.6 21.3 1.0
ND2 B:ASN138 4.7 25.0 1.0
O B:ASP86 4.7 19.4 1.0
OD1 B:ASP86 4.8 21.7 1.0
CE1 B:HIS146 4.9 18.3 1.0

Reference:

L.Buts, A.Garcia-Pino, A.Imberty, N.Amiot, G.-J.Boons, S.Beeckmans, W.Versees, L.Wyns, R.Loris. Structural Basis For the Recognition of Complex-Type Biantennary Oligosaccharides By Pterocarpus Angolensis Lectin. Febs J. V. 273 2407 2006.
ISSN: ISSN 1742-464X
PubMed: 16704415
DOI: 10.1111/J.1742-4658.2006.05248.X
Page generated: Sat Dec 12 03:31:42 2020

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