Zinc in PDB 8u3b: Cryo-Em Structure of E. Coli Narl-Transcription Activation Complex at 3.2A

All present enzymatic activity of Cryo-Em Structure of E. Coli Narl-Transcription Activation Complex at 3.2A:
2.7.7.6;

The structure of Cryo-Em Structure of E. Coli Narl-Transcription Activation Complex at 3.2A also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of E. Coli Narl-Transcription Activation Complex at 3.2A (pdb code 8u3b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of E. Coli Narl-Transcription Activation Complex at 3.2A, PDB code: 8u3b:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of E. Coli Narl-Transcription Activation Complex at 3.2A


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 E. Coli Narl-Transcription Activation Complex at 3.2A within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1501 b:195.7 occ:1.00 SG D:CYS85 2.3 175.7 1.0 SG D:CYS72 2.3 175.9 1.0 SG D:CYS70 2.3 166.5 1.0 SG D:CYS88 2.3 169.5 1.0 CB D:CYS85 3.1 175.7 1.0 CB D:CYS70 3.2 166.5 1.0 N D:CYS72 3.4 175.9 1.0 CB D:CYS72 3.4 175.9 1.0 N D:GLY73 3.5 178.1 1.0 CB D:CYS88 3.8 169.5 1.0 CA D:CYS72 3.8 175.9 1.0 N D:LEU71 4.0 167.4 1.0 C D:CYS72 4.1 175.9 1.0 C D:CYS70 4.2 166.5 1.0 N D:LYS74 4.3 180.6 1.0 CA D:CYS70 4.3 166.5 1.0 CG D:LYS87 4.4 174.5 1.0 N D:CYS88 4.5 169.5 1.0 CA D:GLY73 4.5 178.1 1.0 C D:LEU71 4.5 167.4 1.0 CA D:CYS85 4.5 175.7 1.0 CA D:CYS88 4.7 169.5 1.0 CA D:LEU71 4.8 167.4 1.0 O D:VAL90 4.8 160.0 1.0 C D:GLY73 4.9 178.1 1.0 O D:CYS70 4.9 166.5 1.0 CD D:LYS87 4.9 174.5 1.0 C D:CYS85 4.9 175.7 1.0 O D:CYS85 4.9 175.7 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of E. Coli Narl-Transcription Activation Complex at 3.2A


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of E. Coli Narl-Transcription Activation Complex at 3.2A within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1502 b:107.1 occ:1.00 SG D:CYS895 2.3 82.8 1.0 SG D:CYS898 2.3 83.6 1.0 SG D:CYS888 2.3 89.2 1.0 SG D:CYS814 2.3 99.1 1.0 CB D:CYS814 3.2 99.1 1.0 CB D:CYS898 3.2 83.6 1.0 CB D:CYS888 3.3 89.2 1.0 CB D:CYS895 3.6 82.8 1.0 CA D:CYS888 3.7 89.2 1.0 N D:CYS814 4.0 99.1 1.0 N D:ASP889 4.0 97.1 1.0 N D:CYS895 4.1 82.8 1.0 CA D:CYS814 4.2 99.1 1.0 N D:CYS898 4.2 83.6 1.0 CA D:CYS898 4.3 83.6 1.0 C D:CYS888 4.4 89.2 1.0 CA D:CYS895 4.4 82.8 1.0 OG1 D:THR816 4.5 106.1 1.0 NH2 D:ARG883 4.5 96.8 1.0 OG1 D:THR890 4.6 90.8 1.0 NE D:ARG883 4.8 96.8 1.0 N D:CYS888 4.9 89.2 1.0 O D:CYS895 4.9 82.8 1.0 C D:CYS895 5.0 82.8 1.0

D.Kompaniiets, L.He, D.Wang, W.Zhou, Y.Yang, Y.Hu, B.Liu. Structural Basis For Transcription Activation By the Nitrate-Responsive Regulator Narl. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 38197271
DOI: 10.1093/NAR/GKAD1231