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

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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

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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

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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

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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: Sun Aug 22 09:43:00 2021

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