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Zinc in PDB 6n58: Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II

Enzymatic activity of Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II

All present enzymatic activity of Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II:
2.7.7.6;

Other elements in 6n58:

The structure of Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II (pdb code 6n58). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II, PDB code: 6n58:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6n58

Go back to Zinc Binding Sites List in 6n58
Zinc binding site 1 out of 3 in the Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II


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 Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1502

b:74.4
occ:1.00
SG J:CYS85 2.4 45.5 1.0
SG J:CYS70 2.4 42.5 1.0
SG J:CYS72 2.4 40.4 1.0
SG J:CYS88 2.7 44.2 1.0
N J:CYS88 3.0 44.2 1.0
CB J:CYS85 3.0 45.5 1.0
CB J:LYS87 3.3 50.1 1.0
CB J:CYS72 3.5 40.4 1.0
CB J:CYS88 3.6 44.2 1.0
C J:LYS87 3.7 50.1 1.0
CA J:CYS88 3.7 44.2 1.0
CA J:LYS87 3.8 50.1 1.0
N J:CYS72 3.9 40.4 1.0
N J:LYS87 4.0 50.1 1.0
CB J:CYS70 4.1 42.5 1.0
CG J:LYS87 4.1 50.1 1.0
C J:CYS88 4.3 44.2 1.0
CA J:CYS72 4.4 40.4 1.0
CD J:LYS87 4.4 50.1 1.0
CA J:CYS85 4.5 45.5 1.0
N J:GLY89 4.5 42.6 1.0
N J:LEU71 4.7 37.0 1.0
O J:LYS87 4.8 50.1 1.0
C J:CYS85 4.8 45.5 1.0
O J:CYS88 5.0 44.2 1.0

Zinc binding site 2 out of 3 in 6n58

Go back to Zinc Binding Sites List in 6n58
Zinc binding site 2 out of 3 in the Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II


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 Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1503

b:42.1
occ:1.00
SG J:CYS888 2.3 36.0 1.0
SG J:CYS895 2.3 21.1 1.0
SG J:CYS814 2.4 30.8 1.0
SG J:CYS898 2.4 20.1 1.0
CB J:CYS888 2.7 36.0 1.0
CB J:CYS898 3.0 20.1 1.0
CA J:CYS888 3.0 36.0 1.0
CB J:CYS895 3.4 21.1 1.0
CB J:CYS814 3.4 30.8 1.0
NH2 J:ARG883 3.4 25.7 1.0
N J:ASP889 3.6 36.0 1.0
C J:CYS888 3.8 36.0 1.0
N J:CYS888 4.2 36.0 1.0
CA J:CYS898 4.3 20.1 1.0
N J:CYS895 4.3 21.1 1.0
CA J:CYS895 4.4 21.1 1.0
N J:CYS898 4.4 20.1 1.0
CZ J:ARG883 4.4 25.7 1.0
CA J:CYS814 4.6 30.8 1.0
NE J:ARG883 4.6 25.7 1.0
N J:CYS814 4.6 30.8 1.0
OG1 J:THR816 4.7 40.0 1.0
OG1 J:THR890 4.8 30.7 1.0
O J:SER884 4.9 19.0 1.0
C J:CYS895 4.9 21.1 1.0
CA J:ASP889 4.9 36.0 1.0
O J:CYS895 4.9 21.1 1.0
O J:SER887 5.0 25.9 1.0
N J:THR890 5.0 30.7 1.0

Zinc binding site 3 out of 3 in 6n58

Go back to Zinc Binding Sites List in 6n58
Zinc binding site 3 out of 3 in the Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation II within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn101

b:0.8
occ:1.00
SG M:CYS40 2.3 49.3 1.0
SG M:CYS58 2.4 45.3 1.0
SG M:CYS37 2.4 48.5 1.0
SG M:CYS61 2.4 42.9 1.0
CB M:CYS37 2.8 48.5 1.0
CB M:CYS61 3.0 42.9 1.0
CB M:CYS58 3.1 45.3 1.0
N M:CYS58 3.3 45.3 1.0
CB M:CYS40 3.3 49.3 1.0
N M:CYS40 3.7 49.3 1.0
CA M:CYS58 3.8 45.3 1.0
CA M:CYS40 4.1 49.3 1.0
CA M:CYS37 4.2 48.5 1.0
CA M:CYS61 4.2 42.9 1.0
N M:CYS61 4.2 42.9 1.0
C M:LEU57 4.4 41.7 1.0
C M:CYS58 4.5 45.3 1.0
N M:GLY41 4.6 48.1 1.0
CA M:LEU57 4.7 41.7 1.0
O M:CYS58 4.7 45.3 1.0
C M:CYS40 4.8 49.3 1.0
C M:ALA39 4.9 48.4 1.0
N M:ALA39 4.9 48.4 1.0

Reference:

J.Chen, S.Gopalkrishnan, C.Chiu, A.Y.Chen, E.A.Campbell, R.L.Gourse, W.Ross, S.A.Darst. E. Colitrar Allosterically Regulates Transcription Initiation By Altering Rna Polymerase Conformation. Elife V. 8 2019.
ISSN: ESSN 2050-084X
PubMed: 31841111
DOI: 10.7554/ELIFE.49375
Page generated: Wed Dec 16 12:21:11 2020

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