Zinc in PDB 2rkn: X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana

The structure of X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana, PDB code: 2rkn was solved by M.B.Lascombe, T.Prange, N.Buhot, D.Marion, B.Bakan, C.Lamb, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	9.92 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	28.655, 48.217, 54.406, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 25.2

The binding sites of Zinc atom in the X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana (pdb code 2rkn). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana, PDB code: 2rkn:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:33.1 occ:0.70 N A:ALA1 2.0 38.1 1.0 O A:ALA1 2.5 36.1 1.0 CA A:ALA1 2.8 36.8 1.0 C A:ALA1 2.9 35.7 1.0 CB A:ALA1 3.6 37.0 1.0 N A:ILE2 4.2 32.2 1.0 CG2 A:ILE2 4.7 32.9 1.0 CA A:ILE2 4.9 30.1 1.0

Zinc binding site 2 out of 3 in the X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:21.1 occ:0.65 NE2 A:HIS37 1.9 31.6 0.5 OE2 A:GLU11 2.0 35.9 1.0 CE1 A:HIS37 2.0 35.9 0.5 O A:HOH388 2.1 28.6 1.0 NE2 A:HIS37 2.3 38.8 0.5 ZN A:ZN203 2.3 22.3 0.3 CD2 A:HIS37 2.9 29.5 0.5 CE1 A:HIS37 2.9 28.4 0.5 CD A:GLU11 3.0 35.3 1.0 ND1 A:HIS37 3.3 37.3 0.5 OE1 A:GLU11 3.5 34.2 1.0 O A:HOH375 3.5 36.9 1.0 O A:HOH370 3.6 44.3 1.0 CD2 A:HIS37 3.6 39.0 0.5 O A:HOH305 3.9 15.1 0.3 CA A:ALA34 4.0 34.9 1.0 ND1 A:HIS37 4.0 32.0 0.5 CG A:HIS37 4.1 32.5 0.5 CG A:HIS37 4.1 34.7 0.5 CB A:ALA34 4.2 36.4 1.0 CG A:GLU11 4.2 32.5 1.0 O A:HOH327 4.4 37.8 1.0 O A:ALA34 4.8 34.8 1.0 O A:HOH368 4.9 36.8 1.0 N A:ALA34 4.9 35.3 1.0 C A:ALA34 5.0 35.2 1.0

Zinc binding site 3 out of 3 in the X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of X-Ray Structure of the Self-Defense and Signaling Protein DIR1 From Arabidopsis Taliana within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:22.3 occ:0.35 O A:HOH305 1.8 15.1 0.3 OE1 A:GLU11 2.1 34.2 1.0 CE1 A:HIS37 2.1 28.4 0.5 NE2 A:HIS37 2.2 38.8 0.5 ZN A:ZN202 2.3 21.1 0.7 OE2 A:GLU11 2.4 35.9 1.0 NE2 A:HIS37 2.4 31.6 0.5 CD A:GLU11 2.5 35.3 1.0 CE1 A:HIS37 3.1 35.9 0.5 CD2 A:HIS37 3.1 39.0 0.5 ND1 A:HIS37 3.3 32.0 0.5 CD2 A:HIS37 3.6 29.5 0.5 O A:GLY6 3.7 41.1 1.0 CG A:GLU11 4.0 32.5 1.0 CG A:HIS37 4.1 32.5 0.5 ND1 A:HIS37 4.2 37.3 0.5 CG A:HIS37 4.3 34.7 0.5 O A:HOH388 4.3 28.6 1.0 O A:HOH370 4.4 44.3 1.0 N A:SER8 4.4 34.6 1.0 O A:HOH374 4.4 49.8 1.0 CA A:MET7 4.7 35.6 0.5 CA A:MET7 4.7 34.5 0.5 C A:GLY6 4.8 37.1 1.0 OG A:SER8 4.8 35.7 1.0 CB A:GLU11 4.9 34.7 1.0 CB A:SER8 4.9 36.4 1.0 CB A:ALA34 5.0 36.4 1.0

M.B.Lascombe, B.Bakan, N.Buhot, D.Marion, J.P.Blein, V.Larue, C.Lamb, T.Prange. The Structure of "Defective in Induced Resistance" Protein of Arabidopsis Thaliana, DIR1, Reveals A New Type of Lipid Transfer Protein. Protein Sci. V. 17 1522 2008.
ISSN: ISSN 0961-8368
PubMed: 18552128
DOI: 10.1110/PS.035972.108