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Magnesium 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:

Zinc (Zn) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 3 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4wqt

Go back to Magnesium Binding Sites List in 4wqt
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg2002

b:0.5
occ:1.00
OD2 D:ASP741 1.9 0.4 1.0
OD1 D:ASP739 2.2 0.1 1.0
CG D:ASP741 2.2 0.4 1.0
OD1 D:ASP741 2.3 0.4 1.0
OD2 D:ASP743 2.4 0.4 1.0
CG D:ASP743 3.0 0.4 1.0
OD1 D:ASP743 3.0 0.4 1.0
CG D:ASP739 3.2 0.1 1.0
CB D:ASP741 3.5 0.4 1.0
OD2 D:ASP739 3.6 0.1 1.0
O D:ASP739 3.8 0.4 1.0
N D:ASP741 4.2 0.3 1.0
CB D:ASP743 4.3 0.4 1.0
CA D:ASP741 4.3 0.3 1.0
N D:ASP743 4.4 0.8 1.0
C D:ASP739 4.4 0.4 1.0
CB D:ASP739 4.5 0.1 1.0
N D:ASP739 4.5 0.4 1.0
N D:GLY742 4.6 0.6 1.0
C D:ASP741 4.6 0.3 1.0
CA D:ASP739 4.8 0.4 1.0
CA D:ASP743 4.9 0.8 1.0

Magnesium binding site 2 out of 3 in 4wqt

Go back to Magnesium Binding Sites List in 4wqt
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1602

b:1.0
occ:1.00
OD2 I:ASP743 2.9 0.7 1.0
OD1 I:ASP743 2.9 0.7 1.0
OD1 I:ASP739 3.1 0.6 1.0
OD2 I:ASP739 3.2 0.6 1.0
CG I:ASP743 3.3 0.7 1.0
OD1 I:ASP741 3.4 0.5 1.0
CG I:ASP739 3.4 0.6 1.0
OD2 I:ASP741 3.6 0.5 1.0
CG I:ASP741 3.9 0.5 1.0
NH1 I:ARG704 4.3 0.1 1.0
N I:ASP739 4.6 0.2 1.0
NH2 I:ARG704 4.7 0.1 1.0
CB I:ASP743 4.8 0.7 1.0
CB I:ASP739 4.9 0.6 1.0
CZ I:ARG704 5.0 0.1 1.0
O I:ASP739 5.0 0.2 1.0

Magnesium binding site 3 out of 3 in 4wqt

Go back to Magnesium Binding Sites List in 4wqt
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg1602

b:0.1
occ:1.00
OD2 N:ASP743 2.1 0.2 1.0
OD2 N:ASP739 2.3 0.8 1.0
CG N:ASP743 2.8 0.2 1.0
OD1 N:ASP743 2.8 0.2 1.0
OD2 N:ASP741 2.8 0.9 1.0
OD1 N:ASP741 3.1 0.9 1.0
CG N:ASP739 3.1 0.8 1.0
CG N:ASP741 3.3 0.9 1.0
OD1 N:ASP739 3.7 0.8 1.0
N N:ASP739 3.9 0.5 1.0
CB N:ASP739 4.2 0.8 1.0
CB N:ASP743 4.3 0.2 1.0
O N:ASP739 4.3 0.5 1.0
CA N:ASP739 4.5 0.5 1.0
C N:ASP739 4.6 0.5 1.0
CB N:ASP741 4.8 0.9 1.0
C N:ALA738 5.0 0.5 1.0
CA N:ALA738 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: Mon Dec 14 19:42:43 2020

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