Zinc in PDB 8ree: Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 9NT Complex

All present enzymatic activity of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 9NT Complex:
2.7.7.6;

The structure of Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 9NT 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 - 9NT Complex (pdb code 8ree). 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 - 9NT Complex, PDB code: 8ree:
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 - 9NT 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 - 9NT Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1502 b:74.8 occ:1.00 O D:LEU71 2.1 41.6 1.0 SG D:CYS88 2.3 48.0 1.0 SG D:CYS70 2.3 46.9 1.0 CB D:CYS85 3.2 47.8 1.0 C D:LEU71 3.3 41.6 1.0 CB D:CYS70 3.6 46.9 1.0 N D:LEU71 3.6 41.6 1.0 CB D:LYS74 3.8 49.1 1.0 CA D:LEU71 3.9 41.6 1.0 C D:CYS70 4.0 46.9 1.0 CB D:CYS88 4.1 48.0 1.0 N D:LYS74 4.2 49.1 1.0 CG1 D:VAL90 4.2 44.5 1.0 N D:CYS72 4.3 48.9 1.0 CB D:CYS72 4.4 48.9 1.0 CA D:CYS70 4.4 46.9 1.0 CB D:LEU71 4.5 41.6 1.0 O D:CYS70 4.5 46.9 1.0 O D:CYS88 4.5 48.0 1.0 CA D:LYS74 4.6 49.1 1.0 SG D:CYS72 4.6 48.9 1.0 N D:TYR75 4.6 53.5 1.0 N D:GLY73 4.7 47.4 1.0 CA D:CYS85 4.7 47.8 1.0 N D:CYS88 4.7 48.0 1.0 CA D:CYS72 4.8 48.9 1.0 CD1 D:TYR75 4.8 53.5 1.0 CA D:CYS88 4.9 48.0 1.0 C D:CYS72 4.9 48.9 1.0

Zinc binding site 2 out of 2 in the Cryo-Em Structure of Bacterial Rna Polymerase-SIGMA54 Initial Transcribing Complex - 9NT 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 - 9NT Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1503 b:50.2 occ:1.00 SG D:CYS898 2.3 25.7 1.0 O D:CYS888 2.5 23.7 1.0 CB D:CYS895 2.6 21.9 1.0 CA D:CYS888 2.7 23.7 1.0 CB D:CYS888 2.8 23.7 1.0 C D:CYS888 3.0 23.7 1.0 CB D:CYS898 3.0 25.7 1.0 N D:CYS895 3.2 21.9 1.0 CA D:CYS895 3.5 21.9 1.0 CB D:CYS814 3.8 32.1 1.0 N D:CYS888 4.2 23.7 1.0 N D:ASP889 4.3 30.1 1.0 CA D:CYS898 4.4 25.7 1.0 C D:CYS895 4.4 21.9 1.0 C D:VAL894 4.4 19.7 1.0 CG2 D:THR890 4.4 31.0 1.0 O D:CYS895 4.5 21.9 1.0 N D:CYS898 4.5 25.7 1.0 N D:THR890 4.6 31.0 1.0 N D:CYS814 4.6 32.1 1.0 CB D:THR890 4.6 31.0 1.0 O D:SER887 4.7 22.3 1.0 CA D:VAL894 4.8 19.7 1.0 C D:SER887 4.9 22.3 1.0 CA D:CYS814 4.9 32.1 1.0 SG D:CYS814 4.9 32.1 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