Magnesium in PDB 7eh0: Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp

Enzymatic activity of Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp, PDB code: 7eh0 was solved by L.Li, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.75 / 2.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.784, 103.433, 295.626, 90, 98.95, 90
R / Rfree (%) 20.3 / 24.3

Other elements in 7eh0:

The structure of Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp (pdb code 7eh0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp, PDB code: 7eh0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7eh0

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Magnesium binding site 1 out of 5 in the Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:77.0
occ:1.00
 OD1 B:ASP191 2.2 86.3 1.0
OD1 B:ASP183 2.2 90.0 1.0
OD1 B:ASP193 2.3 85.6 1.0
O B:ASP191 2.8 75.2 1.0
CG B:ASP191 3.3 89.5 1.0
C B:ASP191 3.3 79.0 1.0
CG B:ASP183 3.5 87.6 1.0
O B:LEU192 3.5 65.8 1.0
CG B:ASP193 3.5 73.0 1.0
C B:LEU192 3.7 64.0 1.0
CA B:ASP191 3.9 82.0 1.0
N B:LEU192 4.0 76.3 1.0
N B:ASP193 4.1 64.5 1.0
OD2 B:ASP191 4.1 86.5 1.0
CB B:ASP191 4.1 83.2 1.0
CA B:ASP193 4.2 64.7 1.0
CA B:LEU192 4.3 70.1 1.0
OD2 B:ASP193 4.3 68.3 1.0
OD2 B:ASP183 4.3 98.4 1.0
CA B:ASP183 4.3 73.5 1.0
CB B:ASP183 4.4 76.9 1.0
CB B:ASP193 4.5 60.1 1.0
CG B:ARG30 4.5 56.1 1.0
CA B:ARG30 4.8 64.5 1.0

Magnesium binding site 2 out of 5 in 7eh0

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Magnesium binding site 2 out of 5 in the Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:40.1
occ:1.00
 O3' I:A2 1.8 58.9 0.8
OD1 D:ASP739 2.1 48.9 1.0
OD1 D:ASP741 2.2 41.7 1.0
OD1 D:ASP743 2.2 45.1 1.0
OD2 D:ASP741 2.8 50.4 1.0
CG D:ASP741 2.8 45.5 1.0
CG D:ASP743 3.0 41.2 1.0
CG D:ASP739 3.0 42.0 1.0
OD2 D:ASP743 3.0 37.5 1.0
OD2 D:ASP739 3.2 47.0 1.0
C3' I:A2 3.2 66.0 0.8
O1A D:2TM2006 3.8 89.8 0.8
C4' I:A2 3.9 66.9 0.8
O2' I:A2 4.1 52.8 0.8
C2' I:A2 4.2 65.2 0.8
CB D:ASP741 4.3 35.5 1.0
CB D:ASP739 4.4 46.7 1.0
C5' I:A2 4.4 67.8 0.8
C4' D:2TM2006 4.4 70.3 0.8
N D:ASP739 4.5 37.2 1.0
CB D:ASP743 4.5 31.1 1.0
C5' D:2TM2006 4.5 75.9 0.8
O4' D:2TM2006 4.7 68.6 0.8
N D:ASP741 4.7 38.8 1.0
O D:ASP739 4.7 37.0 1.0
C D:ASP739 4.8 38.6 1.0
CA D:ASP739 4.8 39.5 1.0
NH2 D:ARG704 4.8 43.8 1.0
N D:ASP743 4.8 38.6 1.0
O5' D:2TM2006 4.9 96.3 0.8
CA D:ASP741 4.9 33.9 1.0
PA D:2TM2006 5.0 107.8 0.8
CA D:ASP743 5.0 35.0 1.0

Magnesium binding site 3 out of 5 in 7eh0

Go back to Magnesium Binding Sites List in 7eh0
Magnesium binding site 3 out of 5 in the Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:59.3
occ:1.00
 O D:LYS840 2.2 61.2 1.0
C D:LYS840 3.3 53.5 1.0
OD2 B:ASP168 3.6 64.8 1.0
OE1 B:GLU154 3.7 81.5 1.0
OD1 B:ASP168 4.0 58.1 1.0
O D:LEU839 4.1 61.7 1.0
CA D:LYS840 4.1 55.4 1.0
CG B:ASP168 4.2 64.0 1.0
N D:TYR841 4.2 56.5 1.0
OE2 B:GLU64 4.4 98.3 1.0
OE2 B:GLU154 4.4 83.1 1.0
CA D:TYR841 4.5 53.1 1.0
CD B:GLU154 4.5 82.6 1.0
N D:VAL842 4.6 50.3 1.0
OE1 B:GLU64 4.8 73.5 1.0
CB B:ALA153 4.9 59.6 1.0
C D:LEU839 5.0 59.2 1.0

Magnesium binding site 4 out of 5 in 7eh0

Go back to Magnesium Binding Sites List in 7eh0
Magnesium binding site 4 out of 5 in the Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:65.6
occ:1.00
 O D:TRP897 2.6 61.5 1.0
O D:ILE900 2.7 71.3 1.0
O D:GLU898 3.2 67.7 1.0
C D:GLU898 3.6 64.1 1.0
C D:TRP897 3.7 60.3 1.0
CA D:GLU898 3.8 55.5 1.0
C D:ILE900 3.9 57.8 1.0
N D:ILE900 4.2 61.5 1.0
N D:GLU898 4.2 54.3 1.0
N D:LEU899 4.5 60.5 1.0
CA D:ILE900 4.6 55.5 1.0
C D:LEU899 4.7 58.6 1.0
CD1 D:TRP897 4.7 73.8 1.0
NE1 D:TRP897 4.8 75.9 1.0
N D:GLN901 4.9 52.1 1.0
CA D:TRP897 5.0 62.8 1.0

Magnesium binding site 5 out of 5 in 7eh0

Go back to Magnesium Binding Sites List in 7eh0
Magnesium binding site 5 out of 5 in the Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus Rna Polymerase Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Upa Rna Primer and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:69.5
occ:1.00
 O F:GLY296 2.3 79.0 1.0
O F:TRP299 2.5 75.6 1.0
O F:ALA292 2.7 76.3 1.0
C F:ALA292 3.5 73.3 1.0
C F:GLY296 3.5 79.1 1.0
C F:TRP299 3.7 72.0 1.0
N F:GLU293 4.1 68.4 1.0
CA F:GLU293 4.1 73.2 1.0
CB F:TRP299 4.2 74.8 1.0
CA F:TRP299 4.3 74.3 1.0
N F:GLY296 4.3 77.4 1.0
N F:TRP299 4.3 73.5 1.0
CB F:ALA292 4.4 68.2 1.0
CA F:GLY296 4.4 75.4 1.0
N F:PRO297 4.4 79.8 1.0
CA F:ALA292 4.4 68.7 1.0
O F:GLU293 4.4 76.6 1.0
CA F:PRO297 4.4 74.9 1.0
C F:GLU293 4.6 72.2 1.0
N F:ASP300 4.7 66.3 1.0
C F:PRO297 5.0 72.6 1.0

Reference:

K.S.Skalenko, L.Li, Y.Zhang, I.O.Vvedenskaya, J.T.Winkelman, A.L.Cope, D.M.Taylor, P.Shah, R.H.Ebright, J.B.Kinney, Y.Zhang, B.E.Nickels. Promoter-Sequence Determinants and Structural Basis of Primer-Dependent Transcription Initiation in Escherichia Coli . Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34187896
DOI: 10.1073/PNAS.2106388118
Page generated: Sat Aug 21 16:24:10 2021

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