Zinc in PDB 6xl9: Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT)

Enzymatic activity of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT)

All present enzymatic activity of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT):
2.7.7.6;

Other elements in 6xl9:

The structure of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT) also contains other interesting chemical elements:

Antimony (Sb) 3 atoms
Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT) (pdb code 6xl9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT), PDB code: 6xl9:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6xl9

Go back to Zinc Binding Sites List in 6xl9
Zinc binding site 1 out of 2 in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT)


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 Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1501

b:142.6
occ:1.00
SG D:CYS85 2.2 108.2 1.0
SG D:CYS72 2.2 105.7 1.0
SG D:CYS70 2.3 102.3 1.0
SG D:CYS88 2.3 106.0 1.0
CB D:CYS70 2.9 102.3 1.0
CB D:CYS85 3.0 108.2 1.0
CB D:CYS72 3.9 105.7 1.0
CB D:CYS88 4.0 106.0 1.0
N D:CYS72 4.1 105.7 1.0
CB D:LYS74 4.2 108.7 1.0
N D:CYS88 4.3 106.0 1.0
CA D:CYS70 4.3 102.3 1.0
N D:LEU71 4.4 98.7 1.0
CA D:CYS85 4.4 108.2 1.0
N D:LYS74 4.5 108.7 1.0
CA D:CYS72 4.5 105.7 1.0
C D:CYS70 4.6 102.3 1.0
CB D:LYS87 4.7 113.1 1.0
CA D:CYS88 4.7 106.0 1.0
N D:GLY73 4.7 107.3 1.0
CA D:LYS74 4.9 108.7 1.0
N D:TYR75 4.9 106.2 1.0

Zinc binding site 2 out of 2 in 6xl9

Go back to Zinc Binding Sites List in 6xl9
Zinc binding site 2 out of 2 in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT)


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 Ecmrr-Rnap-Promoter Initial Transcribing Complex with 3-Nt Rna Transcript (Ecmrr-Rpitc-3NT) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:107.0
occ:1.00
SG D:CYS814 2.1 91.2 1.0
SG D:CYS888 2.2 80.1 1.0
SG D:CYS898 2.2 76.0 1.0
SG D:CYS895 2.3 78.8 1.0
CB D:CYS814 3.2 91.2 1.0
CB D:CYS898 3.4 76.0 1.0
CB D:CYS888 3.4 80.1 1.0
CB D:CYS895 3.6 78.8 1.0
CA D:CYS888 3.8 80.1 1.0
N D:ASP889 4.1 87.9 1.0
N D:CYS814 4.1 91.2 1.0
N D:CYS895 4.2 78.8 1.0
CA D:CYS814 4.3 91.2 1.0
NH2 D:ARG883 4.4 82.8 1.0
CA D:CYS895 4.4 78.8 1.0
C D:CYS888 4.5 80.1 1.0
N D:CYS898 4.5 76.0 1.0
CA D:CYS898 4.5 76.0 1.0
OG1 D:THR890 4.8 84.1 1.0
OG1 D:THR816 4.9 93.7 1.0
N D:THR890 4.9 84.1 1.0

Reference:

Y.Yang, C.Liu, W.Shi, D.G.Schatz, Y.Hu, B.Liu. Structural Visualization of Bacterial Multidrug-Activated Transcription To Be Published.
Page generated: Sat Apr 17 17:43:57 2021

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