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

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

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

Protein crystallography data

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 5 Nt, PDB code: 6kqm 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) 48.89 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.730, 102.750, 295.710, 90.00, 98.86, 90.00
R / Rfree (%) 20.5 / 25.2

Other elements in 6kqm:

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 5 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 5 Nt (pdb code 6kqm). 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 5 Nt, PDB code: 6kqm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6kqm

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

b:54.4
occ:1.00
 OD2 B:ASP183 3.0 70.6 1.0
O B:ASP191 3.2 62.5 1.0
OD1 B:ASP193 3.2 73.5 1.0
CG B:ASP183 4.0 71.7 1.0
CG B:ARG30 4.1 56.5 1.0
C B:ASP191 4.2 63.5 1.0
CG B:ASP193 4.3 58.9 1.0
OD1 B:ASP183 4.4 77.8 1.0
OD2 B:ASP193 4.6 42.8 1.0
CA B:ASP191 4.7 62.9 1.0
O B:LEU192 4.8 56.8 1.0
CB B:ASP191 4.8 73.3 1.0
CD B:ARG30 5.0 49.2 1.0

Magnesium binding site 2 out of 4 in 6kqm

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

b:8.7
occ:1.00
 O3' I:A5 1.9 13.8 1.0
OD1 D:ASP739 2.0 10.4 1.0
OD1 D:ASP743 2.1 13.0 1.0
OD1 D:ASP741 2.2 11.9 1.0
OD2 D:ASP741 2.5 12.7 1.0
CG D:ASP741 2.7 12.8 1.0
CG D:ASP743 2.9 10.9 1.0
CG D:ASP739 2.9 12.8 1.0
OD2 D:ASP743 3.0 8.7 1.0
C3' I:A5 3.1 11.1 1.0
OD2 D:ASP739 3.2 13.3 1.0
O D:HOH2120 3.2 13.5 1.0
C4' I:A5 3.5 6.9 1.0
C5' I:A5 3.9 10.6 1.0
O2' I:A5 4.1 9.9 1.0
CB D:ASP741 4.2 9.7 1.0
C2' I:A5 4.2 10.8 1.0
CB D:ASP739 4.3 12.3 1.0
CB D:ASP743 4.4 10.5 1.0
O D:ASP739 4.4 10.8 1.0
N D:ASP739 4.4 7.4 1.0
NH2 D:ARG704 4.6 7.7 1.0
C D:ASP739 4.6 9.4 1.0
CA D:ASP739 4.7 7.3 1.0
N D:ASP743 4.7 7.3 1.0
N D:ASP741 4.7 7.3 1.0
CA D:ASP741 4.9 7.2 1.0
CA D:ASP743 4.9 10.5 1.0
O4' I:A5 4.9 6.2 1.0

Magnesium binding site 3 out of 4 in 6kqm

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

b:28.6
occ:1.00
 O D:LYS840 2.1 28.2 1.0
O D:HOH2126 2.4 28.2 1.0
C D:LYS840 3.3 36.5 1.0
OE1 B:GLU154 3.5 57.6 1.0
OD2 B:ASP168 3.6 35.3 1.0
OE2 B:GLU154 3.7 55.7 1.0
OD1 B:ASP168 3.7 43.8 1.0
CD B:GLU154 4.0 58.4 1.0
CG B:ASP168 4.1 37.9 1.0
CA D:LYS840 4.2 34.2 1.0
N D:TYR841 4.2 40.7 1.0
CA D:TYR841 4.3 35.5 1.0
O D:LEU839 4.5 34.0 1.0
CB B:ALA153 4.6 43.7 1.0
N D:VAL842 4.8 32.8 1.0
OE2 B:GLU64 4.8 70.7 1.0
CG D:LYS840 4.9 34.7 1.0

Magnesium binding site 4 out of 4 in 6kqm

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

b:48.3
occ:1.00
 O F:GLY296 2.4 67.7 1.0
O F:ALA292 2.6 61.2 1.0
O F:TRP299 2.9 48.4 1.0
C F:GLY296 3.4 65.3 1.0
C F:ALA292 3.5 62.3 1.0
CA F:GLU293 3.9 62.5 1.0
C F:TRP299 4.0 53.4 1.0
O F:GLU293 4.0 50.5 1.0
N F:GLU293 4.1 67.4 1.0
N F:GLY296 4.3 71.3 1.0
N F:PRO297 4.3 67.4 1.0
CA F:GLY296 4.3 68.0 1.0
CB F:TRP299 4.3 47.5 1.0
C F:GLU293 4.3 55.1 1.0
CA F:PRO297 4.4 65.2 1.0
N F:TRP299 4.4 56.1 1.0
CA F:TRP299 4.5 52.3 1.0
CA F:ALA292 4.6 55.0 1.0
CB F:ALA292 4.8 48.5 1.0
C F:PRO297 4.9 58.9 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 09:51:37 2024

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