Atomistry » Zinc » PDB 5drr-5e9a » 5e18
Atomistry »
  Zinc »
    PDB 5drr-5e9a »
      5e18 »

Zinc in PDB 5e18: T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)

Enzymatic activity of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)

All present enzymatic activity of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8):
2.7.7.6;

Protein crystallography data

The structure of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8), PDB code: 5e18 was solved by Y.Zhang, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.35 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.917, 103.241, 298.404, 90.00, 97.93, 90.00
R / Rfree (%) 23.8 / 28.4

Other elements in 5e18:

The structure of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) (pdb code 5e18). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8), PDB code: 5e18:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5e18

Go back to Zinc Binding Sites List in 5e18
Zinc binding site 1 out of 2 in the T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:73.1
occ:1.00
SG D:CYS1201 2.1 84.9 1.0
SG D:CYS1194 2.2 73.9 1.0
SG D:CYS1112 2.2 78.1 1.0
SG D:CYS1204 2.3 73.5 1.0
CB D:CYS1204 2.9 68.4 1.0
CB D:CYS1194 3.2 61.5 1.0
CB D:CYS1112 3.5 80.8 1.0
CA D:CYS1194 3.6 59.1 1.0
CB D:CYS1201 3.6 73.6 1.0
OG1 D:THR1196 3.9 81.2 1.0
CG2 D:THR1114 4.1 77.8 1.0
N D:CYS1201 4.1 79.5 1.0
CA D:CYS1204 4.1 73.7 1.0
N D:CYS1112 4.2 95.9 1.0
N D:GLN1195 4.2 72.3 1.0
N D:CYS1204 4.2 74.5 1.0
C D:CYS1194 4.3 70.8 1.0
CA D:CYS1201 4.4 72.1 1.0
CA D:CYS1112 4.5 83.8 1.0
NH2 D:ARG1189 4.5 79.3 1.0
N D:CYS1194 4.7 56.8 1.0
N D:THR1196 4.9 69.7 1.0
NE D:ARG1189 4.9 70.4 1.0
OD1 D:ASP1111 4.9 88.2 1.0
CB D:THR1114 5.0 83.9 1.0

Zinc binding site 2 out of 2 in 5e18

Go back to Zinc Binding Sites List in 5e18
Zinc binding site 2 out of 2 in the T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.7
occ:1.00
SG D:CYS58 2.3 0.4 1.0
SG D:CYS73 2.3 0.4 1.0
SG D:CYS60 2.3 1.0 1.0
CB D:CYS58 2.9 0.9 1.0
SG D:CYS76 3.0 0.9 1.0
CB D:CYS73 3.1 0.9 1.0
CB D:LYS62 3.3 0.3 1.0
N D:LYS62 3.4 0.6 1.0
CB D:CYS60 3.9 0.5 1.0
N D:GLY61 3.9 0.3 1.0
CA D:LYS62 3.9 0.3 1.0
N D:CYS60 4.0 0.5 1.0
CA D:CYS58 4.3 0.5 1.0
CA D:CYS60 4.3 0.3 1.0
N D:TYR63 4.4 0.5 1.0
N D:ALA59 4.4 0.0 1.0
CB D:CYS76 4.5 0.8 1.0
CD2 D:TYR63 4.5 1.0 1.0
C D:CYS60 4.5 0.2 1.0
C D:GLY61 4.5 0.6 1.0
C D:CYS58 4.5 0.7 1.0
CA D:CYS73 4.5 0.3 1.0
CG D:LYS62 4.6 0.7 1.0
N D:CYS76 4.7 1.0 1.0
C D:LYS62 4.7 0.8 1.0
CA D:GLY61 4.7 0.2 1.0
CD D:LYS62 4.8 0.1 1.0
CE2 D:TYR63 4.9 0.4 1.0

Reference:

J.T.Winkelman, I.O.Vvedenskaya, Y.Zhang, Y.Zhang, J.G.Bird, D.M.Taylor, R.L.Gourse, R.H.Ebright, B.E.Nickels. Multiplexed Protein-Dna Cross-Linking: Scrunching in Transcription Start Site Selection. Science V. 351 1090 2016.
ISSN: ESSN 1095-9203
PubMed: 26941320
DOI: 10.1126/SCIENCE.AAD6881
Page generated: Sun Oct 27 14:56:49 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy