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Zinc in PDB 6pmi: SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1

Enzymatic activity of SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1

All present enzymatic activity of SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1:
2.7.7.6;

Other elements in 6pmi:

The structure of SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1 also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1 (pdb code 6pmi). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1, PDB code: 6pmi:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6pmi

Go back to Zinc Binding Sites List in 6pmi
Zinc binding site 1 out of 2 in the SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1501

b:20.0
occ:1.00
H D:CYS72 1.8 20.0 1.0
HG D:CYS70 2.4 20.0 1.0
SG D:CYS88 2.4 20.0 1.0
SG D:CYS72 2.4 20.0 1.0
SG D:CYS85 2.5 20.0 1.0
SG D:CYS70 2.5 20.0 1.0
N D:CYS72 2.6 20.0 1.0
HB2 D:CYS70 2.8 20.0 1.0
HB3 D:CYS72 2.9 20.0 1.0
CB D:CYS72 3.0 20.0 1.0
HB3 D:CYS88 3.1 20.0 1.0
H D:GLY73 3.2 20.0 1.0
H D:LEU71 3.2 20.0 1.0
HB2 D:CYS85 3.2 20.0 1.0
CB D:CYS85 3.2 20.0 1.0
HB3 D:CYS85 3.2 20.0 1.0
CB D:CYS70 3.2 20.0 1.0
CA D:CYS72 3.3 20.0 1.0
H D:CYS88 3.3 20.0 1.0
CB D:CYS88 3.4 20.0 1.0
N D:LEU71 3.5 20.0 1.0
HB2 D:LEU71 3.6 20.0 1.0
H D:LYS74 3.6 20.0 1.0
C D:LEU71 3.7 20.0 1.0
N D:GLY73 3.7 20.0 1.0
HB3 D:LYS87 3.8 20.0 1.0
HB3 D:CYS70 3.9 20.0 1.0
HB2 D:CYS72 3.9 20.0 1.0
C D:CYS72 3.9 20.0 1.0
CA D:LEU71 4.0 20.0 1.0
HB2 D:CYS88 4.0 20.0 1.0
N D:CYS88 4.1 20.0 1.0
HA D:CYS72 4.1 20.0 1.0
C D:CYS70 4.2 20.0 1.0
CB D:LEU71 4.3 20.0 1.0
HB3 D:LYS74 4.3 20.0 1.0
CA D:CYS88 4.3 20.0 1.0
CA D:CYS70 4.3 20.0 1.0
N D:LYS74 4.5 20.0 1.0
HB2 D:LYS74 4.5 20.0 1.0
HD3 D:LYS87 4.5 20.0 1.0
HB D:VAL90 4.6 20.0 1.0
HG21 D:VAL90 4.7 20.0 1.0
CA D:CYS85 4.7 20.0 1.0
HB3 D:LEU71 4.7 20.0 1.0
CB D:LYS87 4.7 20.0 1.0
O D:LEU71 4.8 20.0 1.0
CB D:LYS74 4.8 20.0 1.0
HA D:CYS70 4.9 20.0 1.0
HA D:LEU71 4.9 20.0 1.0
HA D:CYS85 4.9 20.0 1.0
CA D:GLY73 4.9 20.0 1.0
H D:LYS87 5.0 20.0 1.0

Zinc binding site 2 out of 2 in 6pmi

Go back to Zinc Binding Sites List in 6pmi
Zinc binding site 2 out of 2 in the SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of SIGM28-Transcription Initiation Complex with Specific Promoter at the State 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:20.0
occ:1.00
HG D:CYS898 2.0 20.0 1.0
H D:CYS895 2.1 20.0 1.0
SG D:CYS895 2.2 20.0 1.0
HB3 D:CYS895 2.3 20.0 1.0
SG D:CYS888 2.3 20.0 1.0
SG D:CYS814 2.4 20.0 1.0
CB D:CYS895 2.6 20.0 1.0
N D:CYS895 2.8 20.0 1.0
HB2 D:CYS888 2.8 20.0 1.0
HH22 D:ARG883 2.8 20.0 1.0
HB2 D:CYS898 2.9 20.0 1.0
SG D:CYS898 3.0 20.0 1.0
CB D:CYS888 3.1 20.0 1.0
CA D:CYS895 3.1 20.0 1.0
HB3 D:CYS814 3.3 20.0 1.0
HB2 D:CYS895 3.5 20.0 1.0
CB D:CYS898 3.5 20.0 1.0
NH2 D:ARG883 3.5 20.0 1.0
CB D:CYS814 3.5 20.0 1.0
HG1 D:THR816 3.5 20.0 1.0
H D:CYS898 3.6 20.0 1.0
HH12 D:ARG883 3.7 20.0 1.0
H D:CYS814 3.7 20.0 1.0
O D:CYS895 3.7 20.0 1.0
C D:CYS895 3.8 20.0 1.0
HA D:CYS888 3.8 20.0 1.0
HB3 D:CYS888 3.8 20.0 1.0
HH21 D:ARG883 3.9 20.0 1.0
C D:VAL894 3.9 20.0 1.0
HB D:VAL894 4.0 20.0 1.0
HA D:CYS895 4.0 20.0 1.0
CA D:CYS888 4.0 20.0 1.0
HA D:VAL894 4.1 20.0 1.0
HB3 D:CYS898 4.1 20.0 1.0
HG1 D:THR890 4.1 20.0 1.0
OG1 D:THR816 4.1 20.0 1.0
HB2 D:CYS814 4.1 20.0 1.0
NH1 D:ARG883 4.2 20.0 1.0
CZ D:ARG883 4.3 20.0 1.0
N D:CYS814 4.4 20.0 1.0
N D:CYS898 4.4 20.0 1.0
OG1 D:THR890 4.4 20.0 1.0
CA D:VAL894 4.4 20.0 1.0
HG21 D:THR816 4.6 20.0 1.0
CA D:CYS898 4.6 20.0 1.0
CA D:CYS814 4.6 20.0 1.0
H D:ASP889 4.6 20.0 1.0
CB D:VAL894 4.7 20.0 1.0
H D:THR890 4.8 20.0 1.0
N D:ALA896 4.9 20.0 1.0
O D:VAL894 4.9 20.0 1.0
OD1 D:ASP813 4.9 20.0 1.0
C D:CYS888 4.9 20.0 1.0
HH11 D:ARG883 5.0 20.0 1.0

Reference:

W.Shi, W.Zhou, B.Zhang, S.Huang, Y.Jiang, A.Schammel, Y.Hu, B.Liu. Structural Basis of Bacterial SIGMA28-Mediated Transcription Reveals Roles of the Rna Polymerase Zinc-Binding Domain Embo J. 2020.
ISSN: ESSN 1460-2075
DOI: 10.15252/EMBJ.2020104389
Page generated: Tue Oct 29 05:12:11 2024

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