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Zinc in PDB 4wqt: Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein)

Enzymatic activity of Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein)

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein):
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein), PDB code: 4wqt was solved by Y.Murayama, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.79 / 4.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 189.568, 263.770, 195.848, 90.00, 116.83, 90.00
R / Rfree (%) 26 / 31.3

Other elements in 4wqt:

The structure of Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein) also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein) (pdb code 4wqt). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein), PDB code: 4wqt:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 4wqt

Go back to Zinc Binding Sites List in 4wqt
Zinc binding site 1 out of 3 in the Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein)


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 Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2001

b:0.9
occ:1.00
 N D:CYS1201 2.2 0.7 1.0
CB D:CYS1201 2.3 0.2 1.0
CA D:CYS1201 2.7 0.7 1.0
SG D:CYS1194 3.0 0.6 1.0
CG1 D:VAL1200 3.1 0.4 1.0
SG D:CYS1112 3.2 0.9 1.0
CB D:CYS1204 3.3 1.0 1.0
C D:VAL1200 3.3 0.6 1.0
CB D:CYS1112 3.4 0.9 1.0
CA D:VAL1200 3.6 0.6 1.0
CB D:CYS1194 3.7 0.6 1.0
C D:CYS1201 3.7 0.7 1.0
OG1 D:THR1196 3.8 0.9 1.0
SG D:CYS1204 3.8 1.0 1.0
O D:CYS1201 3.9 0.7 1.0
SG D:CYS1201 3.9 0.2 1.0
CB D:VAL1200 4.0 0.4 1.0
O D:VAL1200 4.3 0.6 1.0
N D:CYS1204 4.4 0.5 1.0
CB D:THR1196 4.5 0.9 1.0
CA D:CYS1204 4.5 0.5 1.0
CA D:CYS1194 4.5 0.6 1.0
CA D:CYS1112 4.5 0.8 1.0
N D:CYS1112 4.6 0.8 1.0
CG D:GLU1109 4.8 0.8 1.0
N D:GLN1202 4.9 0.3 1.0

Zinc binding site 2 out of 3 in 4wqt

Go back to Zinc Binding Sites List in 4wqt
Zinc binding site 2 out of 3 in the Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein)


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 Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1601

b:0.2
occ:1.01
 SG I:CYS1194 1.9 0.7 1.0
CB I:CYS1204 2.0 1.0 1.0
SG I:CYS1204 2.1 1.0 1.0
CG1 I:VAL1200 2.3 0.2 1.0
CB I:CYS1194 2.4 0.7 1.0
SG I:CYS1112 2.5 0.3 1.0
N I:CYS1201 3.3 0.8 1.0
SG I:CYS1201 3.3 0.3 1.0
CA I:CYS1204 3.6 0.7 1.0
CB I:VAL1200 3.6 0.2 1.0
CA I:CYS1194 3.8 0.6 1.0
CA I:VAL1200 3.9 0.6 1.0
CB I:CYS1201 4.1 0.3 1.0
C I:VAL1200 4.1 0.6 1.0
N I:CYS1204 4.2 0.7 1.0
CA I:CYS1201 4.2 0.8 1.0
CB I:CYS1112 4.2 0.3 1.0
C I:CYS1204 4.3 0.7 1.0
O I:CYS1201 4.4 0.8 1.0
CA I:PRO1191 4.6 0.6 1.0
CG2 I:VAL1200 4.6 0.2 1.0
N I:TYR1205 4.6 0.0 1.0
C I:CYS1201 4.7 0.8 1.0
N I:CYS1194 4.7 0.6 1.0
C I:CYS1194 4.7 0.6 1.0

Zinc binding site 3 out of 3 in 4wqt

Go back to Zinc Binding Sites List in 4wqt
Zinc binding site 3 out of 3 in the Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermus Thermophilus Rna Polymerase Complexed with An Rna Cleavage Stimulating Factor (A Grea/GFH1 Chimeric Protein) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1601

b:0.1
occ:1.00
 SG N:CYS1201 2.3 1.0 1.0
SG N:CYS1112 2.6 0.5 1.0
SG N:CYS1204 2.8 0.1 1.0
CB N:CYS1204 2.9 0.1 1.0
CB N:CYS1112 3.0 0.5 1.0
CA N:CYS1194 3.0 0.3 1.0
CB N:CYS1194 3.1 0.0 1.0
SG N:CYS1194 3.4 0.0 1.0
N N:GLN1195 3.9 0.9 1.0
C N:CYS1194 3.9 0.3 1.0
N N:CYS1194 4.1 0.3 1.0
CB N:CYS1201 4.1 1.0 1.0
CA N:CYS1204 4.3 0.2 1.0
CA N:CYS1112 4.4 0.9 1.0
O N:THR1193 4.5 0.1 1.0
N N:CYS1201 4.5 1.0 1.0
N N:CYS1204 4.6 0.2 1.0
C N:THR1193 4.6 0.1 1.0
OG1 N:THR1196 4.7 0.4 1.0
CG2 N:THR1114 4.8 0.8 1.0
N N:CYS1112 4.8 0.9 1.0
CA N:CYS1201 4.9 1.0 1.0
N N:THR1196 5.0 0.5 1.0

Reference:

S.I.Sekine, Y.Murayama, V.Svetlov, E.Nudler, S.Yokoyama. The Ratcheted and Ratchetable Structural States of Rna Polymerase Underlie Multiple Transcriptional Functions. Mol.Cell V. 57 408 2015.
ISSN: ISSN 1097-2765
PubMed: 25601758
DOI: 10.1016/J.MOLCEL.2014.12.014
Page generated: Sun Oct 27 10:02:00 2024

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