Chlorine in PDB 6ycq: Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna

Protein crystallography data

The structure of Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna, PDB code: 6ycq was solved by I.Crespo, D.Weijers, D.R.Boer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.57 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.304, 102.784, 127.039, 90.00, 98.04, 90.00
R / Rfree (%) 17.2 / 19.9

Other elements in 6ycq:

The structure of Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna (pdb code 6ycq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna, PDB code: 6ycq:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6ycq

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Chlorine binding site 1 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


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 Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:53.0
occ:1.00
 N A:LEU34 3.0 26.6 1.0
O A:HOH670 3.2 52.3 1.0
CE1 A:HIS25 3.2 27.4 1.0
CA A:THR33 3.5 24.1 1.0
O A:LEU34 3.5 26.3 1.0
C A:THR33 3.7 25.2 1.0
CB A:THR33 3.9 31.3 1.0
ND1 A:HIS25 3.9 28.6 1.0
CA A:LEU34 4.0 24.1 1.0
NE2 A:HIS25 4.0 31.8 1.0
C A:LEU34 4.2 27.0 1.0
CB A:LEU34 4.3 19.5 1.0
CG2 A:THR33 4.3 34.2 1.0
O A:HOH664 4.3 38.7 1.0
O A:VAL32 4.5 26.5 1.0
N A:THR33 4.7 21.5 1.0
CG A:HIS25 4.9 29.2 1.0
O A:THR33 4.9 31.8 1.0
CG A:LEU34 5.0 22.9 1.0
CD2 A:HIS25 5.0 24.7 1.0

Chlorine binding site 2 out of 12 in 6ycq

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Chlorine binding site 2 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


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 Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:58.2
occ:1.00
 N A:THR127 3.4 21.8 1.0
O A:HOH633 3.8 36.3 1.0
CA A:LYS126 3.9 22.9 1.0
O A:HOH526 3.9 40.2 1.0
CG A:LYS126 4.0 22.4 1.0
O A:HOH788 4.0 60.5 1.0
CB A:THR127 4.1 24.6 1.0
C A:LYS126 4.1 22.0 1.0
OG1 A:THR127 4.2 27.7 1.0
O A:CYS125 4.2 27.8 1.0
CA A:THR127 4.3 18.8 1.0
CB A:LYS126 4.5 20.6 1.0
OE2 A:GLU302 4.6 0.3 1.0
O A:THR127 4.6 21.9 1.0
CD1 A:LEU142 4.7 23.7 1.0
O D:HOH105 4.8 39.8 1.0
OE1 A:GLU302 4.8 0.5 1.0
N A:LYS126 4.9 22.8 1.0
C A:CYS125 5.0 25.6 1.0
C A:THR127 5.0 22.8 1.0

Chlorine binding site 3 out of 12 in 6ycq

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Chlorine binding site 3 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


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 Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:76.3
occ:1.00
 N A:ARG293 3.3 24.7 1.0
CA A:MET292 3.7 23.5 1.0
C A:MET292 4.0 21.1 1.0
O A:GLY291 4.2 28.8 1.0
CB A:ARG293 4.2 26.6 1.0
CB A:MET292 4.3 20.6 1.0
CA A:ARG293 4.3 25.7 1.0
CG A:MET292 4.4 34.9 1.0
CG A:ARG293 4.5 32.3 1.0
O A:ARG293 4.7 25.7 1.0
N A:MET292 4.8 20.6 1.0
CD A:ARG293 4.8 33.0 1.0
C A:GLY291 4.9 20.2 1.0
O A:HOH529 5.0 38.9 1.0
C A:ARG293 5.0 25.7 1.0

Chlorine binding site 4 out of 12 in 6ycq

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Chlorine binding site 4 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


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 Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:31.0
occ:1.00
 O C:HOH234 2.7 44.5 1.0
N A:GLY138 3.3 28.0 1.0
O C:HOH202 3.3 37.6 1.0
NH2 A:ARG181 3.4 22.1 1.0
O A:HOH767 3.6 46.8 1.0
CA A:GLY137 3.9 37.0 1.0
C6 C:DC15 4.0 30.6 1.0
CG2 A:THR190 4.0 18.5 1.0
O C:HOH215 4.1 26.3 1.0
C5 C:DC16 4.1 27.7 1.0
C A:GLY137 4.1 30.3 1.0
CA A:GLY138 4.1 24.0 1.0
C2' C:DC15 4.1 42.4 1.0
C5 C:DC15 4.2 27.2 1.0
CD1 A:LEU188 4.7 23.5 1.0
N4 C:DC16 4.7 26.6 1.0
CZ A:ARG181 4.7 21.7 1.0
N1 C:DC15 4.7 31.9 1.0
CB A:THR190 4.8 24.0 1.0
OP2 C:DC15 4.9 40.8 1.0
C4 C:DC16 4.9 23.8 1.0
C6 C:DC16 5.0 23.2 1.0

Chlorine binding site 5 out of 12 in 6ycq

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Chlorine binding site 5 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


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 Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:54.2
occ:1.00
 NH1 A:ARG83 3.2 28.5 1.0
O A:HOH738 3.3 41.1 1.0
O A:HOH744 3.4 50.9 1.0
CZ A:ARG83 4.1 30.8 1.0
NE A:ARG83 4.1 25.5 1.0
OE1 A:GLN81 4.6 31.3 1.0

Chlorine binding site 6 out of 12 in 6ycq

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Chlorine binding site 6 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


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 Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:40.0
occ:1.00
 N A:TRP335 3.2 24.4 1.0
CA A:GLN334 3.7 18.6 1.0
CD1 A:TRP335 3.8 18.9 1.0
C A:GLN334 3.9 21.7 1.0
CB A:GLN334 4.2 21.9 1.0
CB A:TRP335 4.2 23.4 1.0
CA A:TRP335 4.2 25.7 1.0
O A:TRP335 4.3 23.1 1.0
CG A:TRP335 4.4 23.5 1.0
CG A:GLN334 4.5 23.1 1.0
O A:HOH725 4.6 51.9 1.0
O A:VAL333 4.6 26.2 1.0
C A:TRP335 4.8 25.3 1.0
N A:GLN334 4.9 18.4 1.0
NE1 A:TRP335 4.9 19.1 1.0

Chlorine binding site 7 out of 12 in 6ycq

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Chlorine binding site 7 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


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 Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:63.9
occ:1.00
 N B:THR127 3.1 24.4 1.0
CA B:LYS126 3.6 30.2 1.0
CG B:LYS126 3.8 26.6 1.0
C B:LYS126 3.8 32.5 1.0
O B:HOH587 3.9 35.8 1.0
O B:CYS125 4.0 36.7 1.0
CB B:THR127 4.0 34.5 1.0
OG1 B:THR127 4.0 37.2 1.0
CA B:THR127 4.1 31.3 1.0
CB B:LYS126 4.2 29.1 1.0
O B:THR127 4.5 30.9 1.0
N B:LYS126 4.6 30.8 1.0
C B:CYS125 4.7 36.0 1.0
O C:HOH207 4.8 46.6 1.0
C B:THR127 4.8 26.7 1.0
CD1 B:LEU142 4.8 28.1 1.0
OE1 B:GLU302 4.8 81.3 1.0

Chlorine binding site 8 out of 12 in 6ycq

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Chlorine binding site 8 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:40.9
occ:1.00
 O D:HOH102 2.6 41.5 1.0
O D:HOH117 2.9 40.1 1.0
N B:GLY138 3.4 33.9 1.0
NH1 B:ARG181 3.5 36.3 1.0
CG2 B:THR190 3.8 23.3 1.0
C6 D:DC15 3.9 39.9 1.0
CA B:GLY137 3.9 45.2 1.0
C2' D:DC15 4.0 44.8 1.0
C B:GLY137 4.1 40.6 1.0
C5 D:DC15 4.2 37.2 1.0
C5 D:DC16 4.2 34.8 1.0
CA B:GLY138 4.3 27.8 1.0
O B:HOH529 4.4 31.9 1.0
OP2 D:DC15 4.5 53.5 1.0
CB B:THR190 4.5 23.9 1.0
N1 D:DC15 4.7 41.6 1.0
CZ B:ARG181 4.7 34.1 1.0
O5' D:DC15 4.8 51.7 1.0
C3' D:DC15 4.9 42.5 1.0
N4 D:DC16 4.9 32.6 1.0
CD1 B:LEU188 5.0 26.3 1.0
C1' D:DC15 5.0 44.5 1.0

Chlorine binding site 9 out of 12 in 6ycq

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Chlorine binding site 9 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:56.1
occ:1.00
 N B:SER276 3.5 19.1 1.0
O B:HOH579 3.6 33.1 1.0
CB B:SER276 3.8 27.4 1.0
O B:HOH683 3.9 45.0 1.0
OG B:SER276 3.9 27.8 1.0
CA B:SER276 4.3 25.1 1.0
CA B:VAL275 4.4 20.1 1.0
C B:VAL275 4.4 22.6 1.0
CA B:PRO35 4.4 25.5 1.0
N B:PRO35 4.5 23.8 1.0
CB B:PRO35 4.5 27.3 1.0
O B:HOH541 4.5 40.4 1.0
O B:ILE274 4.5 23.4 1.0
OG1 B:THR33 4.7 34.7 1.0
O B:HOH520 4.7 51.2 1.0
C B:LEU34 4.8 26.2 1.0
CD B:PRO35 4.9 20.1 1.0
CB B:ARG279 4.9 21.9 1.0
O B:LEU34 4.9 28.5 1.0

Chlorine binding site 10 out of 12 in 6ycq

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Chlorine binding site 10 out of 12 in the Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of the Dna Binding Domain of Arabidopsis Thaliana Auxin Response Factor 1 (ATARF1) in Complex with High Affinity Dna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:68.5
occ:1.00
 N B:VAL315 3.1 33.0 1.0
CA B:GLY314 3.4 23.7 1.0
O B:HOH734 3.5 42.1 1.0
C B:GLY314 3.8 26.5 1.0
OE2 B:GLU317 3.9 59.6 1.0
CG2 B:VAL315 3.9 31.8 1.0
CG2 B:VAL290 4.0 27.4 1.0
N B:GLN316 4.1 36.3 1.0
CA B:VAL315 4.2 32.0 1.0
C B:VAL315 4.6 38.4 1.0
CB B:VAL315 4.6 32.5 1.0
N B:GLY314 4.7 21.0 1.0
O B:VAL313 4.7 27.1 1.0

Reference:

A.Freire-Rios, K.Tanaka, I.Crespo, E.Van Der Wijk, Y.Sizentsova, V.Levitsky, S.Lindhoud, M.Fontana, J.Hohlbein, D.R.Boer, V.Mironova, D.Weijers. Architecture of Dna Elements Mediating Arf Transcription Factor Binding and Auxin-Responsive Gene Expression in Arabidopsis . Proc.Natl.Acad.Sci.Usa V. 117 24557 2020.
ISSN: ESSN 1091-6490
PubMed: 32929017
DOI: 10.1073/PNAS.2009554117
Page generated: Sat Dec 12 14:41:54 2020

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