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Zinc in PDB 4oio: Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation

Enzymatic activity of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation, PDB code: 4oio was solved by Y.Zhang, R.H.Ebright, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.92 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.110, 103.780, 296.090, 90.00, 98.86, 90.00
R / Rfree (%) 20.5 / 25.6

Other elements in 4oio:

The structure of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation (pdb code 4oio). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation, PDB code: 4oio:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4oio

Go back to Zinc Binding Sites List in 4oio
Zinc binding site 1 out of 2 in the Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:20.4
occ:1.00
SG D:CYS1204 2.2 11.2 1.0
SG D:CYS1194 2.2 10.5 1.0
SG D:CYS1112 2.2 15.5 1.0
SG D:CYS1201 2.4 11.0 1.0
CB D:CYS1112 3.3 19.8 1.0
CB D:CYS1194 3.3 17.5 1.0
CB D:CYS1201 3.4 14.2 1.0
CB D:CYS1204 3.4 13.2 1.0
CA D:CYS1194 3.7 16.0 1.0
OG1 D:THR1196 3.8 24.1 1.0
NH2 D:ARG1189 3.9 17.5 1.0
N D:CYS1112 4.0 19.3 1.0
N D:GLN1195 4.0 17.9 1.0
N D:CYS1201 4.0 13.0 1.0
CA D:CYS1112 4.2 16.3 1.0
CA D:CYS1201 4.3 12.9 1.0
C D:CYS1194 4.3 17.4 1.0
CG2 D:THR1114 4.4 22.0 1.0
N D:CYS1204 4.5 17.3 1.0
CA D:CYS1204 4.5 15.7 1.0
N D:THR1196 4.5 15.7 1.0
CB D:THR1196 4.8 21.5 1.0
N D:CYS1194 4.9 12.0 1.0
C D:CYS1201 4.9 11.1 1.0
CZ D:ARG1189 5.0 22.3 1.0

Zinc binding site 2 out of 2 in 4oio

Go back to Zinc Binding Sites List in 4oio
Zinc binding site 2 out of 2 in the Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:58.0
occ:1.00
SG D:CYS76 2.3 46.2 1.0
SG D:CYS73 2.3 63.2 1.0
SG D:CYS60 2.3 42.3 1.0
SG D:CYS58 2.4 65.2 1.0
CB D:CYS73 2.8 58.5 1.0
CB D:CYS58 3.2 47.1 1.0
CB D:CYS76 3.8 48.0 1.0
CB D:CYS60 3.9 47.5 1.0
N D:CYS60 3.9 55.3 1.0
CB D:LYS62 4.0 59.5 1.0
N D:LYS62 4.1 45.1 1.0
N D:CYS76 4.2 65.5 1.0
N D:GLY61 4.3 56.6 1.0
N D:ALA59 4.3 36.4 1.0
CD2 D:TYR63 4.3 60.5 1.0
CA D:CYS73 4.3 52.6 1.0
CA D:CYS60 4.4 51.6 1.0
CA D:CYS58 4.4 45.6 1.0
C D:CYS58 4.5 38.6 1.0
CA D:CYS76 4.6 60.8 1.0
CA D:LYS62 4.6 56.6 1.0
CE2 D:TYR63 4.6 69.1 1.0
C D:CYS60 4.7 54.9 1.0
N D:TYR63 4.7 62.6 1.0
C D:ALA59 4.9 56.2 1.0

Reference:

Y.Zhang, D.Degen, M.X.Ho, E.Sineva, K.Y.Ebright, Y.W.Ebright, V.Mekler, H.Vahedian-Movahed, Y.Feng, R.Yin, S.Tuske, H.Irschik, R.Jansen, S.Maffioli, S.Donadio, E.Arnold, R.H.Ebright. GE23077 Binds to the Rna Polymerase 'I' and 'I+1' Sites and Prevents the Binding of Initiating Nucleotides. Elife V. 3 02450 2014.
ISSN: ESSN 2050-084X
PubMed: 24755292
Page generated: Sun Oct 27 03:44:52 2024

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