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

Go back to Magnesium Binding Sites List in 6lts
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

Go back to Magnesium Binding Sites List in 6lts
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

Go back to Magnesium Binding Sites List in 6lts
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

Go back to Magnesium Binding Sites List in 6lts
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

Go back to Magnesium Binding Sites List in 6lts
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: Mon Dec 14 23:14:18 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy