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

Protein crystallography data

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

Zinc Binding Sites:

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 2rkn

Go back to Zinc Binding Sites List in 2rkn
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 2rkn

Go back to Zinc Binding Sites List in 2rkn
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 2rkn

Go back to Zinc Binding Sites List in 2rkn
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

Reference:

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
Page generated: Wed Dec 16 03:52:22 2020

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