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Zinc in PDB 4g7h: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex, PDB code: 4g7h 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) 49.27 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.560, 104.570, 297.550, 90.00, 98.32, 90.00
R / Rfree (%) 18.8 / 22.6

Other elements in 4g7h:

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

Magnesium (Mg) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex (pdb code 4g7h). 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, PDB code: 4g7h:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4g7h

Go back to Zinc Binding Sites List in 4g7h
Zinc binding site 1 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:77.6
occ:1.00
 SG D:CYS1204 2.2 48.0 1.0
SG D:CYS1112 2.2 50.1 1.0
SG D:CYS1201 2.3 37.4 1.0
SG D:CYS1194 2.4 48.0 1.0
CB D:CYS1204 3.1 47.7 1.0
CB D:CYS1194 3.3 48.6 1.0
CB D:CYS1112 3.4 49.7 1.0
CA D:CYS1194 3.6 47.7 1.0
CB D:CYS1201 3.6 49.3 1.0
OG1 D:THR1196 3.9 51.3 1.0
N D:CYS1112 4.0 55.5 1.0
N D:GLN1195 4.0 47.9 1.0
NH2 D:ARG1189 4.1 42.9 1.0
CG2 D:THR1114 4.2 54.6 1.0
N D:CYS1204 4.2 50.4 1.0
CA D:CYS1204 4.3 49.5 1.0
N D:CYS1201 4.3 47.1 1.0
CA D:CYS1112 4.3 56.0 1.0
C D:CYS1194 4.3 50.1 1.0
CA D:CYS1201 4.5 45.4 1.0
N D:THR1196 4.7 45.6 1.0
O D:HOH2129 4.8 47.7 1.0
N D:CYS1194 4.8 43.5 1.0
OD1 D:ASP1111 4.9 57.9 1.0
O D:CYS1201 4.9 46.5 1.0

Zinc binding site 2 out of 4 in 4g7h

Go back to Zinc Binding Sites List in 4g7h
Zinc binding site 2 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:73.0
occ:1.00
 SG D:CYS73 2.3 71.0 1.0
SG D:CYS76 2.3 65.8 1.0
SG D:CYS60 2.3 66.1 1.0
SG D:CYS58 2.3 63.2 1.0
CB D:CYS73 3.1 61.8 1.0
CB D:CYS76 3.4 64.2 1.0
CB D:CYS58 3.4 65.8 1.0
N D:CYS60 3.6 69.2 1.0
CB D:CYS60 3.7 66.0 1.0
N D:CYS76 3.9 72.4 1.0
N D:LYS62 4.0 83.9 1.0
N D:GLY61 4.0 81.8 1.0
CB D:LYS62 4.0 80.1 1.0
CA D:CYS60 4.1 70.0 1.0
CA D:CYS76 4.2 63.6 1.0
N D:ALA59 4.2 60.1 1.0
C D:CYS60 4.4 78.7 1.0
C D:CYS58 4.5 64.2 1.0
CA D:CYS58 4.6 65.8 1.0
CA D:CYS73 4.6 63.2 1.0
CA D:LYS62 4.6 77.1 1.0
C D:ALA59 4.7 68.2 1.0
CD2 D:TYR63 4.7 80.1 1.0
CB D:ARG75 4.8 66.7 1.0
CA D:ALA59 4.9 60.0 1.0
CA D:GLY61 5.0 85.7 1.0
N D:TYR63 5.0 79.6 1.0
C D:ARG75 5.0 74.6 1.0
C D:GLY61 5.0 88.5 1.0

Zinc binding site 3 out of 4 in 4g7h

Go back to Zinc Binding Sites List in 4g7h
Zinc binding site 3 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2001

b:54.5
occ:1.00
 SG N:CYS1204 2.2 46.9 1.0
SG N:CYS1201 2.3 44.6 1.0
SG N:CYS1194 2.4 48.9 1.0
SG N:CYS1112 2.4 50.8 1.0
CB N:CYS1204 3.1 48.6 1.0
CB N:CYS1194 3.2 43.8 1.0
CB N:CYS1201 3.5 46.6 1.0
CB N:CYS1112 3.5 54.4 1.0
CA N:CYS1194 3.5 46.2 1.0
N N:GLN1195 4.0 45.0 1.0
CG2 N:THR1114 4.1 50.0 1.0
OG1 N:THR1196 4.1 52.6 1.0
N N:CYS1201 4.1 49.4 1.0
N N:CYS1112 4.2 54.5 1.0
CA N:CYS1204 4.3 50.3 1.0
C N:CYS1194 4.3 46.9 1.0
N N:CYS1204 4.3 49.7 1.0
CA N:CYS1201 4.3 47.3 1.0
NH2 N:ARG1189 4.4 45.4 1.0
CA N:CYS1112 4.5 56.4 1.0
N N:THR1196 4.7 54.4 1.0
N N:CYS1194 4.7 42.8 1.0
O N:HOH2127 4.7 46.2 1.0
O N:CYS1201 4.8 48.0 1.0
C N:CYS1201 4.9 48.0 1.0
OD1 N:ASP1111 5.0 62.7 1.0
CB N:THR1114 5.0 53.9 1.0

Zinc binding site 4 out of 4 in 4g7h

Go back to Zinc Binding Sites List in 4g7h
Zinc binding site 4 out of 4 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn2002

b:95.3
occ:1.00
 SG N:CYS60 2.2 99.6 1.0
SG N:CYS76 2.2 89.8 1.0
SG N:CYS58 2.3 0.6 1.0
SG N:CYS73 2.3 92.6 1.0
CB N:CYS58 3.2 91.2 1.0
CB N:CYS73 3.2 85.1 1.0
CB N:CYS76 3.5 86.3 1.0
CB N:CYS60 3.7 0.6 1.0
N N:CYS60 3.7 95.6 1.0
CB N:LYS62 3.8 0.7 1.0
N N:LYS62 3.9 0.4 1.0
N N:GLY61 4.0 97.7 1.0
N N:CYS76 4.1 97.6 1.0
CA N:CYS60 4.1 97.6 1.0
N N:ALA59 4.2 79.0 1.0
CA N:CYS76 4.4 95.2 1.0
CA N:CYS58 4.4 83.5 1.0
CA N:LYS62 4.4 0.6 1.0
C N:CYS58 4.5 86.3 1.0
C N:CYS60 4.5 0.3 1.0
CA N:CYS73 4.7 86.5 1.0
CD2 N:TYR63 4.7 0.5 1.0
N N:TYR63 4.7 0.4 1.0
C N:ALA59 4.8 92.1 1.0
CB N:ARG75 4.9 96.7 1.0
C N:GLY61 4.9 0.1 1.0
CA N:GLY61 5.0 99.6 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 23:08:22 2024

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