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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: Sun Sep 29 03:27:45 2024

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