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Zinc in PDB 4q5s: Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna

Enzymatic activity of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna, PDB code: 4q5s was solved by K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.98 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 187.089, 102.075, 297.263, 90.00, 98.14, 90.00
R / Rfree (%) 26.9 / 29.4

Other elements in 4q5s:

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna (pdb code 4q5s). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna, PDB code: 4q5s:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4q5s

Go back to Zinc Binding Sites List in 4q5s
Zinc binding site 1 out of 2 in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2002

b:0.1
occ:1.00
SG D:CYS76 2.4 0.3 1.0
SG D:CYS60 2.4 0.4 1.0
SG D:CYS73 2.4 0.4 1.0
SG D:CYS58 2.5 0.8 1.0
CB D:CYS58 2.9 0.4 1.0
CB D:CYS73 3.1 0.8 1.0
N D:CYS60 3.7 0.8 1.0
CB D:CYS60 3.8 0.1 1.0
CB D:CYS76 3.9 0.9 1.0
N D:ALA59 4.0 0.6 1.0
CB D:LYS62 4.0 0.8 1.0
N D:LYS62 4.1 0.4 1.0
CA D:CYS60 4.2 1.0 1.0
N D:GLY61 4.2 0.3 1.0
CA D:CYS58 4.2 0.6 1.0
N D:CYS76 4.3 0.3 1.0
C D:CYS58 4.4 0.3 1.0
CA D:CYS73 4.6 0.9 1.0
C D:CYS60 4.6 0.0 1.0
C D:ALA59 4.7 0.3 1.0
CA D:LYS62 4.7 0.8 1.0
CA D:CYS76 4.7 0.4 1.0
CA D:ALA59 4.8 0.4 1.0
N D:TYR63 4.9 0.9 1.0
N D:GLY77 5.0 0.4 1.0

Zinc binding site 2 out of 2 in 4q5s

Go back to Zinc Binding Sites List in 4q5s
Zinc binding site 2 out of 2 in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2003

b:47.4
occ:1.00
SG D:CYS1201 2.3 56.8 1.0
SG D:CYS1194 2.4 56.0 1.0
SG D:CYS1112 2.5 63.2 1.0
SG D:CYS1204 2.5 58.0 1.0
CB D:CYS1204 3.0 54.5 1.0
CB D:CYS1194 3.2 56.5 1.0
CA D:CYS1194 3.5 59.3 1.0
CB D:CYS1201 3.8 56.1 1.0
CG2 D:THR1114 3.9 66.1 1.0
CB D:CYS1112 3.9 64.3 1.0
N D:GLN1195 4.0 62.8 1.0
OG1 D:THR1196 4.1 57.9 1.0
NH2 D:ARG1189 4.1 64.2 1.0
N D:CYS1201 4.2 52.8 1.0
C D:CYS1194 4.2 61.2 1.0
CA D:CYS1204 4.3 54.4 1.0
N D:CYS1204 4.3 54.2 1.0
N D:CYS1112 4.4 64.2 1.0
CA D:CYS1201 4.6 53.4 1.0
N D:CYS1194 4.6 59.8 1.0
N D:THR1196 4.8 61.0 1.0
CA D:CYS1112 4.8 66.1 1.0
CB D:THR1114 4.8 69.2 1.0
OD1 D:ASP1111 4.9 65.0 1.0

Reference:

R.S.Basu, B.A.Warner, V.Molodtsov, D.Pupov, D.Esyunina, C.Fernandez-Tornero, A.Kulbachinskiy, K.S.Murakami. Structural Basis of Transcription Initiation By Bacterial Rna Polymerase Holoenzyme. J.Biol.Chem. V. 289 24549 2014.
ISSN: ISSN 0021-9258
PubMed: 24973216
DOI: 10.1074/JBC.M114.584037
Page generated: Wed Dec 16 05:42:43 2020

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