Zinc in PDB 7z0r: ATWRKY18 Dna-Binding Domain

The structure of ATWRKY18 Dna-Binding Domain, PDB code: 7z0r was solved by M.Grzechowiak, M.Jaskolski, M.Ruszkowski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.52 / 1.66
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.576, 52.182, 81.043, 90, 90, 90
R / Rfree (%)	17.8 / 21.9

The binding sites of Zinc atom in the ATWRKY18 Dna-Binding Domain (pdb code 7z0r). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the ATWRKY18 Dna-Binding Domain, PDB code: 7z0r:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the ATWRKY18 Dna-Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of ATWRKY18 Dna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn302 b:11.3 occ:1.00 ND1 A:HIS231 2.1 12.0 1.0 NE2 A:HIS233 2.1 12.5 1.0 SG A:CYS207 2.3 12.4 1.0 SG A:CYS201 2.3 12.0 1.0 CE1 A:HIS231 2.9 10.0 1.0 CD2 A:HIS233 3.0 11.7 1.0 CE1 A:HIS233 3.1 11.0 1.0 CG A:HIS231 3.2 10.6 1.0 CB A:CYS207 3.2 11.3 1.0 CB A:CYS201 3.2 15.4 1.0 CB A:HIS231 3.6 9.2 1.0 CA A:HIS231 4.0 10.1 1.0 NE2 A:HIS231 4.1 8.9 1.0 ND1 A:HIS233 4.2 12.3 1.0 CG A:HIS233 4.2 9.0 1.0 CD2 A:HIS231 4.2 10.3 1.0 CB A:PHE203 4.2 13.8 1.0 CG2 A:VAL209 4.3 10.1 1.0 CB A:VAL209 4.4 11.5 1.0 O A:HOH453 4.5 12.9 1.0 CD2 A:PHE179 4.6 12.5 1.0 CA A:CYS207 4.6 11.0 1.0 CA A:CYS201 4.7 11.8 1.0 N A:ASN232 4.8 12.1 1.0 CE2 A:PHE179 4.8 10.7 1.0 CG A:PHE203 4.8 14.7 1.0 C A:HIS231 4.9 13.8 1.0 N A:PHE203 4.9 15.0 1.0

Zinc binding site 2 out of 2 in the ATWRKY18 Dna-Binding Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of ATWRKY18 Dna-Binding Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn303 b:18.0 occ:1.00 NE2 B:HIS233 2.0 20.0 1.0 ND1 B:HIS231 2.1 18.5 1.0 SG B:CYS201 2.2 19.0 1.0 SG B:CYS207 2.3 19.0 1.0 CD2 B:HIS233 2.9 24.1 1.0 CE1 B:HIS231 3.0 18.4 1.0 CE1 B:HIS233 3.1 18.7 1.0 CG B:HIS231 3.1 19.6 1.0 CB B:CYS201 3.2 21.3 1.0 CB B:CYS207 3.3 20.4 1.0 CB B:HIS231 3.5 19.1 1.0 CA B:HIS231 4.0 20.6 1.0 CG B:HIS233 4.1 19.4 1.0 ND1 B:HIS233 4.1 21.7 1.0 NE2 B:HIS231 4.1 18.5 1.0 CB B:PHE203 4.2 23.0 1.0 CD2 B:HIS231 4.2 20.3 1.0 N B:ASN232 4.5 23.2 1.0 CG2 B:VAL209 4.5 18.7 1.0 CD1 B:PHE203 4.6 26.6 1.0 O B:HOH443 4.6 19.4 1.0 CA B:CYS201 4.6 17.4 1.0 CA B:CYS207 4.7 22.7 1.0 CB B:VAL209 4.7 17.3 1.0 C B:HIS231 4.7 20.6 1.0 CD2 B:PHE179 4.7 17.4 1.0 CG B:PHE203 4.8 22.3 1.0 N B:PHE203 4.9 25.0 1.0 CE2 B:PHE179 4.9 17.2 1.0

M.Grzechowiak, A.Ruszkowska, J.Sliwiak, A.Urbanowicz, M.Jaskolski, M.Ruszkowski. New Aspects of Dna Recognition By Group II Wrky Transcription Factor Revealed By Structural and Functional Study of ATWRKY18 Dna Binding Domain. Int.J.Biol.Macromol. V. 213 589 2022.
ISSN: ISSN 0141-8130
PubMed: 35660042
DOI: 10.1016/J.IJBIOMAC.2022.05.186