Zinc in PDB 9jta: Crystal Structure of RNF213 Ring Domain Bound to IPAH1.4 Lrr Domain

All present enzymatic activity of Crystal Structure of RNF213 Ring Domain Bound to IPAH1.4 Lrr Domain:
2.3.2.27;

The structure of Crystal Structure of RNF213 Ring Domain Bound to IPAH1.4 Lrr Domain, PDB code: 9jta was solved by X.D.Zhou, Y.R.Wang, L.F.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.38 / 1.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.609, 68.609, 147.694, 90, 90, 90
R / Rfree (%)	19.3 / 22

The binding sites of Zinc atom in the Crystal Structure of RNF213 Ring Domain Bound to IPAH1.4 Lrr Domain (pdb code 9jta). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of RNF213 Ring Domain Bound to IPAH1.4 Lrr Domain, PDB code: 9jta:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of RNF213 Ring Domain Bound to IPAH1.4 Lrr Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of RNF213 Ring Domain Bound to IPAH1.4 Lrr Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn4101 b:37.8 occ:1.00 ND1 C:HIS4014 2.0 41.2 1.0 SG C:CYS4032 2.3 46.5 1.0 SG C:CYS4035 2.3 39.4 1.0 SG C:CYS4012 2.3 46.8 1.0 CE1 C:HIS4014 3.0 37.7 1.0 CG C:HIS4014 3.0 41.0 1.0 CB C:CYS4032 3.1 47.0 1.0 CB C:CYS4012 3.4 45.9 1.0 CB C:HIS4014 3.4 45.0 1.0 CB C:CYS4035 3.5 36.2 1.0 N C:CYS4035 3.9 38.2 1.0 NE2 C:HIS4014 4.1 38.4 1.0 CD2 C:HIS4014 4.1 40.5 1.0 CA C:CYS4035 4.2 35.9 1.0 O C:CYS4012 4.3 47.2 1.0 CA C:CYS4032 4.6 49.8 1.0 CA C:CYS4012 4.6 48.5 1.0 CA C:HIS4014 4.6 45.9 1.0 C C:CYS4012 4.7 52.3 1.0 N C:HIS4014 4.7 46.7 1.0 O C:HOH4216 4.7 54.8 1.0 O B:HOH465 4.7 39.0 1.0 CB C:TYR4034 4.8 45.8 1.0 C C:CYS4035 4.9 35.8 1.0 C C:TYR4034 4.9 39.3 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of RNF213 Ring Domain Bound to IPAH1.4 Lrr Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of RNF213 Ring Domain Bound to IPAH1.4 Lrr Domain within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn4102 b:61.7 occ:1.00 SG C:CYS4017 2.3 76.5 1.0 SG C:CYS3997 2.4 76.2 1.0 SG C:CYS4020 2.4 94.1 1.0 SG C:CYS4000 2.7 75.7 1.0 CB C:CYS4017 3.2 82.0 1.0 CB C:CYS3997 3.4 73.3 1.0 CB C:CYS4020 3.4 80.2 1.0 N C:CYS4017 3.5 74.8 1.0 CA C:CYS4017 3.9 74.7 1.0 CB C:CYS4000 4.1 80.4 1.0 C C:HIS4016 4.7 59.8 1.0 N C:CYS4000 4.7 83.7 1.0 O C:CYS4017 4.8 79.4 1.0 CA C:CYS3997 4.8 73.7 1.0 CA C:CYS4020 4.8 91.5 1.0 C C:CYS4017 4.8 78.3 1.0 CA C:HIS4016 5.0 62.0 1.0

X.Zhou, H.Zhang, Y.Wang, D.Wang, Z.Lin, Y.Zhang, Y.Tang, J.Liu, Y.F.Yao, Y.Zhang, L.Pan. Shigella Effector IPAH1.4 Subverts Host E3 Ligase RNF213 to Evade Antibacterial Immunity. Nat Commun V. 16 3099 2025.
ISSN: ESSN 2041-1723
PubMed: 40164614
DOI: 10.1038/S41467-025-58432-Y