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Magnesium in PDB 6lts: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger, PDB code: 6lts was solved by Y.Zhang, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.23 / 3.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.698, 103.847, 295.410, 90.00, 98.61, 90.00
R / Rfree (%) 22 / 25.8

Other elements in 6lts:

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger (pdb code 6lts). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger, PDB code: 6lts:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 6lts

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Magnesium binding site 1 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:0.1
occ:1.00
 OD1 B:ASP193 2.5 0.5 1.0
OD2 B:ASP183 2.7 0.4 1.0
O B:ASP191 3.5 0.0 1.0
OD1 B:ASP191 3.6 0.4 1.0
CG B:ASP193 3.6 0.3 1.0
CG B:ASP183 3.7 0.8 1.0
OD2 B:ASP193 4.0 97.0 1.0
OD1 B:ASP183 4.1 0.3 1.0
CG B:ARG30 4.1 0.2 1.0
O B:LEU192 4.3 0.6 1.0
C B:ASP191 4.5 0.1 1.0
C B:LEU192 4.7 0.4 1.0
CG B:ASP191 4.7 0.7 1.0
N B:GLY31 4.8 93.5 1.0
CB B:ASP193 4.8 96.5 1.0
CA B:ASP193 4.9 97.5 1.0
CB B:ASP183 4.9 0.8 1.0
CA B:ARG30 4.9 93.6 1.0
CA B:ASP183 4.9 0.7 1.0
CB B:ARG30 5.0 100.0 1.0

Magnesium binding site 2 out of 5 in 6lts

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Magnesium binding site 2 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:53.5
occ:1.00
 OD1 D:ASP739 2.2 64.1 1.0
OD1 D:ASP743 2.4 64.6 1.0
OD1 D:ASP741 2.4 55.1 1.0
OD2 D:ASP741 2.7 58.8 1.0
CG D:ASP741 2.9 56.0 1.0
CG D:ASP739 3.1 70.1 1.0
CG D:ASP743 3.1 60.3 1.0
OD2 D:ASP743 3.2 54.2 1.0
OD2 D:ASP739 3.4 76.2 1.0
CB D:ASP741 4.4 55.2 1.0
CB D:ASP739 4.5 56.0 1.0
CB D:ASP743 4.6 54.5 1.0
N D:ASP739 4.6 66.8 1.0
O D:ASP739 4.6 58.6 1.0
NH2 D:ARG704 4.7 60.4 1.0
C D:ASP739 4.8 55.0 1.0
CA D:ASP739 4.9 56.3 1.0
N D:ASP743 5.0 54.5 1.0

Magnesium binding site 3 out of 5 in 6lts

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Magnesium binding site 3 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:62.0
occ:1.00
 O D:LYS840 2.0 71.6 1.0
C D:LYS840 3.1 77.6 1.0
OD2 B:ASP168 3.4 90.1 1.0
N D:TYR841 3.9 82.0 1.0
CA D:TYR841 4.0 77.4 1.0
O D:LEU839 4.0 72.8 1.0
OD1 B:ASP168 4.1 98.6 1.0
CA D:LYS840 4.1 76.3 1.0
OE2 B:GLU154 4.1 96.6 1.0
CG B:ASP168 4.1 95.2 1.0
N D:VAL842 4.2 80.7 1.0
OE1 B:GLU64 4.3 0.2 1.0
C D:TYR841 4.6 75.7 1.0
OE2 B:GLU64 4.6 0.7 1.0
CD B:GLU64 4.9 1.0 1.0
C D:LEU839 4.9 78.8 1.0
OE1 B:GLU154 4.9 0.7 1.0
CD B:GLU154 4.9 0.7 1.0

Magnesium binding site 4 out of 5 in 6lts

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Magnesium binding site 4 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:91.2
occ:1.00
 O D:TRP897 2.4 82.2 1.0
O D:ILE900 3.0 84.6 1.0
C D:TRP897 3.6 85.0 1.0
O D:GLU898 3.6 91.1 1.0
C D:GLU898 3.9 85.4 1.0
CA D:GLU898 4.0 81.7 1.0
C D:ILE900 4.1 76.2 1.0
N D:GLU898 4.3 82.9 1.0
NE1 D:TRP897 4.4 89.4 1.0
CD1 D:TRP897 4.5 88.2 1.0
N D:ILE900 4.6 77.4 1.0
CE2 D:TRP897 4.6 92.4 1.0
CG D:TRP897 4.7 87.0 1.0
CA D:TRP897 4.7 89.0 1.0
CD2 D:TRP897 4.7 90.7 1.0
CA D:ILE900 4.8 72.3 1.0
N D:LEU899 4.8 84.3 1.0
CB D:ILE900 5.0 78.3 1.0

Magnesium binding site 5 out of 5 in 6lts

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Magnesium binding site 5 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex Comprising A Truncated Sigma Finger within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:91.7
occ:1.00
 O F:GLY296 2.5 0.5 1.0
O F:TRP299 2.5 92.1 1.0
O F:ALA292 2.8 0.8 1.0
C F:GLY296 3.5 0.7 1.0
C F:ALA292 3.6 0.9 1.0
C F:TRP299 3.7 95.2 1.0
CA F:GLU293 4.1 94.6 1.0
N F:GLU293 4.2 97.8 1.0
N F:TRP299 4.3 96.2 1.0
CA F:TRP299 4.3 93.0 1.0
CA F:GLY296 4.4 1.0 1.0
CB F:TRP299 4.4 89.9 1.0
N F:PRO297 4.4 0.5 1.0
N F:GLY296 4.4 0.4 1.0
CA F:PRO297 4.5 0.1 1.0
O F:GLU293 4.6 0.8 1.0
CA F:ALA292 4.6 98.3 1.0
CB F:ALA292 4.6 96.2 1.0
C F:GLU293 4.7 95.7 1.0
N F:ASP300 4.7 96.9 1.0
C F:PRO297 5.0 99.7 1.0
N F:GLY298 5.0 96.8 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 10:36:13 2024

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