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Zinc in PDB 5e17: T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)

Enzymatic activity of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)

All present enzymatic activity of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7):
2.7.7.6;

Protein crystallography data

The structure of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7), PDB code: 5e17 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) 39.82 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.007, 103.566, 294.935, 90.00, 99.20, 90.00
R / Rfree (%) 21.5 / 26

Other elements in 5e17:

The structure of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) 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 Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) (pdb code 5e17). 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 Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7), PDB code: 5e17:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5e17

Go back to Zinc Binding Sites List in 5e17
Zinc binding site 1 out of 2 in the T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)


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 Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1602

b:6.0
occ:1.00
 SG D:CYS1201 2.1 17.1 1.0
SG D:CYS1112 2.1 20.8 1.0
SG D:CYS1194 2.2 11.8 1.0
SG D:CYS1204 2.2 20.1 1.0
CB D:CYS1194 3.2 24.7 1.0
CB D:CYS1204 3.3 30.9 1.0
CA D:CYS1194 3.4 25.3 1.0
CB D:CYS1112 3.4 21.9 1.0
CB D:CYS1201 3.6 29.2 1.0
OG1 D:THR1196 3.9 25.1 1.0
N D:GLN1195 3.9 20.2 1.0
NH2 D:ARG1189 4.0 32.5 1.0
N D:CYS1112 4.1 26.3 1.0
C D:CYS1194 4.1 21.9 1.0
N D:CYS1201 4.3 27.9 1.0
CA D:CYS1112 4.3 24.2 1.0
CG2 D:THR1114 4.4 29.1 1.0
CA D:CYS1204 4.5 30.5 1.0
CA D:CYS1201 4.5 29.3 1.0
N D:CYS1194 4.5 22.3 1.0
N D:CYS1204 4.6 29.1 1.0
N D:THR1196 4.6 25.9 1.0
OD1 D:ASP1111 4.7 28.7 1.0
O D:HOH2120 4.9 21.0 1.0
CB D:THR1196 4.9 25.8 1.0

Zinc binding site 2 out of 2 in 5e17

Go back to Zinc Binding Sites List in 5e17
Zinc binding site 2 out of 2 in the T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)


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 Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1603

b:45.8
occ:1.00
 SG D:CYS60 2.2 49.6 1.0
SG D:CYS73 2.2 65.0 1.0
SG D:CYS58 2.2 76.1 1.0
SG D:CYS76 2.3 46.5 1.0
CB D:CYS73 2.9 68.3 1.0
CB D:CYS58 2.9 64.1 1.0
CB D:LYS62 3.3 90.1 1.0
N D:LYS62 3.6 78.2 1.0
CB D:CYS60 3.9 63.8 1.0
CB D:CYS76 4.0 54.8 1.0
CA D:LYS62 4.0 88.6 1.0
CD1 D:TYR63 4.1 87.5 1.0
N D:GLY61 4.1 58.5 1.0
N D:CYS60 4.2 63.6 1.0
N D:CYS76 4.2 70.9 1.0
N D:TYR63 4.3 87.7 1.0
CA D:CYS73 4.3 69.9 1.0
CA D:CYS58 4.3 63.1 1.0
CE1 D:TYR63 4.4 82.7 1.0
CG D:LYS62 4.4 90.8 1.0
CA D:CYS60 4.5 64.2 1.0
C D:CYS58 4.6 55.0 1.0
CD D:LYS62 4.6 95.1 1.0
C D:LYS62 4.7 90.0 1.0
C D:CYS60 4.7 54.3 1.0
CA D:CYS76 4.7 67.5 1.0
C D:GLY61 4.7 72.0 1.0
N D:ALA59 4.8 56.2 1.0
CB D:ARG75 4.9 72.6 1.0
CA D:GLY61 5.0 68.1 1.0
C D:CYS73 5.0 69.0 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

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