Atomistry » Magnesium » PDB 5ds5-5e75 » 5e17
Atomistry »
  Magnesium »
    PDB 5ds5-5e75 »
      5e17 »

Magnesium in PDB 5e17: T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)

Enzymatic activity of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)

All present enzymatic activity of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7):
2.7.7.6;

Protein crystallography data

The structure of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7), PDB code: 5e17 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) 39.82 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 183.007, 103.566, 294.935, 90.00, 99.20, 90.00
R / Rfree (%) 21.5 / 26

Other elements in 5e17:

The structure of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) (pdb code 5e17). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7), PDB code: 5e17:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5e17

Go back to Magnesium Binding Sites List in 5e17
Magnesium binding site 1 out of 4 in the T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:64.7
occ:1.00
 O B:ASP191 2.1 73.4 1.0
OD1 B:ASP183 2.8 75.5 1.0
OD1 B:ASP193 3.1 65.3 1.0
C B:ASP191 3.1 77.9 1.0
CA B:ASP191 3.7 83.8 1.0
CG B:ASP183 3.9 68.4 1.0
CG B:ARG30 3.9 59.0 1.0
O B:LEU192 4.0 58.9 1.0
CB B:ASP191 4.0 86.7 1.0
O B:HOH2102 4.1 65.1 1.0
N B:LEU192 4.2 75.8 1.0
C B:LEU192 4.3 64.4 1.0
CG B:ASP193 4.3 58.0 1.0
OD2 B:ASP183 4.4 72.2 1.0
CB B:ARG30 4.5 62.1 1.0
CA B:LEU192 4.7 67.0 1.0
CD B:ARG30 4.7 55.6 1.0
CA B:ARG30 4.7 58.5 1.0
N B:ASP193 4.8 60.1 1.0
CB B:ASP183 4.9 63.5 1.0

Magnesium binding site 2 out of 4 in 5e17

Go back to Magnesium Binding Sites List in 5e17
Magnesium binding site 2 out of 4 in the T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1601

b:37.4
occ:1.00
 O B:HOH2105 2.1 40.8 1.0
O B:HOH2110 2.1 37.8 1.0
O D:HOH2117 2.3 39.3 1.0
O D:LYS840 2.5 30.6 1.0
OD2 B:ASP168 3.4 39.4 1.0
OD1 B:ASP168 3.6 42.3 1.0
C D:LYS840 3.6 38.9 1.0
OE1 B:GLU154 3.7 49.0 1.0
CG B:ASP168 3.9 40.9 1.0
OE1 B:GLU64 4.3 62.4 1.0
OE2 B:GLU64 4.4 62.1 1.0
OE2 B:GLU154 4.4 46.3 1.0
CA D:LYS840 4.4 44.4 1.0
CD B:GLU154 4.5 56.1 1.0
CB B:ALA153 4.5 49.3 1.0
O D:LEU839 4.5 41.7 1.0
N D:TYR841 4.6 49.5 1.0
CA D:TYR841 4.7 45.5 1.0
N D:VAL842 4.7 39.1 1.0
CD B:GLU64 4.8 70.4 1.0

Magnesium binding site 3 out of 4 in 5e17

Go back to Magnesium Binding Sites List in 5e17
Magnesium binding site 3 out of 4 in the T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:19.3
occ:1.00
 OD1 D:ASP739 2.0 22.2 1.0
O D:HOH2104 2.1 23.6 1.0
OD1 D:ASP743 2.1 22.2 1.0
OD1 D:ASP741 2.1 22.5 1.0
O D:HOH2105 2.1 20.4 1.0
O3' I:A7 2.4 30.2 1.0
OD2 D:ASP741 2.6 27.0 1.0
CG D:ASP741 2.7 27.0 1.0
CG D:ASP743 2.7 22.2 1.0
OD2 D:ASP743 2.8 19.8 1.0
CG D:ASP739 3.0 24.2 1.0
OD2 D:ASP739 3.2 18.7 1.0
C3' I:A7 3.4 30.5 1.0
C5' I:A7 3.4 31.2 1.0
C4' I:A7 3.7 25.0 1.0
CB D:ASP741 4.2 24.2 1.0
CB D:ASP743 4.2 21.2 1.0
O D:ASP739 4.3 26.6 1.0
CB D:ASP739 4.3 23.6 1.0
O5' I:A7 4.4 31.0 1.0
N D:ASP743 4.4 23.1 1.0
N D:ASP739 4.4 20.2 1.0
NH2 D:ARG704 4.5 21.3 1.0
C D:ASP739 4.6 23.9 1.0
CA D:ASP743 4.7 26.4 1.0
CA D:ASP739 4.7 20.1 1.0
N D:ASP741 4.7 22.4 1.0
C2' I:A7 4.7 34.7 1.0
CA D:ASP741 4.8 22.2 1.0
C D:ASP741 4.9 24.4 1.0

Magnesium binding site 4 out of 4 in 5e17

Go back to Magnesium Binding Sites List in 5e17
Magnesium binding site 4 out of 4 in the T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of T. Thermophilus Transcription Initiation Complex Having A Rrr Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 7 (Rpo-Ggg-7) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:62.1
occ:1.00
 O F:ALA292 2.3 69.4 1.0
O F:GLY296 2.4 65.5 1.0
O F:TRP299 3.1 54.7 1.0
C F:GLY296 3.3 74.7 1.0
C F:ALA292 3.3 69.1 1.0
CA F:GLU293 3.6 65.5 1.0
N F:GLU293 3.9 70.1 1.0
CA F:GLY296 3.9 77.5 1.0
N F:GLY296 4.0 72.5 1.0
O F:GLU293 4.0 60.2 1.0
C F:GLU293 4.1 54.8 1.0
C F:TRP299 4.2 58.5 1.0
N F:PRO297 4.2 71.7 1.0
CB F:TRP299 4.5 61.2 1.0
CA F:PRO297 4.5 64.8 1.0
CA F:ALA292 4.5 66.0 1.0
N F:TRP299 4.6 60.6 1.0
CA F:TRP299 4.6 61.5 1.0
CB F:ALA292 4.8 68.5 1.0
CB F:GLU293 4.9 80.0 1.0
C F:MET295 5.0 66.1 1.0

Reference:

J.T.Winkelman, I.O.Vvedenskaya, Y.Zhang, Y.Zhang, J.G.Bird, D.M.Taylor, R.L.Gourse, R.H.Ebright, B.E.Nickels. Multiplexed Protein-Dna Cross-Linking: Scrunching in Transcription Start Site Selection. Science V. 351 1090 2016.
ISSN: ESSN 1095-9203
PubMed: 26941320
DOI: 10.1126/SCIENCE.AAD6881
Page generated: Mon Dec 14 20:13:31 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy