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

Enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 Nt

All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 Nt:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 Nt, PDB code: 6kqn 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) 48.79 / 3.49
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.621, 101.920, 296.110, 90.00, 98.83, 90.00
R / Rfree (%) 21.3 / 25.8

Other elements in 6kqn:

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

Magnesium binding site 1 out of 4 in 6kqn

Go back to Magnesium Binding Sites List in 6kqn
Magnesium binding site 1 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 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 6 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:0.2
occ:1.00
 OD2 B:ASP183 2.5 0.6 1.0
OD1 B:ASP193 3.1 0.4 1.0
O B:ASP191 3.5 0.9 1.0
CG B:ASP183 3.5 0.5 1.0
CG B:ASP193 3.9 1.0 1.0
OD1 B:ASP183 4.0 0.4 1.0
OD2 B:ASP193 4.2 0.7 1.0
CG B:ARG30 4.3 0.2 1.0
C B:ASP191 4.4 0.2 1.0
O B:LEU192 4.6 0.9 1.0
CB B:ASP183 4.7 0.8 1.0
CA B:ASP191 4.9 0.5 1.0

Magnesium binding site 2 out of 4 in 6kqn

Go back to Magnesium Binding Sites List in 6kqn
Magnesium binding site 2 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 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 6 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:84.3
occ:1.00
 O3' I:A7 1.8 91.8 1.0
OD1 D:ASP739 2.0 85.6 1.0
OD1 D:ASP743 2.1 85.7 1.0
OD1 D:ASP741 2.1 78.3 1.0
OD2 D:ASP741 2.6 86.6 1.0
CG D:ASP741 2.7 80.9 1.0
CG D:ASP739 2.8 94.7 1.0
C3' I:A7 2.9 87.0 1.0
OD2 D:ASP739 2.9 0.1 1.0
CG D:ASP743 3.0 82.7 1.0
C4' I:A7 3.2 81.9 1.0
OD2 D:ASP743 3.3 77.0 1.0
C5' I:A7 3.3 85.3 1.0
C2' I:A7 4.1 87.7 1.0
CB D:ASP741 4.2 79.8 1.0
CB D:ASP739 4.2 83.0 1.0
O2' I:A7 4.2 88.4 1.0
CB D:ASP743 4.4 79.0 1.0
N D:ASP743 4.5 83.3 1.0
N D:ASP739 4.6 85.7 1.0
O4' I:A7 4.6 86.1 1.0
O5' I:A7 4.7 91.5 1.0
O D:ASP739 4.7 81.5 1.0
NH2 D:ARG704 4.7 92.2 1.0
CA D:ASP739 4.8 79.7 1.0
N D:ASP741 4.8 79.9 1.0
C D:ASP739 4.8 76.9 1.0
CA D:ASP743 4.8 81.7 1.0
CA D:ASP741 4.8 80.0 1.0
C D:ASP741 5.0 83.1 1.0

Magnesium binding site 3 out of 4 in 6kqn

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Magnesium binding site 3 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 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 6 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:67.6
occ:1.00
 O D:LYS840 2.1 75.5 1.0
C D:LYS840 3.3 91.9 1.0
OD2 B:ASP168 3.5 0.1 1.0
OD1 B:ASP168 3.5 0.6 1.0
OE1 B:GLU154 3.6 0.8 1.0
OE2 B:GLU154 3.7 0.9 1.0
CG B:ASP168 3.9 0.6 1.0
CD B:GLU154 4.1 0.9 1.0
N D:TYR841 4.2 0.3 1.0
CA D:TYR841 4.2 94.4 1.0
CA D:LYS840 4.3 89.4 1.0
CB B:ALA153 4.6 0.8 1.0
O D:LEU839 4.7 84.8 1.0
N D:VAL842 4.8 90.4 1.0
CG D:LYS840 4.8 81.5 1.0
CD2 D:TYR841 4.9 88.7 1.0
OE2 B:GLU64 5.0 0.6 1.0

Magnesium binding site 4 out of 4 in 6kqn

Go back to Magnesium Binding Sites List in 6kqn
Magnesium binding site 4 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 6 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 6 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:1.0
occ:1.00
 O F:TRP299 2.1 0.5 1.0
O F:ALA292 2.2 0.9 1.0
O F:GLY296 2.6 0.2 1.0
C F:ALA292 3.1 0.1 1.0
C F:TRP299 3.2 0.9 1.0
CB F:TRP299 3.7 0.1 1.0
C F:GLY296 3.7 0.7 1.0
CA F:TRP299 3.8 0.9 1.0
N F:TRP299 3.9 0.5 1.0
CB F:ALA292 3.9 0.5 1.0
N F:GLU293 3.9 0.6 1.0
CA F:ALA292 3.9 0.8 1.0
CA F:GLU293 4.1 1.0 1.0
N F:GLY296 4.3 0.8 1.0
N F:ASP300 4.4 0.1 1.0
CA F:GLY296 4.5 0.5 1.0
N F:PRO297 4.6 0.2 1.0
C F:GLU293 4.7 0.9 1.0
O F:GLU293 4.7 0.3 1.0
CA F:ASP300 4.8 0.9 1.0
CA F:PRO297 4.8 0.6 1.0
N F:GLY298 4.9 0.0 1.0
C F:PRO297 5.0 0.3 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 09:51:38 2024

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