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Antimony in PDB 6xlj: Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT)

Enzymatic activity of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT)

All present enzymatic activity of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT):
2.7.7.6;

Other elements in 6xlj:

The structure of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Magnesium (Mg) 2 atoms

Antimony Binding Sites:

The binding sites of Antimony atom in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT) (pdb code 6xlj). This binding sites where shown within 5.0 Angstroms radius around Antimony atom.
In total 3 binding sites of Antimony where determined in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT), PDB code: 6xlj:
Jump to Antimony binding site number: 1; 2; 3;

Antimony binding site 1 out of 3 in 6xlj

Go back to Antimony Binding Sites List in 6xlj
Antimony binding site 1 out of 3 in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT)


Mono view


Stereo pair view

A full contact list of Antimony with other atoms in the Sb binding site number 1 of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Sb1402

b:99.2
occ:1.00
SB C:1181402 0.0 99.2 1.0
C1C C:1181402 2.1 99.2 1.0
C1A C:1181402 2.1 99.2 1.0
C1D C:1181402 2.1 99.2 1.0
C1B C:1181402 2.1 99.2 1.0
C2B C:1181402 3.0 99.2 1.0
C2D C:1181402 3.0 99.2 1.0
C2C C:1181402 3.0 99.2 1.0
C6C C:1181402 3.0 99.2 1.0
C2A C:1181402 3.0 99.2 1.0
C6A C:1181402 3.1 99.2 1.0
C6D C:1181402 3.1 99.2 1.0
C6B C:1181402 3.1 99.2 1.0
O C:GLU541 3.5 88.5 1.0
C3B C:1181402 4.3 99.2 1.0
C3C C:1181402 4.3 99.2 1.0
C3A C:1181402 4.3 99.2 1.0
C5C C:1181402 4.3 99.2 1.0
C3D C:1181402 4.4 99.2 1.0
C5A C:1181402 4.4 99.2 1.0
C5D C:1181402 4.4 99.2 1.0
C5B C:1181402 4.4 99.2 1.0
C C:GLU541 4.5 88.5 1.0
C2' T:DG11 4.8 85.7 1.0
CA C:GLU541 4.8 88.5 1.0
C4C C:1181402 4.9 99.2 1.0
C4A C:1181402 4.9 99.2 1.0
C4B C:1181402 4.9 99.2 1.0
C4D C:1181402 4.9 99.2 1.0
N3 T:DG11 4.9 85.7 1.0
CB C:GLU541 5.0 88.5 1.0

Antimony binding site 2 out of 3 in 6xlj

Go back to Antimony Binding Sites List in 6xlj
Antimony binding site 2 out of 3 in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT)


Mono view


Stereo pair view

A full contact list of Antimony with other atoms in the Sb binding site number 2 of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Sb302

b:219.3
occ:1.00
SB G:118302 0.0 219.3 1.0
C1B G:118302 2.1 219.3 1.0
C1D G:118302 2.1 219.3 1.0
C1A G:118302 2.1 219.3 1.0
C1C G:118302 2.1 219.3 1.0
C2B G:118302 3.0 219.3 1.0
C2D G:118302 3.0 219.3 1.0
C2A G:118302 3.1 219.3 1.0
C6A G:118302 3.1 219.3 1.0
C2C G:118302 3.1 219.3 1.0
C6C G:118302 3.1 219.3 1.0
C6D G:118302 3.1 219.3 1.0
C6B G:118302 3.1 219.3 1.0
CE3 G:TRP250 4.0 213.2 1.0
C3B G:118302 4.3 219.3 1.0
CD2 G:TRP250 4.3 213.2 1.0
C3D G:118302 4.4 219.3 1.0
C3A G:118302 4.4 219.3 1.0
C5A G:118302 4.4 219.3 1.0
C3C G:118302 4.4 219.3 1.0
C5D G:118302 4.4 219.3 1.0
C5C G:118302 4.4 219.3 1.0
C5B G:118302 4.4 219.3 1.0
CZ3 G:TRP250 4.6 213.2 1.0
CG G:TRP250 4.6 213.2 1.0
CB G:TRP250 4.6 213.2 1.0
C4B G:118302 4.9 219.3 1.0
C4D G:118302 4.9 219.3 1.0
C4A G:118302 4.9 219.3 1.0
C4C G:118302 4.9 219.3 1.0

Antimony binding site 3 out of 3 in 6xlj

Go back to Antimony Binding Sites List in 6xlj
Antimony binding site 3 out of 3 in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT)


Mono view


Stereo pair view

A full contact list of Antimony with other atoms in the Sb binding site number 3 of Cryo-Em Structure of Ecmrr-Rnap-Promoter Initial Transcribing Complex with 4-Nt Rna Transcript (Ecmrr-Rpitc-4NT) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Sb302

b:205.8
occ:1.00
SB H:118302 0.0 205.8 1.0
C1B H:118302 2.1 205.8 1.0
C1C H:118302 2.1 205.8 1.0
C1D H:118302 2.1 205.8 1.0
C1A H:118302 2.1 205.8 1.0
C2B H:118302 3.0 205.8 1.0
C2C H:118302 3.1 205.8 1.0
C2D H:118302 3.1 205.8 1.0
C2A H:118302 3.1 205.8 1.0
C6D H:118302 3.1 205.8 1.0
C6C H:118302 3.1 205.8 1.0
C6A H:118302 3.1 205.8 1.0
C6B H:118302 3.1 205.8 1.0
C3B H:118302 4.3 205.8 1.0
C3D H:118302 4.4 205.8 1.0
C3C H:118302 4.4 205.8 1.0
C3A H:118302 4.4 205.8 1.0
C5D H:118302 4.4 205.8 1.0
C5A H:118302 4.4 205.8 1.0
C5C H:118302 4.4 205.8 1.0
C5B H:118302 4.4 205.8 1.0
CD2 H:TRP250 4.6 198.7 1.0
CG H:TRP250 4.6 198.7 1.0
CD1 H:TRP250 4.8 198.7 1.0
CE2 H:TRP250 4.8 198.7 1.0
C4B H:118302 4.9 205.8 1.0
C4D H:118302 4.9 205.8 1.0
NE1 H:TRP250 4.9 198.7 1.0
C4C H:118302 4.9 205.8 1.0
C4A H:118302 4.9 205.8 1.0
CE3 H:TRP250 5.0 198.7 1.0
CB H:TRP250 5.0 198.7 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 17:14:17 2021

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