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Magnesium in PDB 6l74: Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt

Enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt

All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt, PDB code: 6l74 was solved by Y.Zhang, L.Li, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.92 / 3.12
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.071, 103.498, 295.128, 90.00, 99.17, 90.00
R / Rfree (%) 19.1 / 23.6

Other elements in 6l74:

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt (pdb code 6l74). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt, PDB code: 6l74:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6l74

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Magnesium binding site 1 out of 5 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:0.5
occ:1.00
 OD1 B:ASP183 2.2 0.3 1.0
OD1 B:ASP193 2.2 0.6 1.0
OD1 B:ASP191 2.2 0.3 1.0
O B:ASP191 3.0 96.7 1.0
CG B:ASP183 3.4 0.4 1.0
CG B:ASP191 3.5 1.0 1.0
CG B:ASP193 3.5 91.8 1.0
C B:ASP191 3.6 99.1 1.0
O B:LEU192 3.7 84.9 1.0
C B:LEU192 4.0 80.2 1.0
CA B:ASP191 4.1 98.0 1.0
OD2 B:ASP193 4.1 82.4 1.0
OD2 B:ASP183 4.2 0.9 1.0
CB B:ASP191 4.3 99.4 1.0
CB B:ASP183 4.3 99.0 1.0
OD2 B:ASP191 4.4 98.7 1.0
CA B:ASP183 4.4 90.7 1.0
N B:LEU192 4.4 98.0 1.0
N B:ASP193 4.4 83.6 1.0
CA B:ASP193 4.5 81.8 1.0
CB B:ASP193 4.6 73.6 1.0
CG B:ARG30 4.6 72.6 1.0
CA B:LEU192 4.7 85.9 1.0
CA B:ARG30 4.9 81.6 1.0

Magnesium binding site 2 out of 5 in 6l74

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Magnesium binding site 2 out of 5 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:75.8
occ:1.00
 O D:LYS840 2.4 72.1 1.0
OD2 B:ASP168 3.1 94.3 1.0
OE1 B:GLU154 3.2 90.6 1.0
OD1 B:ASP168 3.3 81.9 1.0
C D:LYS840 3.6 71.9 1.0
CG B:ASP168 3.6 85.2 1.0
CD B:GLU154 4.2 99.4 1.0
N D:TYR841 4.4 73.3 1.0
CA D:TYR841 4.4 71.0 1.0
OE2 B:GLU154 4.5 0.4 1.0
CB B:ALA153 4.5 86.2 1.0
OE2 B:GLU64 4.5 0.3 1.0
CA D:LYS840 4.5 72.5 1.0
O D:LEU839 4.6 71.4 1.0
N D:VAL842 4.6 68.5 1.0
OE1 B:GLU64 4.7 0.2 1.0

Magnesium binding site 3 out of 5 in 6l74

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Magnesium binding site 3 out of 5 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:47.0
occ:1.00
 OD1 D:ASP739 1.9 51.3 1.0
O3' I:A7 2.0 63.4 0.9
OD1 D:ASP741 2.1 54.0 1.0
OD1 D:ASP743 2.1 56.3 1.0
O I:HOH101 2.2 67.9 1.0
O D:HOH2135 2.5 60.6 1.0
CG D:ASP741 2.8 57.0 1.0
OD2 D:ASP741 2.8 65.8 1.0
CG D:ASP743 2.9 53.9 1.0
CG D:ASP739 3.0 56.2 1.0
OD2 D:ASP743 3.0 51.8 1.0
C3' I:A7 3.3 61.8 0.9
OD2 D:ASP739 3.4 59.8 1.0
C4' I:A7 3.7 67.5 0.9
C5' I:A7 4.0 68.0 0.9
O D:ASP739 4.2 52.4 1.0
CB D:ASP741 4.3 53.1 1.0
CB D:ASP739 4.3 56.6 1.0
N D:ASP739 4.3 55.2 1.0
CB D:ASP743 4.4 46.9 1.0
O2' I:A7 4.4 60.8 0.9
C2' I:A7 4.4 64.1 0.9
C D:ASP739 4.4 53.6 1.0
N D:ASP741 4.5 53.5 1.0
CA D:ASP739 4.6 51.8 1.0
N D:ASP743 4.7 47.9 1.0
NH2 D:ARG704 4.8 55.8 1.0
CA D:ASP741 4.8 51.5 1.0
CA D:ASP743 4.9 46.3 1.0
C D:ASP741 5.0 55.2 1.0

Magnesium binding site 4 out of 5 in 6l74

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Magnesium binding site 4 out of 5 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:79.0
occ:1.00
 O D:ILE900 2.6 84.2 1.0
O D:TRP897 2.8 75.6 1.0
C D:ILE900 3.6 72.0 1.0
O D:GLU898 4.0 78.4 1.0
C D:TRP897 4.1 74.0 1.0
C D:GLU898 4.3 73.2 1.0
N D:ILE900 4.4 72.7 1.0
CA D:GLU898 4.5 67.1 1.0
N D:GLN901 4.5 67.5 1.0
CA D:GLN901 4.5 73.7 1.0
CA D:ILE900 4.5 69.3 1.0
N D:LEU902 4.6 77.9 1.0
N D:GLU898 4.8 72.8 1.0
CB D:ILE900 4.9 77.1 1.0
NE1 D:TRP897 4.9 97.6 1.0
CE2 D:TRP897 4.9 94.1 1.0
CD1 D:TRP897 5.0 91.5 1.0

Magnesium binding site 5 out of 5 in 6l74

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Magnesium binding site 5 out of 5 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 2 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:90.5
occ:1.00
 O F:GLY296 2.1 0.0 1.0
O F:ALA292 2.2 0.6 1.0
O F:TRP299 2.9 95.9 1.0
C F:GLY296 3.2 0.4 1.0
C F:ALA292 3.2 0.1 1.0
N F:GLY296 3.7 0.4 1.0
O F:GLU293 3.8 99.6 1.0
CA F:GLU293 3.8 0.6 1.0
N F:GLU293 3.8 0.1 1.0
CA F:GLY296 3.9 0.3 1.0
C F:TRP299 4.0 97.4 1.0
C F:GLU293 4.1 96.5 1.0
N F:PRO297 4.2 0.8 1.0
CB F:TRP299 4.2 94.2 1.0
CA F:ALA292 4.3 98.6 1.0
CA F:PRO297 4.4 0.7 1.0
N F:TRP299 4.5 97.5 1.0
CA F:TRP299 4.5 96.4 1.0
CB F:ALA292 4.5 98.7 1.0
C F:MET295 4.7 0.3 1.0
C F:PRO297 4.9 96.8 1.0
N F:MET295 4.9 94.7 1.0

Reference:

L.Li, V.Molodtsov, W.Lin, R.H.Ebright, Y.Zhang. Rna Extension Drives A Stepwise Displacement of An Initiation-Factor Structural Module in Initial Transcription. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1920747117
Page generated: Tue Oct 1 10:21:47 2024

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