Zinc in PDB 8ibx: Structure of R2 with 3'Utr and Dna in Unwinding State

The binding sites of Zinc atom in the Structure of R2 with 3'Utr and Dna in Unwinding State (pdb code 8ibx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of R2 with 3'Utr and Dna in Unwinding State, PDB code: 8ibx:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of R2 with 3'Utr and Dna in Unwinding State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of R2 with 3'Utr and Dna in Unwinding State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1201 b:141.1 occ:1.00 NE2 C:HIS135 2.0 109.0 1.0 NE2 C:HIS130 2.0 114.0 1.0 SG C:CYS114 2.3 120.2 1.0 SG C:CYS117 2.3 125.0 1.0 CB C:CYS117 2.6 125.0 1.0 N C:CYS117 2.8 125.0 1.0 CE1 C:HIS135 2.9 109.0 1.0 CE1 C:HIS130 2.9 114.0 1.0 CB C:CYS114 3.1 120.2 1.0 CD2 C:HIS135 3.1 109.0 1.0 CD2 C:HIS130 3.1 114.0 1.0 CA C:CYS117 3.3 125.0 1.0 C C:PHE116 3.9 118.1 1.0 ND1 C:HIS135 4.0 109.0 1.0 ND1 C:HIS130 4.1 114.0 1.0 CG C:HIS135 4.2 109.0 1.0 C C:CYS117 4.2 125.0 1.0 CG C:HIS130 4.2 114.0 1.0 N C:PHE116 4.3 118.1 1.0 CB C:PHE116 4.4 118.1 1.0 N C:GLU118 4.4 126.8 1.0 CA C:PHE116 4.4 118.1 1.0 CA C:CYS114 4.5 120.2 1.0 CD1 C:PHE116 4.6 118.1 1.0 CB C:ALA134 4.7 113.0 1.0 C C:CYS114 4.8 120.2 1.0 O C:PHE116 4.9 118.1 1.0 N C:GLN115 4.9 118.4 1.0

Zinc binding site 2 out of 2 in the Structure of R2 with 3'Utr and Dna in Unwinding State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of R2 with 3'Utr and Dna in Unwinding State within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1202 b:167.8 occ:1.00 CB C:CYS934 2.3 132.8 1.0 NE2 C:HIS946 2.3 118.8 1.0 SG C:CYS938 2.3 138.8 1.0 SG C:CYS934 2.3 132.8 1.0 CB C:CYS938 2.3 138.8 1.0 CE1 C:HIS946 2.9 118.8 1.0 CA C:CYS938 3.4 138.8 1.0 N C:CYS938 3.4 138.8 1.0 CD2 C:HIS946 3.5 118.8 1.0 CA C:CYS934 3.8 132.8 1.0 ND1 C:HIS946 4.2 118.8 1.0 C C:CYS938 4.2 138.8 1.0 CG2 C:VAL940 4.4 136.5 1.0 N C:CYS934 4.5 132.8 1.0 CG C:HIS946 4.5 118.8 1.0 SG C:CYS951 4.5 117.2 1.0 C C:CYS934 4.5 132.8 1.0 N C:LYS939 4.6 140.5 1.0 CB C:ALA936 4.7 127.7 1.0 CB C:CYS951 4.7 117.2 1.0 C C:GLY937 4.7 133.1 1.0 N C:GLY937 4.8 133.1 1.0 O C:CYS934 4.8 132.8 1.0 O C:VAL940 4.9 136.5 1.0 N C:ALA936 5.0 127.7 1.0 O C:CYS938 5.0 138.8 1.0

P.Deng, S.Q.Tan, Q.Y.Yang, L.Fu, Y.Wu, H.Z.Zhu, L.Sun, Z.Bao, Y.Lin, Q.C.Zhang, H.Wang, J.Wang, J.G.Liu. Structural Rna Components Supervise the Sequential Dna Cleavage in R2 Retrotransposon. Cell V. 186 2865 2023.
ISSN: ISSN 1097-4172
PubMed: 37301196
DOI: 10.1016/J.CELL.2023.05.032