Zinc in PDB 7vg2: Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 40-Bp Rna

The structure of Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 40-Bp Rna also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 40-Bp Rna (pdb code 7vg2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 40-Bp Rna, PDB code: 7vg2:

Zinc binding site 1 out of 1 in the Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 40-Bp Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of Arabidopsis DCL3 in Complex with A 40-Bp Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2003 b:49.8 occ:1.00 ND1 A:HIS1123 2.1 28.7 1.0 SG A:CYS1119 2.4 29.7 1.0 SG A:CYS1093 2.4 40.0 1.0 SG A:CYS1091 2.4 37.8 1.0 CB A:CYS1093 2.6 40.0 1.0 CG A:HIS1123 3.0 28.7 1.0 CB A:HIS1123 3.2 28.7 1.0 CE1 A:HIS1123 3.2 28.7 1.0 CB A:CYS1091 3.6 37.8 1.0 CB A:CYS1119 3.7 29.7 1.0 CA A:CYS1093 3.8 40.0 1.0 N A:CYS1093 3.9 40.0 1.0 CA A:CYS1091 4.0 37.8 1.0 CD2 A:HIS1123 4.2 28.7 1.0 NE2 A:HIS1123 4.2 28.7 1.0 CA A:HIS1123 4.2 28.7 1.0 N A:HIS1123 4.2 28.7 1.0 C A:CYS1091 4.5 37.8 1.0 CB A:MET1121 4.5 31.7 1.0 O A:HIS1123 4.7 28.7 1.0 C A:CYS1093 4.7 40.0 1.0 C A:HIS1123 4.8 28.7 1.0 N A:LYS1092 4.9 38.0 1.0 CG2 A:ILE1095 4.9 38.8 1.0 O A:ILE1095 4.9 38.8 1.0 O A:CYS1091 5.0 37.8 1.0

Q.Wang, Y.Xue, L.Zhang, Z.Zhong, S.Feng, C.Wang, L.Xiao, Z.Yang, C.J.Harris, Z.Wu, J.Zhai, M.Yang, S.Li, S.E.Jacobsen, J.Du. Mechanism of Sirna Production By A Plant Dicer-Rna Complex in Dicing-Competent Conformation. Science L4546 2021.
ISSN: ESSN 1095-9203
PubMed: 34648373
DOI: 10.1126/SCIENCE.ABL4546