Zinc in PDB 4yln: E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna

Enzymatic activity of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna

All present enzymatic activity of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna:
2.7.7.6;

Protein crystallography data

The structure of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna, PDB code: 4yln was solved by Y.Zuo, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.90 / 5.50
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 237.401, 206.052, 248.690, 90.00, 116.55, 90.00
R / Rfree (%) 24.5 / 32.8

Other elements in 4yln:

The structure of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna (pdb code 4yln). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna, PDB code: 4yln:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 4yln

Go back to Zinc Binding Sites List in 4yln
Zinc binding site 1 out of 6 in the E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1501

b:0.3
occ:1.00
 SG D:CYS88 1.9 0.1 1.0
SG D:CYS72 2.0 0.2 1.0
SG D:CYS85 2.9 0.9 1.0
CB D:CYS72 3.1 0.5 1.0
N D:CYS72 3.1 0.7 1.0
SG D:CYS70 3.2 0.5 1.0
CB D:CYS88 3.2 0.9 1.0
CA D:CYS72 3.6 0.0 1.0
CB D:CYS85 3.7 0.7 1.0
CB D:CYS70 3.9 0.2 1.0
N D:LEU71 4.0 0.8 1.0
N D:GLY73 4.2 0.2 1.0
N D:CYS88 4.2 0.9 1.0
C D:LEU71 4.2 0.1 1.0
CA D:CYS88 4.3 0.5 1.0
C D:CYS72 4.3 0.6 1.0
CB D:LEU71 4.4 0.8 1.0
CA D:LEU71 4.4 0.1 1.0
C D:CYS70 4.6 0.1 1.0
CA D:CYS70 4.9 0.9 1.0
CG2 D:VAL90 4.9 0.6 1.0
CB D:VAL90 5.0 0.1 1.0

Zinc binding site 2 out of 6 in 4yln

Go back to Zinc Binding Sites List in 4yln
Zinc binding site 2 out of 6 in the E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:0.3
occ:1.00
 SG D:CYS895 1.5 0.8 1.0
SG D:CYS898 1.9 0.5 1.0
SG D:CYS814 2.5 0.0 1.0
NH2 D:ARG883 2.5 0.6 1.0
CB D:CYS895 2.8 0.6 1.0
SG D:CYS888 3.3 0.5 1.0
CZ D:ARG883 3.3 0.3 1.0
NE D:ARG883 3.4 0.1 1.0
CB D:CYS898 3.6 0.2 1.0
CB D:CYS888 4.0 0.1 1.0
CA D:CYS888 4.0 0.6 1.0
OG1 D:THR890 4.0 0.3 1.0
N D:ASP889 4.1 0.1 1.0
CA D:CYS895 4.1 0.9 1.0
N D:CYS814 4.1 0.1 1.0
OG1 D:THR816 4.1 0.5 1.0
N D:CYS895 4.2 0.3 1.0
CB D:CYS814 4.3 0.8 1.0
NH1 D:ARG883 4.5 0.5 1.0
N D:CYS898 4.6 0.7 1.0
OD1 D:ASP813 4.6 0.3 1.0
C D:CYS888 4.6 0.3 1.0
CA D:CYS898 4.7 0.4 1.0
CD D:ARG883 4.8 0.0 1.0
CA D:CYS814 4.8 0.7 1.0
N D:THR890 4.9 0.3 1.0
CB D:THR816 5.0 0.0 1.0

Zinc binding site 3 out of 6 in 4yln

Go back to Zinc Binding Sites List in 4yln
Zinc binding site 3 out of 6 in the E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1501

b:0.9
occ:1.00
 SG J:CYS85 2.3 0.7 1.0
SG J:CYS70 2.3 0.7 1.0
SG J:CYS72 2.4 0.1 1.0
SG J:CYS88 2.4 0.0 1.0
CB J:CYS85 3.1 0.1 1.0
CB J:CYS70 3.3 0.2 1.0
CB J:CYS72 3.8 0.2 1.0
N J:CYS72 4.0 0.2 1.0
N J:LYS74 4.1 0.0 1.0
CB J:CYS88 4.1 0.2 1.0
N J:CYS88 4.1 0.4 1.0
CB J:LYS74 4.2 0.5 1.0
CB J:LYS87 4.2 0.1 1.0
N J:GLY73 4.3 0.8 1.0
CA J:CYS72 4.3 0.8 1.0
N J:TYR75 4.5 0.2 1.0
CA J:CYS85 4.6 0.1 1.0
N J:LEU71 4.6 0.9 1.0
CA J:CYS70 4.6 0.1 1.0
CA J:LYS74 4.7 0.4 1.0
C J:CYS72 4.7 0.3 1.0
C J:CYS70 4.8 0.4 1.0
CA J:CYS88 4.8 0.2 1.0
CA J:LYS87 4.9 0.1 1.0
N J:LYS87 4.9 0.0 1.0
CG J:LYS87 4.9 0.8 1.0
C J:LYS87 5.0 0.6 1.0

Zinc binding site 4 out of 6 in 4yln

Go back to Zinc Binding Sites List in 4yln
Zinc binding site 4 out of 6 in the E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1502

b:0.0
occ:1.00
 SG J:CYS814 1.2 0.8 1.0
SG J:CYS888 2.4 0.8 1.0
SG J:CYS898 2.8 0.2 1.0
NH2 J:ARG883 2.8 0.6 1.0
CB J:CYS814 2.9 0.9 1.0
CB J:CYS895 2.9 0.4 1.0
OG1 J:THR890 2.9 0.0 1.0
SG J:CYS895 3.2 0.0 1.0
N J:CYS814 3.7 1.0 1.0
CB J:CYS888 3.7 0.1 1.0
N J:ASP889 3.8 0.6 1.0
CA J:CYS814 3.8 0.6 1.0
N J:THR890 4.0 0.5 1.0
CZ J:ARG883 4.0 0.1 1.0
CA J:CYS888 4.1 0.5 1.0
CB J:THR890 4.1 0.2 1.0
CA J:CYS895 4.2 0.1 1.0
NE J:ARG883 4.3 0.1 1.0
N J:CYS895 4.3 0.4 1.0
C J:CYS888 4.4 0.1 1.0
CB J:CYS898 4.5 1.0 1.0
CA J:THR890 4.6 0.7 1.0
C J:CYS814 4.7 0.6 1.0
CA J:ASP889 4.7 0.2 1.0
N J:GLY815 4.7 0.9 1.0
C J:ASP889 4.7 0.3 1.0
C J:ASP813 4.9 0.0 1.0

Zinc binding site 5 out of 6 in 4yln

Go back to Zinc Binding Sites List in 4yln
Zinc binding site 5 out of 6 in the E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1501

b:0.0
occ:1.00
 SG P:CYS88 2.0 0.5 1.0
SG P:CYS85 2.2 0.6 1.0
SG P:CYS70 2.5 0.4 1.0
CB P:CYS70 2.6 0.7 1.0
CB P:CYS85 2.7 0.1 1.0
SG P:CYS72 3.1 0.6 1.0
CB P:CYS88 3.6 0.8 1.0
CA P:CYS70 4.1 0.5 1.0
CA P:CYS85 4.2 0.4 1.0
N P:LEU71 4.2 0.9 1.0
N P:CYS88 4.4 0.9 1.0
CD2 P:TYR75 4.4 0.0 1.0
CA P:CYS88 4.4 0.3 1.0
C P:CYS70 4.4 0.1 1.0
N P:CYS72 4.4 0.7 1.0
CB P:CYS72 4.6 0.0 1.0
N P:TYR75 4.7 0.9 1.0
N P:LYS74 4.7 0.0 1.0
N P:VAL90 4.8 0.8 1.0
N P:GLY89 4.8 0.2 1.0
C P:CYS85 4.8 0.5 1.0
O P:VAL90 4.8 0.8 1.0
C P:CYS88 4.9 0.0 1.0
CB P:VAL90 4.9 0.2 1.0
N P:GLY73 4.9 0.4 1.0
CB P:TYR75 4.9 0.3 1.0
CB P:LYS74 4.9 0.3 1.0
O P:CYS85 5.0 0.4 1.0

Zinc binding site 6 out of 6 in 4yln

Go back to Zinc Binding Sites List in 4yln
Zinc binding site 6 out of 6 in the E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of E. Coli Transcription Initiation Complex - 17-Bp Spacer and 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1502

b:1.0
occ:1.00
 SG P:CYS898 1.8 0.5 1.0
SG P:CYS814 1.9 0.9 1.0
NH2 P:ARG883 2.3 0.6 1.0
SG P:CYS895 2.6 0.1 1.0
SG P:CYS888 2.7 0.0 1.0
CB P:CYS895 3.0 0.2 1.0
CZ P:ARG883 3.2 0.4 1.0
NE P:ARG883 3.3 0.3 1.0
CB P:CYS814 3.6 0.3 1.0
CB P:CYS898 3.6 0.5 1.0
OG1 P:THR890 3.8 0.1 1.0
CB P:CYS888 3.8 0.2 1.0
N P:CYS814 4.0 0.4 1.0
CA P:CYS888 4.2 0.9 1.0
CA P:CYS895 4.3 0.1 1.0
CA P:CYS814 4.4 0.9 1.0
NH1 P:ARG883 4.4 0.9 1.0
N P:CYS898 4.4 0.2 1.0
N P:CYS895 4.4 0.5 1.0
N P:ASP889 4.5 0.3 1.0
CA P:CYS898 4.6 0.9 1.0
CD P:ARG883 4.7 0.5 1.0
N P:GLY815 4.8 0.6 1.0
C P:CYS888 4.9 0.1 1.0
N P:THR890 5.0 0.3 1.0
CB P:THR890 5.0 0.1 1.0

Reference:

Y.Zuo, T.A.Steitz. Crystal Structures of the E. Coli Transcription Initiation Complexes with A Complete Bubble. Mol.Cell V. 58 534 2015.
ISSN: ISSN 1097-2765
PubMed: 25866247
DOI: 10.1016/J.MOLCEL.2015.03.010
Page generated: Wed Dec 16 05:57:59 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy