Magnesium 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:

Zinc	(Zn)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Cryoem Structure of E.Coli Transcription Elongation Complex Bound to Ppgpp, PDB code: 8fvw:
Jump to Magnesium binding site number: 1; 2;

Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1504 b:19.6 occ:1.00 O3' C:A16 2.0 37.4 1.0 O G:HOH1602 2.1 23.9 1.0 OD1 G:ASP460 2.2 32.9 1.0 OD1 G:ASP464 2.2 26.2 1.0 O G:HOH1617 2.2 20.9 1.0 OD1 G:ASP462 2.2 26.7 1.0 CG G:ASP462 3.0 19.1 1.0 CG G:ASP460 3.0 25.9 1.0 CG G:ASP464 3.1 18.9 1.0 OD2 G:ASP462 3.1 28.6 1.0 OD2 G:ASP460 3.1 30.7 1.0 C3' C:A16 3.3 35.6 1.0 OD2 G:ASP464 3.3 23.3 1.0 O2' C:A16 3.7 45.1 1.0 C4' C:A16 3.8 31.9 1.0 C2' C:A16 4.1 37.5 1.0 CB G:ASP462 4.4 18.6 1.0 CB G:ASP460 4.4 14.8 1.0 C5' C:A16 4.4 28.5 1.0 CB G:ASP464 4.5 17.9 1.0 N G:ASP462 4.6 19.4 1.0 N G:ASP460 4.6 16.0 1.0 O G:ASP460 4.7 24.4 1.0 N G:ASP464 4.7 22.5 1.0 C G:ASP460 4.7 14.6 1.0 CA G:ASP460 4.8 20.4 1.0 CA G:ASP462 4.8 16.6 1.0 C G:ASP462 4.9 15.6 1.0 CA G:ASP464 5.0 20.2 1.0

Magnesium 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 Magnesium with other atoms in the Mg 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 H:Mg101 b:56.9 occ:1.00 O G:HOH1630 2.0 31.7 0.6 O3B G:G4P1501 2.2 45.5 1.0 O2A G:G4P1501 2.2 48.4 1.0 O G:HOH1677 2.2 35.8 0.6 O H:HOH205 2.4 46.0 0.6 PB G:G4P1501 3.5 59.0 1.0 PA G:G4P1501 3.5 54.0 1.0 O3A G:G4P1501 3.7 39.6 1.0 O G:HOH1679 3.8 43.7 1.0 O1B G:G4P1501 4.1 48.5 1.0 O1C G:G4P1501 4.1 41.4 1.0 NH1 H:ARG3 4.4 39.7 1.0 O1A G:G4P1501 4.5 48.5 1.0 O5' G:G4P1501 4.6 46.5 1.0 O2B G:G4P1501 4.6 48.0 1.0 C5' G:G4P1501 4.7 35.1 1.0 NH2 G:ARG417 4.7 43.6 1.0 OE1 H:GLU42 5.0 57.7 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