Zinc in PDB 8fvw: Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp

All present enzymatic activity of Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp:
2.7.7.6;

The structure of Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Zinc atom in the Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp (pdb code 8fvw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp, PDB code: 8fvw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1502 b:173.6 occ:1.00 SG G:CYS72 2.3 113.8 1.0 SG G:CYS88 2.3 119.1 1.0 SG G:CYS85 2.3 113.5 1.0 SG G:CYS70 2.3 115.5 1.0 CB G:CYS85 3.2 110.8 1.0 CB G:CYS70 3.4 111.4 1.0 CB G:CYS88 3.5 114.4 1.0 N G:CYS88 3.7 115.4 1.0 CB G:CYS72 3.7 113.1 1.0 N G:CYS72 3.9 113.6 1.0 CA G:CYS88 4.2 114.7 1.0 N G:GLY73 4.2 111.2 1.0 CA G:CYS72 4.3 113.5 1.0 N G:LEU71 4.4 107.9 1.0 CB G:LYS87 4.4 117.8 1.0 C G:CYS70 4.4 110.0 1.0 CA G:CYS70 4.5 110.1 1.0 N G:LYS74 4.6 121.0 1.0 CA G:CYS85 4.6 110.5 1.0 C G:CYS72 4.7 113.5 1.0 CB G:LYS74 4.8 121.5 1.0 C G:LYS87 4.8 117.7 1.0 N G:LYS87 4.9 117.3 1.0 N G:GLY89 4.9 106.3 1.0 CA G:LYS87 4.9 117.6 1.0 O G:CYS70 4.9 110.8 1.0 C G:LEU71 4.9 110.0 1.0 C G:CYS85 5.0 111.2 1.0

Zinc binding site 2 out of 2 in the Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1503 b:71.4 occ:1.00 SG G:CYS898 2.3 49.5 1.0 SG G:CYS814 2.3 48.5 1.0 SG G:CYS895 2.3 39.6 1.0 SG G:CYS888 2.3 40.8 1.0 NH2 G:ARG883 3.0 40.2 1.0 CB G:CYS888 3.3 39.9 1.0 CB G:CYS898 3.4 30.6 1.0 CB G:CYS895 3.4 24.6 1.0 CB G:CYS814 3.4 43.8 1.0 CA G:CYS888 3.7 39.6 1.0 N G:CYS814 4.0 39.6 1.0 CG2 G:THR816 4.0 54.5 1.0 N G:ASP889 4.1 45.1 1.0 N G:CYS895 4.1 27.1 1.0 CZ G:ARG883 4.1 41.4 1.0 OG1 G:THR890 4.2 46.8 1.0 CA G:CYS895 4.3 27.2 1.0 N G:CYS898 4.3 25.4 1.0 CA G:CYS814 4.3 44.0 1.0 C G:CYS888 4.4 39.6 1.0 CA G:CYS898 4.4 27.1 1.0 NE G:ARG883 4.5 40.4 1.0 N G:THR890 4.7 45.4 1.0 CB G:THR816 4.8 57.5 1.0 C G:CYS895 4.9 23.5 1.0 N G:CYS888 4.9 45.4 1.0 O G:CYS895 4.9 31.3 1.0

J.W.Weaver, S.Proshkin, W.Duan, V.Epshtein, M.Gowder, B.Bharati, E.Afanaseva, A.Mironov, A.Serganov, E.Nudler. Control of Transcription Elongation and Dna Repair By Alarmone Ppgpp Nat.Struct.Mol.Biol. 2023.
ISSN: ESSN 1545-9985
DOI: 10.1038/S41594-023-00948-2