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Sodium in PDB 3e85: Crystal Structure of Pathogenesis-Related Protein Llpr-10.2B From Yellow Lupine in Complex with Diphenylurea

Protein crystallography data

The structure of Crystal Structure of Pathogenesis-Related Protein Llpr-10.2B From Yellow Lupine in Complex with Diphenylurea, PDB code: 3e85 was solved by H.C.Fernandes, G.Bujacz, A.Bujacz, M.M.Sikorski, M.Jaskolski, 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 C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 34.362, 73.256, 99.956, 90.00, 90.00, 90.00
R / Rfree (%) 18.8 / 24.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Pathogenesis-Related Protein Llpr-10.2B From Yellow Lupine in Complex with Diphenylurea (pdb code 3e85). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Pathogenesis-Related Protein Llpr-10.2B From Yellow Lupine in Complex with Diphenylurea, PDB code: 3e85:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3e85

Go back to Sodium Binding Sites List in 3e85
Sodium binding site 1 out of 2 in the Crystal Structure of Pathogenesis-Related Protein Llpr-10.2B From Yellow Lupine in Complex with Diphenylurea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Pathogenesis-Related Protein Llpr-10.2B From Yellow Lupine in Complex with Diphenylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na162

b:34.4
occ:1.00
O A:PRO31 2.2 35.5 1.0
O A:ILE37 2.4 36.4 1.0
O A:HOH209 2.4 40.0 1.0
O A:VAL34 2.5 37.3 1.0
O A:HOH259 2.7 51.0 1.0
O A:HOH226 2.7 43.2 1.0
C A:PRO31 3.4 36.4 1.0
C A:VAL34 3.4 36.2 1.0
C A:ILE37 3.5 36.6 1.0
CA A:GLU35 3.8 36.1 1.0
N A:GLU35 3.9 36.6 1.0
CA A:PRO31 3.9 34.6 1.0
C A:GLU35 4.0 35.0 1.0
O A:GLU35 4.0 35.2 1.0
N A:ILE37 4.2 36.5 1.0
CA A:ILE37 4.4 36.3 1.0
N A:VAL34 4.4 35.3 1.0
CA A:GLN38 4.4 36.1 1.0
N A:GLN38 4.4 36.6 1.0
CA A:VAL34 4.5 35.7 1.0
N A:LYS32 4.5 37.3 1.0
CB A:PRO31 4.6 35.3 1.0
N A:THR36 4.7 35.6 1.0
C A:LYS32 4.8 38.8 1.0
CA A:LYS32 4.8 38.8 1.0
O A:ILE30 4.8 34.6 1.0
CB A:ILE37 4.9 34.1 1.0
O A:LYS32 4.9 39.7 1.0
O A:GLN38 4.9 34.4 1.0
C A:GLN38 4.9 35.0 1.0

Sodium binding site 2 out of 2 in 3e85

Go back to Sodium Binding Sites List in 3e85
Sodium binding site 2 out of 2 in the Crystal Structure of Pathogenesis-Related Protein Llpr-10.2B From Yellow Lupine in Complex with Diphenylurea


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Pathogenesis-Related Protein Llpr-10.2B From Yellow Lupine in Complex with Diphenylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na163

b:41.0
occ:1.00
O A:HOH229 2.1 43.7 1.0
O A:GLY123 2.5 34.0 1.0
O A:HOH231 2.5 44.9 1.0
OG1 A:THR121 2.5 31.1 1.0
O A:HOH246 2.6 48.7 1.0
O A:THR121 2.9 33.6 1.0
C A:THR121 3.5 35.4 1.0
C A:GLY123 3.7 34.2 1.0
CB A:THR121 3.7 35.0 1.0
CA A:THR121 3.9 34.7 1.0
N A:THR121 3.9 36.7 1.0
O A:ALA125 4.0 33.7 1.0
C A:LYS122 4.3 36.2 1.0
N A:LYS122 4.4 36.2 1.0
N A:GLY123 4.4 35.2 1.0
O A:HOH275 4.4 55.5 1.0
CA A:ASP124 4.4 33.7 1.0
N A:ASP124 4.5 33.9 1.0
N A:ALA125 4.5 33.5 1.0
O A:LYS122 4.5 36.6 1.0
C A:ASP124 4.6 34.4 1.0
CE2 A:PHE3 4.6 28.2 1.0
CA A:GLY123 4.7 34.6 1.0
CA A:LYS122 4.7 36.7 1.0
CG2 A:THR121 4.7 31.2 1.0

Reference:

H.Fernandes, A.Bujacz, G.Bujacz, F.Jelen, M.Jasinski, P.Kachlicki, J.Otlewski, M.M.Sikorski, M.Jaskolski. Cytokinin-Induced Structural Adaptability of A Lupinus Luteus Pr-10 Protein. Febs J. V. 276 1596 2009.
ISSN: ISSN 1742-464X
PubMed: 19220853
DOI: 10.1111/J.1742-4658.2009.06892.X
Page generated: Tue Dec 15 06:09:34 2020

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