Atomistry » Zinc » PDB 7ea8-7emf » 7eh2
Atomistry »
  Zinc »
    PDB 7ea8-7emf »
      7eh2 »

Zinc in PDB 7eh2: Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer

Enzymatic activity of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer

All present enzymatic activity of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer, PDB code: 7eh2 was solved by L.Li, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.82 / 3.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 184.85, 104.2, 296.65, 90, 98.42, 90
R / Rfree (%) 20.1 / 24.8

Other elements in 7eh2:

The structure of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer (pdb code 7eh2). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer, PDB code: 7eh2:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7eh2

Go back to Zinc Binding Sites List in 7eh2
Zinc binding site 1 out of 4 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:78.6
occ:1.00
 SG D:CYS1112 2.2 66.1 1.0
SG D:CYS1204 2.2 78.6 1.0
SG D:CYS1201 2.3 71.0 1.0
SG D:CYS1194 2.3 67.9 1.0
CB D:CYS1194 3.0 66.4 1.0
CB D:CYS1204 3.0 68.1 1.0
CA D:CYS1194 3.5 66.0 1.0
CB D:CYS1201 3.7 75.7 1.0
CB D:CYS1112 3.9 74.3 1.0
NH2 D:ARG1189 3.9 61.0 1.0
N D:CYS1204 4.1 76.4 1.0
CG2 D:THR1114 4.1 75.2 1.0
CA D:CYS1204 4.1 75.1 1.0
N D:CYS1112 4.3 76.6 1.0
N D:GLN1195 4.4 62.9 1.0
N D:CYS1201 4.4 66.0 1.0
C D:CYS1194 4.5 71.4 1.0
N D:CYS1194 4.6 56.2 1.0
CA D:CYS1201 4.6 69.8 1.0
CA D:CYS1112 4.7 78.0 1.0
CZ D:ARG1189 4.9 65.8 1.0
NE D:ARG1189 5.0 67.0 1.0

Zinc binding site 2 out of 4 in 7eh2

Go back to Zinc Binding Sites List in 7eh2
Zinc binding site 2 out of 4 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:95.9
occ:1.00
 SG D:CYS76 2.3 93.6 1.0
SG D:CYS73 2.3 87.8 1.0
SG D:CYS60 2.3 98.2 1.0
SG D:CYS58 2.4 96.9 1.0
CB D:CYS73 3.1 86.5 1.0
CB D:CYS58 3.3 89.5 1.0
CB D:CYS76 3.4 80.0 1.0
N D:CYS60 3.5 102.4 1.0
CB D:CYS60 3.7 97.5 1.0
N D:GLY61 4.0 106.5 1.0
N D:ALA59 4.0 79.5 1.0
CA D:CYS60 4.0 98.5 1.0
N D:CYS76 4.1 101.8 1.0
N D:LYS62 4.1 104.3 1.0
C D:CYS58 4.3 87.4 1.0
CA D:CYS76 4.3 90.9 1.0
CB D:LYS62 4.4 105.8 1.0
CA D:CYS58 4.4 89.0 1.0
C D:CYS60 4.4 105.8 1.0
C D:ALA59 4.5 95.9 1.0
CA D:CYS73 4.6 88.5 1.0
CD1 D:TYR63 4.7 98.4 1.0
CA D:ALA59 4.8 78.9 1.0
CA D:LYS62 4.9 105.3 1.0
O D:CYS58 4.9 88.3 1.0
CB D:ARG75 4.9 96.5 1.0
CA D:GLY61 5.0 105.5 1.0

Zinc binding site 3 out of 4 in 7eh2

Go back to Zinc Binding Sites List in 7eh2
Zinc binding site 3 out of 4 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1601

b:94.0
occ:1.00
 SG N:CYS1201 2.2 65.3 1.0
SG N:CYS1112 2.2 73.2 1.0
SG N:CYS1204 2.2 86.7 1.0
SG N:CYS1194 2.3 65.3 1.0
CB N:CYS1204 3.0 73.7 1.0
CB N:CYS1194 3.0 64.3 1.0
CA N:CYS1194 3.4 65.1 1.0
CB N:CYS1201 3.7 69.0 1.0
CB N:CYS1112 3.8 76.8 1.0
CG2 N:THR1114 3.8 72.0 1.0
NH2 N:ARG1189 3.9 71.5 1.0
N N:GLN1195 4.0 69.3 1.0
CA N:CYS1204 4.2 72.4 1.0
C N:CYS1194 4.2 68.7 1.0
N N:CYS1204 4.3 74.7 1.0
N N:CYS1201 4.3 74.0 1.0
OG1 N:THR1196 4.4 77.4 1.0
N N:CYS1194 4.5 60.8 1.0
N N:CYS1112 4.5 77.3 1.0
CA N:CYS1201 4.5 71.7 1.0
CA N:CYS1112 4.7 73.8 1.0
NE N:ARG1189 4.8 65.7 1.0
CZ N:ARG1189 4.8 65.7 1.0
CB N:THR1114 4.9 72.3 1.0

Zinc binding site 4 out of 4 in 7eh2

Go back to Zinc Binding Sites List in 7eh2
Zinc binding site 4 out of 4 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1602

b:129.9
occ:1.00
 O N:HOH1704 2.1 132.0 1.0
SG N:CYS76 2.3 125.2 1.0
SG N:CYS60 2.3 133.6 1.0
SG N:CYS58 2.3 141.3 1.0
SG N:CYS73 2.4 126.7 1.0
O N:HOH1702 2.6 140.4 1.0
CB N:CYS73 3.1 125.8 1.0
CB N:CYS58 3.1 128.7 1.0
CB N:CYS76 3.5 125.5 1.0
CB N:CYS60 3.7 131.2 1.0
N N:CYS60 3.7 128.3 1.0
N N:GLY61 4.1 132.8 1.0
N N:LYS62 4.1 128.1 1.0
CA N:CYS60 4.2 133.2 1.0
CB N:LYS62 4.2 134.2 1.0
N N:ALA59 4.3 117.1 1.0
N N:CYS76 4.3 135.6 1.0
CA N:CYS58 4.4 126.8 1.0
CA N:CYS76 4.5 131.2 1.0
CA N:CYS73 4.6 125.0 1.0
C N:CYS58 4.6 125.2 1.0
C N:CYS60 4.6 133.5 1.0
CA N:LYS62 4.8 130.4 1.0
C N:ALA59 4.8 123.9 1.0
CD1 N:TYR63 5.0 138.0 1.0

Reference:

K.S.Skalenko, L.Li, Y.Zhang, I.O.Vvedenskaya, J.T.Winkelman, A.L.Cope, D.M.Taylor, P.Shah, R.H.Ebright, J.B.Kinney, Y.Zhang, B.E.Nickels. Promoter-Sequence Determinants and Structural Basis of Primer-Dependent Transcription Initiation in Escherichia Coli . Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34187896
DOI: 10.1073/PNAS.2106388118
Page generated: Tue Oct 29 19:49:58 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy