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

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

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

Protein crystallography data

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 5 Nt, PDB code: 6kqf 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) 48.85 / 2.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.644, 103.640, 296.186, 90.00, 98.95, 90.00
R / Rfree (%) 19.9 / 23

Other elements in 6kqf:

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

Magnesium binding site 1 out of 4 in 6kqf

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

b:64.2
occ:1.00
 OD1 B:ASP183 2.6 87.5 1.0
OD1 B:ASP193 2.6 68.4 1.0
O B:ASP191 2.8 61.3 1.0
O B:HOH2115 3.0 60.4 1.0
O B:LEU192 3.2 58.2 1.0
C B:ASP191 3.4 67.8 1.0
CG B:ASP183 3.5 83.5 1.0
C B:LEU192 3.7 58.7 1.0
CG B:ASP193 3.9 61.9 1.0
CA B:ASP191 4.1 76.1 1.0
N B:LEU192 4.1 66.8 1.0
OD2 B:ASP183 4.2 77.7 1.0
CA B:ASP183 4.3 66.2 1.0
CB B:ASP183 4.3 69.8 1.0
N B:ASP193 4.3 54.8 1.0
CG B:ARG30 4.3 56.9 1.0
CA B:LEU192 4.4 56.9 1.0
CA B:ASP193 4.5 52.0 1.0
CB B:ASP191 4.6 84.5 1.0
OD2 B:ASP193 4.6 58.3 1.0
CA B:ARG30 4.8 55.5 1.0
CB B:ASP193 4.8 55.0 1.0
CB B:ARG30 4.9 55.2 1.0

Magnesium binding site 2 out of 4 in 6kqf

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

b:37.5
occ:1.00
 OD1 D:ASP739 2.0 42.0 1.0
O D:HOH2122 2.1 35.3 1.0
O3' I:A5 2.1 45.5 1.0
O D:HOH2173 2.1 34.5 1.0
OD1 D:ASP741 2.1 38.7 1.0
OD1 D:ASP743 2.1 39.7 1.0
CG D:ASP741 2.9 39.1 1.0
CG D:ASP739 3.0 37.5 1.0
CG D:ASP743 3.0 37.3 1.0
OD2 D:ASP741 3.1 45.5 1.0
OD2 D:ASP743 3.3 35.2 1.0
OD2 D:ASP739 3.4 44.4 1.0
C3' I:A5 3.5 51.9 1.0
C4' I:A5 4.1 49.2 1.0
O2' I:A5 4.1 42.3 1.0
O I:HOH104 4.2 62.9 1.0
O D:HOH2149 4.3 41.6 1.0
CB D:ASP741 4.3 34.5 1.0
C2' I:A5 4.3 43.2 1.0
CB D:ASP739 4.4 27.1 1.0
N D:ASP741 4.4 31.1 1.0
CB D:ASP743 4.4 33.1 1.0
N D:ASP739 4.5 33.6 1.0
C D:ASP739 4.5 31.8 1.0
O D:ASP739 4.5 36.1 1.0
C5' I:A5 4.6 42.1 1.0
N D:ASP743 4.6 33.0 1.0
CA D:ASP739 4.7 33.6 1.0
CA D:ASP741 4.7 32.5 1.0
C D:ASP741 4.8 35.9 1.0
CA D:ASP743 4.9 29.8 1.0

Magnesium binding site 3 out of 4 in 6kqf

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

b:74.6
occ:1.00
 O D:HOH2188 2.1 54.2 1.0
O D:HOH2182 2.1 68.1 1.0
O B:HOH2103 2.1 57.9 1.0
O B:HOH2123 2.1 72.0 1.0
O B:HOH2106 2.1 59.8 1.0
O D:LYS840 2.2 55.0 1.0
C D:LYS840 3.3 52.8 1.0
OD2 B:ASP168 3.8 59.4 1.0
OD1 B:ASP168 4.0 59.5 1.0
CA D:LYS840 4.1 53.2 1.0
OE2 B:GLU154 4.2 80.0 1.0
N D:TYR841 4.3 56.8 1.0
O D:LEU839 4.3 55.7 1.0
CG B:ASP168 4.4 61.9 1.0
O B:HOH2112 4.4 61.1 1.0
CA D:TYR841 4.4 56.4 1.0
OE1 B:GLU154 4.5 66.8 1.0
OE2 B:GLU64 4.5 85.3 1.0
N D:VAL842 4.6 51.8 1.0
O B:HOH2105 4.8 72.8 1.0
OE1 B:GLU64 4.8 90.2 1.0
CD B:GLU154 4.8 77.3 1.0
CB B:ALA153 4.8 63.6 1.0
CG D:LYS840 5.0 50.2 1.0

Magnesium binding site 4 out of 4 in 6kqf

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

b:52.1
occ:1.00
 O F:HOH2117 2.0 57.6 1.0
O F:TRP299 2.4 51.6 1.0
O F:GLY296 2.7 59.0 1.0
O F:ALA292 3.0 54.3 1.0
C F:TRP299 3.6 52.8 1.0
C F:ALA292 3.6 52.0 1.0
C F:GLY296 3.7 63.7 1.0
N F:GLU293 4.1 53.7 1.0
CA F:GLU293 4.2 50.5 1.0
N F:TRP299 4.2 57.1 1.0
CA F:TRP299 4.2 53.0 1.0
CB F:TRP299 4.2 49.0 1.0
CB F:ALA292 4.4 51.8 1.0
N F:PRO297 4.4 64.0 1.0
N F:GLY296 4.5 61.4 1.0
CA F:GLY296 4.5 65.6 1.0
CA F:PRO297 4.5 63.0 1.0
CA F:ALA292 4.5 53.0 1.0
O F:GLU293 4.6 59.8 1.0
N F:ASP300 4.7 50.8 1.0
C F:GLU293 4.7 53.3 1.0
N F:GLY298 4.9 53.4 1.0
C F:PRO297 5.0 58.4 1.0
CA F:ASP300 5.0 57.6 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 07:34:16 2024

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