Zinc in PDB 6pb5: The E. Coli Class-II Cap-Dependent Transcription Activation Complex at the State 1 Architecture

Enzymatic activity of The E. Coli Class-II Cap-Dependent Transcription Activation Complex at the State 1 Architecture

All present enzymatic activity of The E. Coli Class-II Cap-Dependent Transcription Activation Complex at the State 1 Architecture:
2.7.7.6;

Other elements in 6pb5:

The structure of The E. Coli Class-II Cap-Dependent Transcription Activation Complex at the State 1 Architecture also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the The E. Coli Class-II Cap-Dependent Transcription Activation Complex at the State 1 Architecture (pdb code 6pb5). 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 at the State 1 Architecture, PDB code: 6pb5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6pb5

Go back to Zinc Binding Sites List in 6pb5
Zinc binding site 1 out of 2 in the The E. Coli Class-II Cap-Dependent Transcription Activation Complex at the State 1 Architecture


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 at the State 1 Architecture 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 2.0 20.0 1.0
HB2 D:CYS70 2.0 20.0 1.0
HG D:CYS88 2.1 20.0 1.0
SG D:CYS72 2.3 20.0 1.0
H D:GLY73 2.4 20.0 1.0
N D:CYS72 2.5 20.0 1.0
SG D:CYS70 2.5 20.0 1.0
CB D:CYS70 2.6 20.0 1.0
SG D:CYS88 3.0 20.0 1.0
N D:LEU71 3.0 20.0 1.0
H D:LEU71 3.0 20.0 1.0
SG D:CYS85 3.0 20.0 1.0
C D:CYS70 3.0 20.0 1.0
CB D:CYS72 3.1 20.0 1.0
N D:GLY73 3.1 20.0 1.0
H D:LYS74 3.1 20.0 1.0
CA D:CYS72 3.1 20.0 1.0
HB3 D:CYS72 3.2 20.0 1.0
CA D:CYS70 3.4 20.0 1.0
HB3 D:CYS70 3.4 20.0 1.0
HB3 D:CYS85 3.4 20.0 1.0
C D:LEU71 3.5 20.0 1.0
O D:CYS70 3.5 20.0 1.0
C D:CYS72 3.5 20.0 1.0
CB D:CYS85 3.6 20.0 1.0
HB2 D:CYS85 3.7 20.0 1.0
CA D:LEU71 3.7 20.0 1.0
HB2 D:LEU71 3.9 20.0 1.0
N D:LYS74 3.9 20.0 1.0
HB2 D:CYS72 4.0 20.0 1.0
HA D:CYS70 4.0 20.0 1.0
HB3 D:LYS87 4.0 20.0 1.0
HA D:CYS72 4.0 20.0 1.0
HB2 D:LYS74 4.2 20.0 1.0
HB3 D:LYS74 4.2 20.0 1.0
CA D:GLY73 4.2 20.0 1.0
H D:CYS70 4.2 20.0 1.0
H D:CYS88 4.3 20.0 1.0
N D:CYS70 4.4 20.0 1.0
HA2 D:GLY73 4.4 20.0 1.0
CB D:LEU71 4.4 20.0 1.0
HZ3 D:LYS74 4.4 20.0 1.0
HB3 D:CYS88 4.4 20.0 1.0
CB D:CYS88 4.5 20.0 1.0
HB D:VAL90 4.5 20.0 1.0
HD3 D:LYS87 4.5 20.0 1.0
HA D:LEU71 4.6 20.0 1.0
CB D:LYS74 4.6 20.0 1.0
O D:LEU71 4.6 20.0 1.0
C D:GLY73 4.6 20.0 1.0
H D:TYR75 4.7 20.0 1.0
O D:CYS72 4.7 20.0 1.0
CA D:LYS74 4.9 20.0 1.0
HZ2 D:LYS74 4.9 20.0 1.0
N D:CYS88 4.9 20.0 1.0
CB D:LYS87 4.9 20.0 1.0

Zinc binding site 2 out of 2 in 6pb5

Go back to Zinc Binding Sites List in 6pb5
Zinc binding site 2 out of 2 in the The E. Coli Class-II Cap-Dependent Transcription Activation Complex at the State 1 Architecture


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 at the State 1 Architecture within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:20.0
occ:1.00
 HG D:CYS814 1.8 20.0 1.0
HB2 D:CYS888 1.9 20.0 1.0
SG D:CYS898 2.3 20.0 1.0
CB D:CYS888 2.3 20.0 1.0
SG D:CYS888 2.3 20.0 1.0
SG D:CYS895 2.4 20.0 1.0
HA D:CYS888 2.4 20.0 1.0
HB2 D:CYS898 2.7 20.0 1.0
CA D:CYS888 2.8 20.0 1.0
SG D:CYS814 2.9 20.0 1.0
HH22 D:ARG883 2.9 20.0 1.0
CB D:CYS898 3.0 20.0 1.0
H D:CYS895 3.1 20.0 1.0
HB3 D:CYS888 3.2 20.0 1.0
HB3 D:CYS895 3.3 20.0 1.0
HH12 D:ARG883 3.4 20.0 1.0
CB D:CYS895 3.4 20.0 1.0
NH2 D:ARG883 3.5 20.0 1.0
HB3 D:CYS898 3.5 20.0 1.0
HB3 D:CYS814 3.5 20.0 1.0
N D:CYS888 3.7 20.0 1.0
N D:CYS895 3.8 20.0 1.0
H D:CYS888 3.8 20.0 1.0
H D:CYS814 3.8 20.0 1.0
CB D:CYS814 3.9 20.0 1.0
H D:CYS898 3.9 20.0 1.0
O D:SER884 3.9 20.0 1.0
NH1 D:ARG883 3.9 20.0 1.0
HH21 D:ARG883 4.0 20.0 1.0
HG1 D:THR816 4.0 20.0 1.0
C D:CYS888 4.0 20.0 1.0
H D:ASP889 4.0 20.0 1.0
CZ D:ARG883 4.1 20.0 1.0
CA D:CYS895 4.1 20.0 1.0
OG1 D:THR816 4.1 20.0 1.0
HA D:VAL885 4.2 20.0 1.0
HB2 D:CYS895 4.2 20.0 1.0
O D:CYS895 4.3 20.0 1.0
CA D:CYS898 4.3 20.0 1.0
HB D:VAL894 4.3 20.0 1.0
N D:ASP889 4.4 20.0 1.0
N D:CYS898 4.4 20.0 1.0
HB3 D:ARG883 4.4 20.0 1.0
HB2 D:CYS814 4.4 20.0 1.0
C D:CYS895 4.5 20.0 1.0
HH11 D:ARG883 4.6 20.0 1.0
N D:CYS814 4.6 20.0 1.0
C D:SER887 4.6 20.0 1.0
HA D:CYS898 4.6 20.0 1.0
H D:THR890 4.7 20.0 1.0
HG D:SER887 4.7 20.0 1.0
O D:SER887 4.8 20.0 1.0
OD1 D:ASP813 4.8 20.0 1.0
C D:SER884 4.8 20.0 1.0
HA D:VAL894 4.8 20.0 1.0
HG1 D:THR890 4.8 20.0 1.0
C D:VAL894 4.9 20.0 1.0
CA D:CYS814 4.9 20.0 1.0
HB2 D:ARG883 4.9 20.0 1.0
HA D:CYS895 5.0 20.0 1.0
HG21 D:THR816 5.0 20.0 1.0
O D:CYS888 5.0 20.0 1.0

Reference:

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
Page generated: Wed Dec 16 12:29:31 2020

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