Zinc in PDB 6pb4: The E. Coli Class-II Cap-Dependent Transcription Activation Complex with De Novo Rna Transcript at the State 2

All present enzymatic activity of The E. Coli Class-II Cap-Dependent Transcription Activation Complex with De Novo Rna Transcript at the State 2:
2.7.7.6;

The structure of The E. Coli Class-II Cap-Dependent Transcription Activation Complex with De Novo Rna Transcript at the State 2 also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Zinc atom in the The E. Coli Class-II Cap-Dependent Transcription Activation Complex with De Novo Rna Transcript at the State 2 (pdb code 6pb4). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the The E. Coli Class-II Cap-Dependent Transcription Activation Complex with De Novo Rna Transcript at the State 2, PDB code: 6pb4:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the The E. Coli Class-II Cap-Dependent Transcription Activation Complex with De Novo Rna Transcript at the State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The E. Coli Class-II Cap-Dependent Transcription Activation Complex with De Novo Rna Transcript at the State 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1501 b:20.0 occ:1.00 H D:CYS72 1.7 20.0 1.0 HG D:CYS85 1.8 20.0 1.0 N D:CYS72 2.3 20.0 1.0 HG D:CYS88 2.3 20.0 1.0 H D:GLY73 2.4 20.0 1.0 HB2 D:CYS70 2.5 20.0 1.0 SG D:CYS72 2.6 20.0 1.0 SG D:CYS70 2.7 20.0 1.0 H D:LYS74 2.7 20.0 1.0 N D:GLY73 2.9 20.0 1.0 N D:LEU71 2.9 20.0 1.0 H D:LEU71 2.9 20.0 1.0 CA D:CYS72 2.9 20.0 1.0 CB D:CYS70 3.0 20.0 1.0 SG D:CYS85 3.0 20.0 1.0 C D:CYS70 3.1 20.0 1.0 C D:CYS72 3.1 20.0 1.0 C D:LEU71 3.2 20.0 1.0 CB D:CYS72 3.2 20.0 1.0 SG D:CYS88 3.3 20.0 1.0 CA D:LEU71 3.5 20.0 1.0 O D:CYS70 3.5 20.0 1.0 HB3 D:CYS72 3.6 20.0 1.0 N D:LYS74 3.6 20.0 1.0 CA D:CYS70 3.6 20.0 1.0 HB3 D:CYS85 3.7 20.0 1.0 HB2 D:LEU71 3.7 20.0 1.0 CB D:CYS85 3.8 20.0 1.0 HB2 D:CYS85 3.8 20.0 1.0 HB3 D:CYS70 3.8 20.0 1.0 HA D:CYS72 3.9 20.0 1.0 HB2 D:LYS74 3.9 20.0 1.0 CA D:GLY73 4.0 20.0 1.0 HB3 D:LYS74 4.0 20.0 1.0 HB2 D:CYS72 4.1 20.0 1.0 O D:CYS72 4.2 20.0 1.0 HA2 D:GLY73 4.2 20.0 1.0 HA D:CYS70 4.2 20.0 1.0 O D:LEU71 4.2 20.0 1.0 CB D:LEU71 4.2 20.0 1.0 C D:GLY73 4.3 20.0 1.0 CB D:LYS74 4.3 20.0 1.0 HA D:LEU71 4.4 20.0 1.0 H D:TYR75 4.4 20.0 1.0 CA D:LYS74 4.6 20.0 1.0 HB D:VAL90 4.6 20.0 1.0 HB3 D:CYS88 4.7 20.0 1.0 HB3 D:LEU71 4.7 20.0 1.0 N D:CYS70 4.7 20.0 1.0 H D:CYS88 4.7 20.0 1.0 CB D:CYS88 4.7 20.0 1.0 HA3 D:GLY73 4.8 20.0 1.0 HZ3 D:LYS74 4.8 20.0 1.0 H D:CYS70 4.8 20.0 1.0 HB3 D:LYS87 4.9 20.0 1.0

Zinc binding site 2 out of 2 in the The E. Coli Class-II Cap-Dependent Transcription Activation Complex with De Novo Rna Transcript at the State 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The E. Coli Class-II Cap-Dependent Transcription Activation Complex with De Novo Rna Transcript at the State 2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1502 b:20.0 occ:1.00 HB2 D:CYS888 1.8 20.0 1.0 HB2 D:CYS898 2.4 20.0 1.0 CB D:CYS888 2.4 20.0 1.0 SG D:CYS814 2.4 20.0 1.0 SG D:CYS898 2.4 20.0 1.0 SG D:CYS895 2.4 20.0 1.0 HH22 D:ARG883 2.5 20.0 1.0 SG D:CYS888 2.6 20.0 1.0 HA D:CYS888 2.7 20.0 1.0 HG D:CYS888 2.7 20.0 1.0 CB D:CYS898 2.9 20.0 1.0 HH12 D:ARG883 2.9 20.0 1.0 CA D:CYS888 3.0 20.0 1.0 HG1 D:THR816 3.1 20.0 1.0 NH2 D:ARG883 3.2 20.0 1.0 HB3 D:CYS888 3.2 20.0 1.0 H D:CYS898 3.3 20.0 1.0 H D:CYS895 3.3 20.0 1.0 HB3 D:CYS898 3.5 20.0 1.0 HB3 D:CYS895 3.5 20.0 1.0 NH1 D:ARG883 3.5 20.0 1.0 CB D:CYS895 3.6 20.0 1.0 HB3 D:CYS814 3.6 20.0 1.0 CB D:CYS814 3.7 20.0 1.0 HH21 D:ARG883 3.8 20.0 1.0 CZ D:ARG883 3.8 20.0 1.0 H D:CYS888 3.8 20.0 1.0 OG1 D:THR816 3.8 20.0 1.0 N D:CYS888 3.8 20.0 1.0 N D:CYS898 3.9 20.0 1.0 H D:CYS814 4.0 20.0 1.0 CA D:CYS898 4.0 20.0 1.0 H D:ASP889 4.0 20.0 1.0 N D:CYS895 4.1 20.0 1.0 HB2 D:CYS814 4.2 20.0 1.0 HH11 D:ARG883 4.2 20.0 1.0 C D:CYS888 4.3 20.0 1.0 O D:SER884 4.3 20.0 1.0 CA D:CYS895 4.3 20.0 1.0 HB2 D:CYS895 4.4 20.0 1.0 HG21 D:THR816 4.4 20.0 1.0 O D:CYS895 4.4 20.0 1.0 HA D:CYS898 4.4 20.0 1.0 HB D:VAL894 4.4 20.0 1.0 N D:ASP889 4.5 20.0 1.0 HA D:VAL885 4.6 20.0 1.0 N D:CYS814 4.7 20.0 1.0 C D:CYS895 4.7 20.0 1.0 HB2 D:HIS897 4.7 20.0 1.0 HG1 D:THR890 4.8 20.0 1.0 HB3 D:ARG883 4.8 20.0 1.0 CA D:CYS814 4.8 20.0 1.0 HH12 D:ARG1258 4.8 20.0 1.0 HG23 D:THR816 4.9 20.0 1.0 H D:THR890 4.9 20.0 1.0 HG D:SER887 4.9 20.0 1.0 HA D:VAL894 4.9 20.0 1.0 C D:SER887 4.9 20.0 1.0 CG2 D:THR816 4.9 20.0 1.0 CB D:THR816 5.0 20.0 1.0

W.Shi, Y.Jiang, Y.Deng, Z.Dong, B.Liu. Visualization of Two Architectures in Class-II Cap-Dependent Transcription Activation Plos Biol. 2020.
ISSN: ESSN 1545-7885