Chlorine in PDB 4ldv: Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1

The structure of Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1, PDB code: 4ldv was solved by D.R.Boer, A.Freire-Rios, W.M.A.Van Den Berg, D.Weijers, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.08 / 1.45
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	88.362, 126.256, 83.672, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 24.3

The structure of Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1 also contains other interesting chemical elements:

Iodine

(I)

1 atom

The binding sites of Chlorine atom in the Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1 (pdb code 4ldv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1, PDB code: 4ldv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in the Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:19.3 occ:1.00 O A:HOH599 3.2 40.1 1.0 O A:HOH595 3.4 26.4 0.5 N A:ARG293 3.5 9.3 1.0 CB A:ARG293 4.0 8.2 1.0 CG A:ARG293 4.2 8.2 1.0 CA A:MET292 4.2 10.3 0.5 O A:LEU355 4.2 36.9 1.0 CA A:MET292 4.2 10.5 0.5 SD A:MET292 4.3 15.5 0.5 CA A:ARG293 4.3 8.8 1.0 C A:MET292 4.4 9.9 1.0 CB A:MET292 4.6 11.3 0.5 CD A:ARG293 4.7 8.8 1.0 O A:ARG293 4.7 10.1 1.0 CB A:MET292 4.7 11.7 0.5 CG A:MET292 4.7 12.3 0.5 C A:ARG293 4.9 9.3 1.0 O A:GLY291 5.0 10.0 1.0

Chlorine binding site 2 out of 7 in the Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:48.0 occ:1.00 O A:HOH624 3.2 37.1 1.0 N A:GLU37 3.3 13.2 1.0 O A:HOH601 3.7 34.3 1.0 CG A:GLU37 3.8 12.5 1.0 CD1 A:ILE80 3.9 15.1 1.0 CA A:ARG36 4.0 15.0 1.0 CB A:GLU37 4.1 13.4 1.0 C A:ARG36 4.1 13.0 1.0 CD A:GLU37 4.3 12.4 1.0 CA A:GLU37 4.3 12.3 1.0 NH1 A:ARG82 4.4 19.4 1.0 CB A:ARG36 4.5 17.3 1.0 OE2 A:GLU37 4.6 10.7 1.0 O A:PRO35 4.6 16.1 1.0 O A:HOH650 4.7 36.3 1.0 OE1 A:GLU37 4.8 15.1 1.0 CB A:ILE80 4.8 9.8 1.0 NH2 A:ARG82 4.8 21.2 1.0 CG1 A:ILE80 4.9 11.3 1.0

Chlorine binding site 3 out of 7 in the Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:53.9 occ:1.00 N A:ARG346 3.3 12.7 1.0 N A:GLU345 3.5 15.7 1.0 O A:ARG346 3.7 11.7 1.0 CB A:ARG346 3.9 13.3 1.0 CB A:PRO344 4.0 18.0 1.0 CA A:ARG346 4.1 12.2 1.0 CA A:PRO344 4.2 17.3 1.0 CA A:GLU345 4.2 15.3 0.5 C A:GLU345 4.3 14.4 1.0 CA A:GLU345 4.3 15.1 0.5 CB A:GLU345 4.3 16.9 0.5 C A:PRO344 4.3 16.1 1.0 CD A:ARG329 4.3 12.0 1.0 C A:ARG346 4.3 11.8 1.0 CB A:GLU345 4.5 16.4 0.5 CG A:ARG346 4.7 14.6 1.0 NH1 A:ARG329 4.8 10.6 1.0 CG A:GLU345 4.9 18.2 0.5 NE A:ARG329 4.9 11.9 1.0

Chlorine binding site 4 out of 7 in the Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:32.5 occ:1.00 NH1 A:ARG279 3.1 16.6 0.5 N A:SER276 3.3 8.2 1.0 NE A:ARG279 3.5 15.1 0.5 CD A:ARG279 3.7 15.7 0.5 CG2 A:THR33 3.8 20.6 1.0 N A:PRO35 3.8 13.9 1.0 CA A:VAL275 3.9 8.9 1.0 CB A:SER276 4.0 9.1 1.0 O A:ILE274 4.0 12.4 1.0 C A:VAL275 4.0 8.7 1.0 C A:LEU34 4.1 13.3 1.0 O A:THR33 4.1 20.5 1.0 CA A:PRO35 4.1 13.5 1.0 CZ A:ARG279 4.2 17.6 0.5 CA A:SER276 4.2 8.2 1.0 CD A:PRO35 4.2 13.5 1.0 OG A:SER276 4.2 10.9 1.0 NH2 A:ARG279 4.3 15.8 0.5 CB A:PRO35 4.3 13.6 1.0 CZ A:ARG279 4.4 15.5 0.5 NE A:ARG279 4.4 17.0 0.5 CD A:ARG279 4.4 14.6 0.5 O A:LEU34 4.4 14.3 1.0 C A:THR33 4.4 17.7 1.0 CB A:THR33 4.5 19.3 1.0 OE2 A:GLU272 4.6 29.4 0.5 CA A:LEU34 4.7 14.6 1.0 CG A:ARG279 4.7 14.1 0.5 C A:ILE274 4.7 10.6 1.0 N A:VAL275 4.7 9.1 1.0 CG A:PRO35 4.8 14.1 1.0 N A:LEU34 4.8 15.0 1.0 O A:HOH713 4.8 18.6 0.5 CG1 A:VAL275 4.9 8.9 1.0

Chlorine binding site 5 out of 7 in the Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl406 b:33.9 occ:1.00 NE1 A:TRP323 3.1 17.8 1.0 NE2 A:HIS243 3.4 5.5 1.0 CZ2 A:TRP323 3.7 15.6 1.0 CE2 A:TRP323 3.7 15.6 1.0 CG A:MET49 3.8 11.2 1.0 CE1 A:HIS243 4.1 6.0 1.0 CB A:MET49 4.2 8.9 1.0 CA A:GLU46 4.2 8.4 1.0 CG A:GLU46 4.3 11.7 1.0 CD1 A:TRP323 4.3 16.9 1.0 CD2 A:HIS243 4.4 5.2 1.0 O A:HOH621 4.5 26.4 1.0 O A:PRO45 4.7 9.2 1.0 N A:GLU46 4.7 8.8 1.0 CB A:GLU46 4.7 10.2 1.0 CD2 A:LEU247 4.7 5.5 1.0 O A:HOH576 4.8 26.6 1.0 CD1 A:LEU247 4.8 4.8 1.0 C A:PRO45 4.9 9.3 1.0 CH2 A:TRP323 5.0 14.1 1.0

Chlorine binding site 6 out of 7 in the Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl407 b:33.0 occ:1.00 O A:HOH528 3.1 28.9 1.0 NE A:ARG177 3.2 13.4 1.0 CG A:GLU163 3.5 19.6 1.0 CB A:GLU163 3.5 15.9 1.0 NH2 A:ARG177 3.6 13.0 1.0 CD A:GLU163 3.6 23.7 1.0 OE1 A:GLU163 3.7 26.6 1.0 CB A:ARG177 3.8 12.6 1.0 CZ A:ARG177 3.8 12.8 1.0 CA A:GLU163 4.1 13.6 1.0 CG A:ARG177 4.1 12.8 1.0 CD A:ARG177 4.2 13.2 1.0 CZ3 A:TRP161 4.3 13.9 1.0 CA A:ARG177 4.3 11.5 1.0 OE2 A:GLU163 4.3 25.6 1.0 N A:ARG177 4.6 10.9 1.0 CB A:THR191 4.7 15.6 1.0 N A:GLU163 4.8 12.3 1.0 CG2 A:THR191 4.9 16.3 1.0 CE3 A:TRP161 4.9 13.4 1.0 O A:HOH675 4.9 45.9 1.0

Chlorine binding site 7 out of 7 in the Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of the Dna Binding Domain of A. Thailana Auxin Response Factor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl408 b:25.8 occ:0.50 NE2 A:GLN157 1.9 14.6 0.5 O A:HOH510 2.8 21.7 1.0 O A:HOH672 3.0 47.4 1.0 CD A:GLN157 3.1 13.1 0.5 O A:HOH752 3.1 48.8 1.0 OE1 A:GLN157 3.5 15.9 0.5 OE1 A:GLN157 3.5 16.5 0.5 CG A:GLN157 3.8 11.4 0.5 CD A:GLN157 4.0 12.6 0.5 CG A:GLN157 4.3 11.8 0.5 CB A:GLN157 4.4 10.3 0.5 CB A:GLN157 4.6 10.5 0.5 CA A:GLN157 4.6 9.9 0.5 CA A:GLN157 4.7 10.1 0.5 O A:HOH703 4.9 27.4 1.0

D.R.Boer, A.Freire-Rios, W.A.Van Den Berg, T.Saaki, I.W.Manfield, S.Kepinski, I.Lopez-Vidrieo, J.M.Franco-Zorrilla, S.C.De Vries, R.Solano, D.Weijers, M.Coll. Structural Basis For Dna Binding Specificity By the Auxin-Dependent Arf Transcription Factors. Cell(Cambridge,Mass.) V. 156 577 2014.
ISSN: ISSN 0092-8674
PubMed: 24485461
DOI: 10.1016/J.CELL.2013.12.027