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Magnesium in PDB 6kql: Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 Nt

Enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 Nt

All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 Nt:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 Nt, PDB code: 6kql 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) 44.84 / 2.89
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.802, 103.166, 295.560, 90.00, 99.12, 90.00
R / Rfree (%) 20.7 / 24.6

Other elements in 6kql:

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

Magnesium binding site 1 out of 4 in 6kql

Go back to Magnesium Binding Sites List in 6kql
Magnesium binding site 1 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 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 4 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:41.7
occ:1.00
 O3' I:A7 1.9 50.4 1.0
OD1 D:ASP739 2.0 47.0 1.0
O D:HOH2105 2.1 47.3 1.0
OD1 D:ASP743 2.1 42.1 1.0
OD1 D:ASP741 2.1 48.9 1.0
OD2 D:ASP741 2.4 53.5 1.0
CG D:ASP741 2.6 50.4 1.0
CG D:ASP739 2.8 47.9 1.0
CG D:ASP743 3.0 44.7 1.0
OD2 D:ASP739 3.1 53.0 1.0
OD2 D:ASP743 3.1 40.7 1.0
C3' I:A7 3.2 46.0 1.0
O2' I:A7 3.8 46.6 1.0
C4' I:A7 3.9 47.0 1.0
C2' I:A7 4.0 49.7 1.0
CB D:ASP741 4.1 37.6 1.0
CB D:ASP739 4.2 43.9 1.0
N D:ASP739 4.4 46.9 1.0
CB D:ASP743 4.4 35.4 1.0
C5' I:A7 4.4 48.6 1.0
O D:ASP739 4.5 40.8 1.0
C D:ASP739 4.6 43.3 1.0
CA D:ASP739 4.6 42.9 1.0
N D:ASP741 4.7 41.4 1.0
N D:ASP743 4.7 40.5 1.0
CA D:ASP741 4.8 38.0 1.0
O D:HOH2223 4.9 50.9 1.0
CA D:ASP743 4.9 39.8 1.0
NH2 D:ARG704 5.0 41.5 1.0

Magnesium binding site 2 out of 4 in 6kql

Go back to Magnesium Binding Sites List in 6kql
Magnesium binding site 2 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 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 4 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:72.6
occ:1.00
 O D:LYS840 2.2 64.6 1.0
C D:LYS840 3.3 62.3 1.0
OD2 B:ASP168 4.0 76.2 1.0
OE2 B:GLU154 4.0 81.1 1.0
CA D:LYS840 4.1 64.9 1.0
O D:LEU839 4.2 71.5 1.0
OE1 B:GLU154 4.3 82.9 1.0
OD1 B:ASP168 4.3 67.4 1.0
N D:TYR841 4.4 66.8 1.0
OE2 B:GLU64 4.4 99.2 1.0
OE1 B:GLU64 4.5 94.6 1.0
CG B:ASP168 4.6 71.4 1.0
CA D:TYR841 4.6 60.7 1.0
CD B:GLU154 4.6 84.6 1.0
CD B:GLU64 4.9 0.8 1.0
N D:VAL842 4.9 62.9 1.0
CB B:ALA153 4.9 65.0 1.0

Magnesium binding site 3 out of 4 in 6kql

Go back to Magnesium Binding Sites List in 6kql
Magnesium binding site 3 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Triphosphate Rna of 4 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 4 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:74.5
occ:1.00
 O D:ILE900 2.6 73.6 1.0
O D:HOH2225 2.7 67.8 1.0
O D:TRP897 2.7 64.2 1.0
O D:GLU898 3.4 68.4 1.0
C D:GLU898 3.7 71.0 1.0
C D:TRP897 3.8 63.6 1.0
C D:ILE900 3.8 62.8 1.0
CA D:GLU898 3.9 65.0 1.0
N D:ILE900 4.3 63.8 1.0
N D:GLU898 4.3 61.0 1.0
N D:LEU899 4.5 63.8 1.0
CA D:ILE900 4.6 59.5 1.0
C D:LEU899 4.7 65.0 1.0
N D:GLN901 4.8 55.6 1.0
CA D:GLN901 4.9 56.2 1.0

Magnesium binding site 4 out of 4 in 6kql

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

b:72.0
occ:1.00
 O F:ALA292 2.5 85.2 1.0
O F:GLY296 2.6 84.7 1.0
O F:TRP299 2.8 75.1 1.0
C F:ALA292 3.2 85.5 1.0
C F:GLY296 3.5 89.6 1.0
CA F:GLU293 3.8 82.5 1.0
N F:GLU293 3.8 86.0 1.0
C F:TRP299 4.0 79.1 1.0
O F:GLU293 4.1 87.6 1.0
N F:GLY296 4.2 89.5 1.0
C F:GLU293 4.2 78.8 1.0
CA F:GLY296 4.3 88.1 1.0
CA F:ALA292 4.3 78.6 1.0
CB F:ALA292 4.4 78.3 1.0
CB F:TRP299 4.4 79.3 1.0
N F:PRO297 4.5 95.9 1.0
CA F:TRP299 4.5 81.5 1.0
N F:TRP299 4.6 84.0 1.0
CA F:PRO297 4.7 90.7 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 09:51:38 2024

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