Zinc in PDB 6xl5: Cryo-Em Structure of Ecmrr-Rnap-Promoter Open Complex (Ecmrr-Rpo)

Enzymatic activity of Cryo-Em Structure of Ecmrr-Rnap-Promoter Open Complex (Ecmrr-Rpo)

All present enzymatic activity of Cryo-Em Structure of Ecmrr-Rnap-Promoter Open Complex (Ecmrr-Rpo):
2.7.7.6;

Other elements in 6xl5:

The structure of Cryo-Em Structure of Ecmrr-Rnap-Promoter Open Complex (Ecmrr-Rpo) also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Antimony (Sb) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Open Complex (Ecmrr-Rpo) (pdb code 6xl5). 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 Open Complex (Ecmrr-Rpo), PDB code: 6xl5:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6xl5

Go back to Zinc Binding Sites List in 6xl5
Zinc binding site 1 out of 2 in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Open Complex (Ecmrr-Rpo)


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 Open Complex (Ecmrr-Rpo) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:78.6
occ:1.00
SG D:CYS72 2.2 62.4 1.0
SG D:CYS85 2.2 61.2 1.0
SG D:CYS70 2.3 60.2 1.0
SG D:CYS88 2.3 58.8 1.0
CB D:CYS85 2.5 61.2 1.0
CB D:CYS70 2.7 60.2 1.0
CB D:CYS88 3.8 58.8 1.0
CB D:CYS72 3.9 62.4 1.0
N D:CYS72 3.9 62.4 1.0
CA D:CYS85 4.0 61.2 1.0
CA D:CYS70 4.1 60.2 1.0
CD2 D:TYR75 4.1 64.5 1.0
N D:CYS88 4.2 58.8 1.0
N D:LEU71 4.2 55.6 1.0
CB D:LYS74 4.3 65.7 1.0
N D:LYS74 4.4 65.7 1.0
CA D:CYS72 4.4 62.4 1.0
C D:CYS70 4.5 60.2 1.0
CA D:CYS88 4.6 58.8 1.0
N D:GLY73 4.6 64.9 1.0
CE2 D:TYR75 4.6 64.5 1.0
N D:TYR75 4.7 64.5 1.0
C D:CYS85 4.8 61.2 1.0
N D:CYS85 4.8 61.2 1.0
C D:CYS72 4.8 62.4 1.0
CA D:LYS74 4.9 65.7 1.0
O D:VAL90 4.9 52.3 1.0
C D:LEU71 5.0 55.6 1.0

Zinc binding site 2 out of 2 in 6xl5

Go back to Zinc Binding Sites List in 6xl5
Zinc binding site 2 out of 2 in the Cryo-Em Structure of Ecmrr-Rnap-Promoter Open Complex (Ecmrr-Rpo)


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 Open Complex (Ecmrr-Rpo) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1503

b:65.0
occ:1.00
SG D:CYS895 2.1 45.9 1.0
SG D:CYS814 2.2 51.7 1.0
SG D:CYS888 2.2 48.6 1.0
SG D:CYS898 2.2 45.5 1.0
CB D:CYS898 3.1 45.5 1.0
CB D:CYS814 3.3 51.7 1.0
CB D:CYS888 3.3 48.6 1.0
CB D:CYS895 3.3 45.9 1.0
CA D:CYS888 3.6 48.6 1.0
NH2 D:ARG883 3.8 50.6 1.0
N D:CYS895 4.0 45.9 1.0
N D:CYS814 4.0 51.7 1.0
N D:CYS898 4.1 45.5 1.0
CA D:CYS898 4.2 45.5 1.0
N D:ASP889 4.2 53.4 1.0
CA D:CYS895 4.2 45.9 1.0
CA D:CYS814 4.3 51.7 1.0
C D:CYS888 4.4 48.6 1.0
OG1 D:THR890 4.5 51.1 1.0
CG2 D:THR816 4.5 55.8 1.0
O D:CYS895 4.7 45.9 1.0
C D:CYS895 4.8 45.9 1.0
CZ D:ARG883 4.8 50.6 1.0
N D:CYS888 4.8 48.6 1.0
NE D:ARG883 4.9 50.6 1.0
N D:THR890 4.9 51.1 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 17:43:58 2021

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