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Zinc in PDB 6n57: Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation I

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

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

Other elements in 6n57:

The structure of Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation I 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 I (pdb code 6n57). 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 I, PDB code: 6n57:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 6n57

Go back to Zinc Binding Sites List in 6n57
Zinc binding site 1 out of 3 in the Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1501

b:60.0
occ:1.00
CB J:CYS888 2.3 38.1 1.0
SG J:CYS888 2.3 38.1 1.0
SG J:CYS898 2.4 24.1 1.0
CB J:CYS898 2.6 24.1 1.0
SG J:CYS895 2.7 21.9 1.0
CA J:CYS888 2.8 38.1 1.0
SG J:CYS814 2.9 34.1 1.0
CB J:CYS814 3.6 34.1 1.0
N J:CYS888 3.8 38.1 1.0
C J:CYS888 3.9 38.1 1.0
CB J:CYS895 3.9 21.9 1.0
CA J:CYS898 4.0 24.1 1.0
N J:ASP889 4.1 38.7 1.0
NH2 J:ARG883 4.3 27.9 1.0
N J:CYS895 4.3 21.9 1.0
N J:CYS898 4.4 24.1 1.0
C J:SER887 4.6 31.6 1.0
CA J:CYS895 4.7 21.9 1.0
O J:SER887 4.7 31.6 1.0
O J:SER884 4.7 21.3 1.0
C J:CYS898 4.9 24.1 1.0
OG1 J:THR816 4.9 38.0 1.0
CA J:CYS814 4.9 34.1 1.0
O J:CYS888 5.0 38.1 1.0

Zinc binding site 2 out of 3 in 6n57

Go back to Zinc Binding Sites List in 6n57
Zinc binding site 2 out of 3 in the Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1503

b:99.0
occ:1.00
SG J:CYS85 2.3 68.1 1.0
SG J:CYS88 2.4 59.0 1.0
SG J:CYS70 2.4 46.9 1.0
SG J:CYS72 2.4 47.0 1.0
CB J:CYS85 2.9 68.1 1.0
N J:CYS88 3.3 59.0 1.0
CB J:CYS88 3.6 59.0 1.0
CB J:CYS72 3.8 47.0 1.0
CA J:CYS88 3.9 59.0 1.0
CB J:LYS87 3.9 65.2 1.0
N J:CYS72 3.9 47.0 1.0
C J:LYS87 4.1 65.2 1.0
CB J:CYS70 4.1 46.9 1.0
CA J:CYS85 4.3 68.1 1.0
N J:LYS87 4.3 65.2 1.0
CA J:LYS87 4.3 65.2 1.0
C J:CYS88 4.4 59.0 1.0
CA J:CYS72 4.4 47.0 1.0
C J:CYS85 4.5 68.1 1.0
N J:LEU71 4.5 37.4 1.0
O J:CYS85 4.6 68.1 1.0
N J:GLY89 4.6 58.0 1.0
N J:GLY73 4.7 48.3 1.0
CG J:LYS87 4.8 65.2 1.0
CB J:LYS74 4.9 56.9 1.0
N J:LYS74 4.9 56.9 1.0
CD J:LYS87 4.9 65.2 1.0
C J:CYS72 4.9 47.0 1.0
O J:CYS88 5.0 59.0 1.0
C J:LEU71 5.0 37.4 1.0

Zinc binding site 3 out of 3 in 6n57

Go back to Zinc Binding Sites List in 6n57
Zinc binding site 3 out of 3 in the Cryo-Em Structure of Escherichia Coli Rnap Polymerase Bound with Trar in Conformation I


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 I within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn101

b:0.5
occ:1.00
CB M:CYS37 2.4 66.5 1.0
SG M:CYS58 2.4 49.4 1.0
SG M:CYS37 2.4 66.5 1.0
CB M:CYS58 2.5 49.4 1.0
SG M:CYS40 2.8 64.0 1.0
N M:CYS58 3.4 49.4 1.0
SG M:CYS61 3.5 48.5 1.0
CA M:CYS58 3.6 49.4 1.0
CA M:CYS37 3.6 66.5 1.0
CB M:ASN42 4.1 68.4 1.0
CB M:CYS61 4.1 48.5 1.0
N M:CYS37 4.4 66.5 1.0
CB M:CYS40 4.4 64.0 1.0
ND2 M:ASN42 4.4 68.4 1.0
N M:ASN42 4.5 68.4 1.0
C M:LEU57 4.6 51.3 1.0
O M:ASN42 4.6 68.4 1.0
N M:CYS40 4.6 64.0 1.0
C M:CYS58 4.7 49.4 1.0
N M:CYS61 4.7 48.5 1.0
CA M:ASN42 4.7 68.4 1.0
C M:CYS37 4.7 66.5 1.0
CG M:ASN42 4.8 68.4 1.0
C M:ASN42 4.9 68.4 1.0
CA M:CYS40 5.0 64.0 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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