Zinc in PDB 8re4: Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 5NT Pre-Translocated Complex

All present enzymatic activity of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 5NT Pre-Translocated Complex:
2.7.7.6;

The structure of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 5NT Pre-Translocated Complex also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 5NT Pre-Translocated Complex (pdb code 8re4). 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 Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 5NT Pre-Translocated Complex, PDB code: 8re4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 5NT Pre-Translocated Complex


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 Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 5NT Pre-Translocated Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1502 b:80.8 occ:1.00 SG D:CYS88 2.3 51.4 1.0 O D:LEU71 2.6 52.7 1.0 SG D:CYS72 2.7 47.2 1.0 CB D:CYS85 3.0 43.2 1.0 SG D:CYS70 3.0 58.7 1.0 C D:LEU71 3.6 52.5 1.0 CB D:CYS88 3.9 50.0 1.0 N D:CYS88 3.9 51.5 1.0 O D:CYS88 4.0 58.7 1.0 CB D:LYS74 4.0 56.6 1.0 CB D:CYS72 4.3 47.9 1.0 CA D:CYS88 4.3 50.9 1.0 N D:LEU71 4.4 47.2 1.0 CB D:CYS70 4.5 46.5 1.0 CB D:LYS87 4.5 56.8 1.0 CA D:CYS85 4.5 49.3 1.0 N D:LYS74 4.5 55.0 1.0 CA D:LEU71 4.5 49.2 1.0 N D:CYS72 4.5 45.4 1.0 C D:CYS88 4.6 54.0 1.0 C D:LYS87 4.8 59.6 1.0 C D:CYS70 4.8 50.6 1.0 CA D:CYS72 4.8 46.7 1.0 N D:GLY73 4.8 53.0 1.0 CB D:LEU71 4.8 47.5 1.0 CA D:LYS74 4.9 55.3 1.0 N D:LYS87 4.9 59.1 1.0 C D:CYS72 4.9 50.7 1.0 CA D:LYS87 5.0 61.4 1.0 C D:CYS85 5.0 52.1 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 5NT Pre-Translocated Complex


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 Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 5NT Pre-Translocated Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1503 b:77.1 occ:1.00 SG D:CYS898 2.3 44.8 1.0 CB D:CYS898 2.8 34.4 1.0 CB D:CYS895 2.9 23.6 1.0 O D:CYS888 3.2 51.4 1.0 CB D:CYS814 3.5 46.2 1.0 CA D:CYS888 3.5 42.3 1.0 N D:CYS898 3.8 34.3 1.0 NH2 D:ARG883 3.8 33.1 1.0 C D:CYS888 3.8 48.1 1.0 CB D:CYS888 3.9 38.7 1.0 CA D:CYS898 3.9 29.4 1.0 N D:CYS895 4.0 31.4 1.0 CA D:CYS895 4.1 24.0 1.0 N D:CYS814 4.2 52.5 1.0 CG2 D:THR816 4.4 42.2 1.0 CA D:CYS814 4.5 46.4 1.0 CG2 D:THR890 4.6 42.3 1.0 SG D:CYS814 4.7 70.9 1.0 CZ D:ARG883 4.7 34.6 1.0 C D:CYS895 4.7 29.3 1.0 NE D:ARG883 4.7 39.2 1.0 N D:CYS888 4.8 40.7 1.0 C D:HIS897 4.9 32.2 1.0 O D:CYS895 4.9 39.4 1.0

F.Gao, F.Ye, B.Zhang, N.Cronin, M.Buck, X.Zhang. Structural Basis of Sigma 54 Displacement and Promoter Escape in Bacterial Transcription. Proc.Natl.Acad.Sci.Usa V. 121 70120 2024.
ISSN: ESSN 1091-6490
PubMed: 38170755
DOI: 10.1073/PNAS.2309670120