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Calcium in PDB 1q8o: Pterocartpus Angolensis Lectin Pal in Complex with the Dimmanoside Man(ALPHA1-2)Man

Protein crystallography data

The structure of Pterocartpus Angolensis Lectin Pal in Complex with the Dimmanoside Man(ALPHA1-2)Man, PDB code: 1q8o was solved by R.Loris, I.Van Walle, H.De Greve, S.Beeckmans, F.Deboeck, L.Wyns, J.Bouckaert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.320, 82.980, 122.000, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 21.8

Other elements in 1q8o:

The structure of Pterocartpus Angolensis Lectin Pal in Complex with the Dimmanoside Man(ALPHA1-2)Man also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Pterocartpus Angolensis Lectin Pal in Complex with the Dimmanoside Man(ALPHA1-2)Man (pdb code 1q8o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Pterocartpus Angolensis Lectin Pal in Complex with the Dimmanoside Man(ALPHA1-2)Man, PDB code: 1q8o:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1q8o

Go back to Calcium Binding Sites List in 1q8o
Calcium binding site 1 out of 2 in the Pterocartpus Angolensis Lectin Pal in Complex with the Dimmanoside Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pterocartpus Angolensis Lectin Pal in Complex with the Dimmanoside Man(ALPHA1-2)Man within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca262

b:12.9
occ:1.00
OD1 A:ASN138 2.3 15.2 1.0
OD2 A:ASP141 2.3 13.6 1.0
O A:PHE132 2.3 19.4 1.0
OD1 A:ASP130 2.4 15.1 1.0
O A:HOH265 2.4 11.2 1.0
OD2 A:ASP130 2.4 16.1 1.0
O A:HOH271 2.6 16.6 1.0
CG A:ASP130 2.7 15.4 1.0
CG A:ASN138 3.3 17.7 1.0
CG A:ASP141 3.4 14.9 1.0
C A:PHE132 3.5 20.8 1.0
CB A:ASN138 3.9 15.9 1.0
OD1 A:ASP141 4.0 15.0 1.0
MN A:MN261 4.2 14.2 1.0
CB A:ASP130 4.2 14.9 1.0
CA A:PHE132 4.4 20.5 1.0
NE1 A:TRP140 4.4 17.1 1.0
N A:TYR133 4.4 21.1 1.0
ND2 A:ASN138 4.5 17.3 1.0
N A:PHE132 4.5 20.3 1.0
CA A:TYR133 4.5 20.8 1.0
O A:GLY106 4.5 16.6 1.0
O A:HOH263 4.5 10.7 1.0
CA A:GLY106 4.5 15.2 1.0
CB A:ASP141 4.6 15.9 1.0
O A:ASP86 4.6 11.9 1.0
CB A:PHE132 4.6 20.5 1.0
OD1 A:ASP86 4.7 16.1 1.0
CE1 A:HIS146 4.9 13.7 1.0

Calcium binding site 2 out of 2 in 1q8o

Go back to Calcium Binding Sites List in 1q8o
Calcium binding site 2 out of 2 in the Pterocartpus Angolensis Lectin Pal in Complex with the Dimmanoside Man(ALPHA1-2)Man


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pterocartpus Angolensis Lectin Pal in Complex with the Dimmanoside Man(ALPHA1-2)Man within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1262

b:13.2
occ:1.00
O B:PHE132 2.3 16.1 1.0
OD2 B:ASP130 2.3 13.2 1.0
OD2 B:ASP141 2.3 15.4 1.0
OD1 B:ASP130 2.4 13.8 1.0
O B:HOH1270 2.4 10.3 1.0
O B:HOH1273 2.5 14.7 1.0
OD1 B:ASN138 2.5 17.1 1.0
CG B:ASP130 2.7 14.2 1.0
CG B:ASP141 3.4 15.4 1.0
CG B:ASN138 3.5 21.0 1.0
C B:PHE132 3.5 18.0 1.0
OD1 B:ASP141 3.9 16.0 1.0
CB B:ASN138 3.9 21.1 1.0
MN B:MN261 4.1 15.4 1.0
CB B:ASP130 4.2 12.8 1.0
CA B:PHE132 4.4 17.1 1.0
NE1 B:TRP140 4.4 14.7 1.0
N B:PHE132 4.4 16.7 1.0
N B:TYR133 4.5 18.8 1.0
CB B:PHE132 4.5 17.6 1.0
O B:ASP86 4.5 13.0 1.0
O B:HOH1265 4.6 7.6 1.0
CB B:ASP141 4.6 17.0 1.0
CA B:TYR133 4.6 19.2 1.0
O B:GLY106 4.6 16.3 1.0
CA B:GLY106 4.7 14.3 1.0
ND2 B:ASN138 4.7 17.8 1.0
CE1 B:HIS146 4.8 13.9 1.0
OD1 B:ASP86 4.8 16.8 1.0

Reference:

R.Loris, I.Van Walle, H.De Greve, S.Beeckmans, F.Deboeck, L.Wyns, J.Bouckaert. Structural Basis of Oligomannose Recognition By the Pterocarpus Angolensis Seed Lectin J.Mol.Biol. V. 335 1227 2004.
ISSN: ISSN 0022-2836
PubMed: 14729339
DOI: 10.1016/J.JMB.2003.11.043
Page generated: Thu Jul 11 14:05:58 2024

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