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Zinc in PDB 4g7o: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna, PDB code: 4g7o 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) 46.61 / 2.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.483, 103.883, 297.340, 90.00, 98.23, 90.00
R / Rfree (%) 20.5 / 24.7

Other elements in 4g7o:

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna (pdb code 4g7o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna, PDB code: 4g7o:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4g7o

Go back to Zinc Binding Sites List in 4g7o
Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna


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 Transcription Initiation Complex Containing 2 Nt of Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:62.4
occ:1.00
 SG D:CYS1201 2.2 46.2 1.0
SG D:CYS1112 2.2 53.8 1.0
SG D:CYS1194 2.2 60.1 1.0
SG D:CYS1204 2.3 61.4 1.0
CB D:CYS1204 2.9 50.6 1.0
CB D:CYS1194 3.0 54.2 1.0
CB D:CYS1112 3.4 53.1 1.0
CB D:CYS1201 3.5 54.7 1.0
CA D:CYS1194 3.6 49.8 1.0
N D:GLN1195 4.0 49.1 1.0
N D:CYS1112 4.1 59.5 1.0
CA D:CYS1204 4.1 49.9 1.0
OG1 D:THR1196 4.1 58.3 1.0
N D:CYS1201 4.2 53.3 1.0
N D:CYS1204 4.2 53.9 1.0
NH2 D:ARG1189 4.2 42.4 1.0
CG2 D:THR1114 4.3 57.7 1.0
C D:CYS1194 4.3 49.2 1.0
CA D:CYS1201 4.4 53.5 1.0
CA D:CYS1112 4.4 56.4 1.0
O D:CYS1201 4.6 52.3 1.0
N D:THR1196 4.8 53.7 1.0
N D:CYS1194 4.8 43.5 1.0
C D:CYS1201 4.8 51.0 1.0

Zinc binding site 2 out of 4 in 4g7o

Go back to Zinc Binding Sites List in 4g7o
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna


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 Transcription Initiation Complex Containing 2 Nt of Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:83.6
occ:1.00
 SG D:CYS76 2.2 88.7 1.0
SG D:CYS73 2.2 86.2 1.0
SG D:CYS58 2.3 81.0 1.0
SG D:CYS60 2.4 76.7 1.0
CB D:CYS73 3.0 80.7 1.0
CB D:CYS58 3.2 80.8 1.0
CB D:CYS76 3.6 73.6 1.0
N D:CYS60 3.7 84.4 1.0
CB D:CYS60 3.7 79.0 1.0
N D:CYS76 4.1 91.9 1.0
CA D:CYS60 4.2 88.8 1.0
N D:ALA59 4.2 70.4 1.0
CB D:LYS62 4.2 89.9 1.0
N D:GLY61 4.3 94.7 1.0
N D:LYS62 4.3 92.9 1.0
C D:CYS58 4.3 73.8 1.0
CA D:CYS58 4.4 73.5 1.0
CA D:CYS73 4.4 81.7 1.0
CA D:CYS76 4.5 85.5 1.0
C D:CYS60 4.6 94.5 1.0
C D:ALA59 4.7 82.4 1.0
CB D:ARG75 4.7 90.3 1.0
C D:CYS73 4.8 88.7 1.0
CA D:LYS62 4.8 90.3 1.0
CA D:ALA59 4.9 73.3 1.0
CD2 D:TYR63 4.9 89.4 1.0
O D:CYS58 4.9 75.9 1.0
N D:GLY77 5.0 76.6 1.0
O D:CYS73 5.0 86.8 1.0
C D:ARG75 5.0 93.4 1.0

Zinc binding site 3 out of 4 in 4g7o

Go back to Zinc Binding Sites List in 4g7o
Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2001

b:62.6
occ:1.00
 SG N:CYS1204 2.2 47.3 1.0
SG N:CYS1201 2.2 45.6 1.0
SG N:CYS1112 2.3 51.3 1.0
SG N:CYS1194 2.3 61.7 1.0
CB N:CYS1204 3.1 46.9 1.0
CB N:CYS1194 3.2 46.0 1.0
CB N:CYS1201 3.4 44.6 1.0
CA N:CYS1194 3.4 48.8 1.0
CB N:CYS1112 3.4 47.0 1.0
N N:GLN1195 3.8 51.5 1.0
CG2 N:THR1114 4.0 55.9 1.0
OG1 N:THR1196 4.1 54.1 1.0
C N:CYS1194 4.1 50.5 1.0
N N:CYS1201 4.2 53.1 1.0
N N:CYS1112 4.2 51.5 1.0
NH2 N:ARG1189 4.3 40.5 1.0
CA N:CYS1204 4.3 46.1 1.0
CA N:CYS1201 4.3 46.0 1.0
N N:CYS1204 4.3 48.3 1.0
CA N:CYS1112 4.4 48.0 1.0
N N:CYS1194 4.6 44.8 1.0
N N:THR1196 4.7 52.6 1.0
O N:CYS1201 4.8 46.5 1.0
C N:CYS1201 4.9 47.1 1.0
CB N:THR1114 4.9 52.9 1.0
OD1 N:ASP1111 5.0 54.6 1.0

Zinc binding site 4 out of 4 in 4g7o

Go back to Zinc Binding Sites List in 4g7o
Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Containing 2 Nt of Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2002

b:0.1
occ:1.00
 SG N:CYS60 2.2 0.1 1.0
SG N:CYS58 2.2 0.4 1.0
SG N:CYS76 2.3 95.9 1.0
SG N:CYS73 2.3 96.7 1.0
CB N:CYS58 3.1 0.0 1.0
CB N:CYS73 3.1 96.3 1.0
N N:CYS60 3.6 0.1 1.0
CB N:CYS60 3.7 1.0 1.0
CB N:CYS76 3.7 96.4 1.0
N N:LYS62 4.0 0.3 1.0
CB N:LYS62 4.0 0.8 1.0
N N:GLY61 4.0 0.9 1.0
CA N:CYS60 4.1 0.6 1.0
N N:ALA59 4.2 89.6 1.0
C N:CYS58 4.2 0.1 1.0
N N:CYS76 4.2 0.6 1.0
CA N:CYS58 4.3 97.4 1.0
C N:CYS60 4.4 0.1 1.0
CA N:LYS62 4.5 0.5 1.0
CA N:CYS73 4.6 0.1 1.0
CA N:CYS76 4.6 0.1 1.0
C N:ALA59 4.7 0.1 1.0
O N:CYS58 4.8 0.2 1.0
N N:TYR63 4.8 0.9 1.0
CD2 N:TYR63 4.9 0.2 1.0
CA N:ALA59 4.9 92.7 1.0
C N:GLY61 4.9 0.6 1.0
CA N:GLY61 5.0 0.1 1.0
CB N:ARG75 5.0 0.8 1.0

Reference:

Y.Zhang, Y.Feng, S.Chatterjee, S.Tuske, M.X.Ho, E.Arnold, R.H.Ebright. Structural Basis of Transcription Initiation. Science V. 338 1076 2012.
ISSN: ISSN 0036-8075
PubMed: 23086998
DOI: 10.1126/SCIENCE.1227786
Page generated: Sat Oct 26 23:08:23 2024

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