Magnesium in PDB 6kqh: Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt

Enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt

All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt, PDB code: 6kqh 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) 39.82 / 3.18
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.007, 103.566, 294.935, 90.00, 99.20, 90.00
R / Rfree (%) 20.3 / 24.7

Other elements in 6kqh:

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 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 7 Nt (pdb code 6kqh). 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 7 Nt, PDB code: 6kqh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6kqh

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Magnesium binding site 1 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 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 7 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:73.4
occ:1.00
O B:ASP191 2.4 81.0 1.0
OD1 B:ASP183 2.7 83.2 1.0
OD1 B:ASP193 3.1 74.1 1.0
C B:ASP191 3.3 82.5 1.0
CG B:ASP183 3.7 78.3 1.0
CA B:ASP191 3.8 90.3 1.0
CG B:ARG30 4.0 59.0 1.0
O B:LEU192 4.0 66.7 1.0
CB B:ASP191 4.1 95.0 1.0
O B:HOH2101 4.2 73.3 1.0
OD2 B:ASP183 4.2 81.8 1.0
N B:LEU192 4.3 79.4 1.0
C B:LEU192 4.3 70.4 1.0
CG B:ASP193 4.4 62.4 1.0
CB B:ARG30 4.6 62.3 1.0
CD B:ARG30 4.8 60.1 1.0
CA B:LEU192 4.8 71.7 1.0
CA B:ARG30 4.8 60.7 1.0
CB B:ASP183 4.8 72.6 1.0
N B:ASP193 4.9 65.3 1.0

Magnesium binding site 2 out of 4 in 6kqh

Go back to Magnesium Binding Sites List in 6kqh
Magnesium binding site 2 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 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 7 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:45.3
occ:1.00
O B:HOH2108 2.0 45.3 1.0
O B:HOH2106 2.1 47.5 1.0
O D:HOH2108 2.5 44.7 1.0
O D:LYS840 2.6 32.7 1.0
OD2 B:ASP168 3.4 48.0 1.0
OD1 B:ASP168 3.6 49.3 1.0
C D:LYS840 3.8 41.5 1.0
OE1 B:GLU154 3.8 57.9 1.0
CG B:ASP168 3.9 47.3 1.0
OE2 B:GLU154 4.3 59.4 1.0
OE1 B:GLU64 4.3 75.7 1.0
OE2 B:GLU64 4.3 70.2 1.0
CB B:ALA153 4.3 48.9 1.0
CD B:GLU154 4.5 62.3 1.0
CA D:LYS840 4.5 42.6 1.0
O D:LEU839 4.6 47.0 1.0
N D:TYR841 4.7 49.6 1.0
CD B:GLU64 4.7 78.0 1.0
CA D:TYR841 4.8 42.6 1.0
N D:VAL842 4.9 42.3 1.0

Magnesium binding site 3 out of 4 in 6kqh

Go back to Magnesium Binding Sites List in 6kqh
Magnesium binding site 3 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 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 7 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:23.7
occ:1.00
OD1 D:ASP739 2.0 31.2 1.0
O D:HOH2124 2.0 29.8 1.0
OD1 D:ASP741 2.0 30.9 1.0
OD1 D:ASP743 2.2 28.9 1.0
O D:HOH2119 2.4 26.7 1.0
O3' I:A7 2.6 37.4 1.0
CG D:ASP741 2.8 31.8 1.0
OD2 D:ASP741 2.9 34.0 1.0
CG D:ASP739 2.9 33.2 1.0
CG D:ASP743 3.0 27.9 1.0
OD2 D:ASP743 3.1 25.5 1.0
OD2 D:ASP739 3.2 30.7 1.0
C5' I:A7 3.5 34.1 1.0
C3' I:A7 3.5 36.3 1.0
C4' I:A7 3.8 33.6 1.0
CB D:ASP741 4.2 27.5 1.0
CB D:ASP739 4.3 29.1 1.0
O5' I:A7 4.4 42.2 1.0
CB D:ASP743 4.4 25.0 1.0
N D:ASP739 4.5 25.1 1.0
N D:ASP741 4.5 27.0 1.0
O D:ASP739 4.5 30.9 1.0
N D:ASP743 4.5 26.2 1.0
C D:ASP739 4.6 28.2 1.0
CA D:ASP739 4.7 23.4 1.0
CA D:ASP741 4.7 24.6 1.0
NH2 D:ARG704 4.8 25.1 1.0
C D:ASP741 4.8 31.4 1.0
CA D:ASP743 4.8 27.7 1.0
C2' I:A7 4.9 40.4 1.0
N D:GLY742 4.9 28.3 1.0

Magnesium binding site 4 out of 4 in 6kqh

Go back to Magnesium Binding Sites List in 6kqh
Magnesium binding site 4 out of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 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 7 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:70.6
occ:1.00
O F:ALA292 2.4 73.3 1.0
O F:GLY296 2.5 76.3 1.0
O F:TRP299 3.1 61.6 1.0
C F:GLY296 3.4 81.8 1.0
C F:ALA292 3.4 70.5 1.0
CA F:GLU293 3.7 66.2 1.0
N F:GLU293 3.9 70.6 1.0
N F:GLY296 4.0 78.7 1.0
CA F:GLY296 4.0 82.8 1.0
O F:GLU293 4.1 63.3 1.0
C F:GLU293 4.2 59.4 1.0
C F:TRP299 4.2 65.9 1.0
N F:PRO297 4.3 76.2 1.0
CA F:PRO297 4.5 73.3 1.0
CB F:TRP299 4.5 63.2 1.0
CA F:ALA292 4.5 68.3 1.0
N F:TRP299 4.6 67.1 1.0
CA F:TRP299 4.7 66.2 1.0
CB F:ALA292 4.8 68.8 1.0
CB F:GLU293 5.0 77.4 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: Mon Dec 14 23:09:08 2020

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