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Magnesium in PDB 7eh1: Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg Rna Primer, and Cmpcpp

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

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

Protein crystallography data

The structure of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg Rna Primer, and Cmpcpp, PDB code: 7eh1 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) 25.27 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.124, 103.319, 295.646, 90, 98.96, 90
R / Rfree (%) 19.1 / 25.3

Other elements in 7eh1:

The structure of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg 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 Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg Rna Primer, and Cmpcpp (pdb code 7eh1). 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 Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg Rna Primer, and Cmpcpp, PDB code: 7eh1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7eh1

Go back to Magnesium Binding Sites List in 7eh1
Magnesium binding site 1 out of 5 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg 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 Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg Rna Primer, and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:57.3
occ:1.00
 OD1 B:ASP183 2.3 67.5 1.0
OD1 B:ASP191 2.5 65.1 1.0
OD1 B:ASP193 2.6 51.6 1.0
O B:ASP191 3.2 45.1 1.0
O B:LEU192 3.4 45.6 1.0
CG B:ASP183 3.5 60.5 1.0
C B:ASP191 3.7 50.1 1.0
CG B:ASP191 3.7 69.3 1.0
CG B:ASP193 3.8 47.6 1.0
C B:LEU192 4.0 43.0 1.0
CA B:ASP191 4.2 51.3 1.0
CB B:ASP183 4.3 48.7 1.0
OD2 B:ASP183 4.3 64.7 1.0
N B:LEU192 4.4 51.4 1.0
CA B:ASP183 4.4 46.4 1.0
CB B:ASP191 4.5 59.2 1.0
N B:ASP193 4.6 38.8 1.0
OD2 B:ASP193 4.6 45.9 1.0
CG B:ARG30 4.6 38.6 1.0
CA B:ASP193 4.6 38.0 1.0
CA B:LEU192 4.6 45.8 1.0
OD2 B:ASP191 4.7 61.6 1.0
CB B:ASP193 4.9 36.5 1.0
CA B:ARG30 4.9 31.0 1.0
CB B:ARG30 5.0 41.3 1.0

Magnesium binding site 2 out of 5 in 7eh1

Go back to Magnesium Binding Sites List in 7eh1
Magnesium binding site 2 out of 5 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg 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 Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg Rna Primer, and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2003

b:41.1
occ:1.00
 O D:LYS840 2.2 44.8 1.0
OE1 B:GLU154 2.9 53.7 1.0
OD2 B:ASP168 3.3 42.0 1.0
C D:LYS840 3.4 41.2 1.0
OD1 B:ASP168 3.8 40.5 1.0
CG B:ASP168 3.9 39.8 1.0
CD B:GLU154 4.1 60.1 1.0
CA D:LYS840 4.3 40.9 1.0
O D:LEU839 4.3 43.6 1.0
N D:TYR841 4.4 43.1 1.0
OE2 B:GLU154 4.5 58.3 1.0
N D:VAL842 4.5 32.0 1.0
CA D:TYR841 4.5 40.4 1.0
OE1 B:GLU64 4.6 60.6 1.0
OE2 B:GLU64 4.7 76.0 1.0
CB B:ALA153 4.8 51.3 1.0

Magnesium binding site 3 out of 5 in 7eh1

Go back to Magnesium Binding Sites List in 7eh1
Magnesium binding site 3 out of 5 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg 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 Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg Rna Primer, and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg2001

b:20.2
occ:1.00
 CD C:ARG640 3.2 57.1 1.0
O C:ILE572 3.5 22.2 1.0
NE C:ARG640 3.7 58.7 1.0
OD2 A:ASP74 3.7 44.1 1.0
CG1 A:VAL76 4.1 23.1 1.0
OD1 A:ASP74 4.1 49.3 1.0
CZ C:ARG640 4.3 53.8 1.0
CG A:ASP74 4.3 41.8 1.0
NH1 C:ARG640 4.4 51.2 1.0
C C:ILE572 4.5 22.7 1.0
CG C:ARG640 4.5 53.8 1.0
CB C:ILE572 4.7 17.7 1.0
CA C:ILE572 4.7 20.2 1.0
CB A:VAL76 4.9 31.4 1.0
OD2 C:ASP638 5.0 54.7 1.0

Magnesium binding site 4 out of 5 in 7eh1

Go back to Magnesium Binding Sites List in 7eh1
Magnesium binding site 4 out of 5 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg 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 Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg Rna Primer, and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:8.9
occ:1.00
 O3' I:G2 2.0 21.8 0.8
OD1 D:ASP739 2.0 15.1 1.0
OD1 D:ASP743 2.2 14.7 1.0
OD1 D:ASP741 2.3 14.1 1.0
CG D:ASP739 2.8 17.1 1.0
OD2 D:ASP739 2.9 26.7 1.0
CG D:ASP741 3.0 15.9 1.0
OD2 D:ASP741 3.0 25.3 1.0
CG D:ASP743 3.1 15.5 1.0
OD2 D:ASP743 3.2 16.6 1.0
C3' I:G2 3.3 19.6 0.8
C4' I:G2 3.9 19.1 0.8
O2' I:G2 3.9 16.4 0.8
C2' I:G2 4.2 17.5 0.8
CB D:ASP739 4.2 14.3 1.0
C5' I:G2 4.4 18.5 0.8
CB D:ASP741 4.4 11.6 1.0
O D:ASP739 4.5 17.9 1.0
CB D:ASP743 4.5 11.0 1.0
C5' I:2TM2101 4.5 30.3 0.8
N D:ASP739 4.6 12.5 1.0
C D:ASP739 4.7 16.7 1.0
O1A I:2TM2101 4.7 53.5 0.8
N D:ASP741 4.7 12.9 1.0
CA D:ASP739 4.8 13.1 1.0
C1 I:2TM2101 4.8 47.5 0.8
O5' I:2TM2101 4.8 49.3 0.8
C4' I:2TM2101 4.8 30.3 0.8
N D:ASP743 4.9 11.7 1.0
CA D:ASP741 5.0 9.9 1.0
O4' I:2TM2101 5.0 29.8 0.8

Magnesium binding site 5 out of 5 in 7eh1

Go back to Magnesium Binding Sites List in 7eh1
Magnesium binding site 5 out of 5 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg 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 Transcription Initiation Complex Containing A Template-Strand Purine at Position Tss-2, Gpg Rna Primer, and Cmpcpp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:28.6
occ:1.00
 O F:GLY296 2.6 47.9 1.0
O F:TRP299 2.8 50.1 1.0
O F:ALA292 3.0 52.3 1.0
C F:ALA292 3.5 51.5 1.0
CA F:GLU293 3.7 53.3 1.0
N F:GLU293 3.8 53.4 1.0
C F:GLY296 3.9 49.2 1.0
C F:TRP299 4.0 43.3 1.0
O F:GLU293 4.2 48.9 1.0
CB F:ALA292 4.4 39.0 1.0
C F:GLU293 4.4 44.9 1.0
CA F:ALA292 4.5 41.8 1.0
CA F:PRO297 4.6 55.0 1.0
CB F:TRP299 4.6 43.7 1.0
N F:PRO297 4.7 56.9 1.0
CA F:TRP299 4.7 42.4 1.0
N F:TRP299 4.8 47.3 1.0
N F:GLY296 4.8 55.2 1.0
CA F:GLY296 4.9 51.5 1.0
CB F:GLU293 4.9 58.4 1.0
N F:ASP300 5.0 39.0 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: Wed Oct 2 20:42:44 2024

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