Atomistry » Magnesium » PDB 7efn-7en1 » 7eh1
Atomistry »
  Magnesium »
    PDB 7efn-7en1 »
      7eh1 »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy