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Calcium in PDB 1ukg: Pterocarps Angolensis Lectin Pal in Complex with Methyl-Alpha-Mannose

Protein crystallography data

The structure of Pterocarps Angolensis Lectin Pal in Complex with Methyl-Alpha-Mannose, PDB code: 1ukg 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 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.820, 83.670, 123.000, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 21.5

Other elements in 1ukg:

The structure of Pterocarps Angolensis Lectin Pal in Complex with Methyl-Alpha-Mannose also contains other interesting chemical elements:

Manganese (Mn) 2 atoms

Calcium Binding Sites:

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

Calcium binding site 1 out of 2 in 1ukg

Go back to Calcium Binding Sites List in 1ukg
Calcium binding site 1 out of 2 in the Pterocarps Angolensis Lectin Pal in Complex with Methyl-Alpha-Mannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Pterocarps Angolensis Lectin Pal in Complex with Methyl-Alpha-Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1262

b:19.4
occ:1.00
OD2 A:ASP141 2.3 22.1 1.0
OD1 A:ASN138 2.4 21.8 1.0
O A:PHE132 2.4 21.1 1.0
O A:HOH1266 2.5 19.7 1.0
O A:HOH1264 2.5 18.8 1.0
OD1 A:ASP130 2.5 18.8 1.0
OD2 A:ASP130 2.5 19.4 1.0
CG A:ASP130 2.8 15.5 1.0
CG A:ASP141 3.4 18.9 1.0
CG A:ASN138 3.4 30.3 1.0
C A:PHE132 3.6 21.0 1.0
OD1 A:ASP141 3.9 17.9 1.0
CB A:ASN138 4.0 22.5 1.0
MN A:MN261 4.2 19.9 1.0
CB A:ASP130 4.3 16.3 1.0
NE1 A:TRP140 4.4 22.5 1.0
CA A:PHE132 4.5 22.1 1.0
N A:PHE132 4.5 20.5 1.0
N A:TYR133 4.6 22.1 1.0
ND2 A:ASN138 4.6 27.5 1.0
O A:HOH1263 4.6 16.7 1.0
CA A:TYR133 4.6 19.1 1.0
O A:GLY106 4.6 21.5 1.0
CB A:ASP141 4.6 19.1 1.0
CA A:GLY106 4.7 21.2 1.0
CB A:PHE132 4.7 21.5 1.0
O A:ASP86 4.7 18.8 1.0
OD1 A:ASP86 4.8 22.3 1.0
CE1 A:HIS146 4.9 21.3 1.0

Calcium binding site 2 out of 2 in 1ukg

Go back to Calcium Binding Sites List in 1ukg
Calcium binding site 2 out of 2 in the Pterocarps Angolensis Lectin Pal in Complex with Methyl-Alpha-Mannose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Pterocarps Angolensis Lectin Pal in Complex with Methyl-Alpha-Mannose within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2262

b:17.7
occ:1.00
OD2 B:ASP141 2.3 19.2 1.0
O B:PHE132 2.3 17.3 1.0
O B:HOH2265 2.4 17.0 1.0
OD1 B:ASN138 2.4 20.4 1.0
O B:HOH2269 2.4 18.5 1.0
OD1 B:ASP130 2.5 15.2 1.0
OD2 B:ASP130 2.5 14.2 1.0
CG B:ASP130 2.8 18.1 1.0
CG B:ASP141 3.4 20.2 1.0
CG B:ASN138 3.5 23.6 1.0
C B:PHE132 3.6 21.5 1.0
OD1 B:ASP141 3.9 15.1 1.0
CB B:ASN138 4.0 23.3 1.0
MN B:MN261 4.2 18.2 1.0
CB B:ASP130 4.3 18.3 1.0
CA B:PHE132 4.4 17.8 1.0
NE1 B:TRP140 4.5 19.9 1.0
N B:PHE132 4.5 18.2 1.0
N B:TYR133 4.5 22.1 1.0
CB B:PHE132 4.6 20.4 1.0
O B:HOH2264 4.6 16.1 1.0
CA B:TYR133 4.6 20.8 1.0
ND2 B:ASN138 4.6 24.2 1.0
CB B:ASP141 4.6 17.4 1.0
O B:GLY106 4.7 20.4 1.0
O B:ASP86 4.7 17.0 1.0
CA B:GLY106 4.7 18.6 1.0
OD1 B:ASP86 4.8 17.5 1.0
CE1 B:HIS146 4.9 16.2 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 23:31:40 2024

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