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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: Thu Aug 21 01:45:51 2025

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