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Magnesium in PDB 5e18: T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)

Enzymatic activity of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)

All present enzymatic activity of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8):
2.7.7.6;

Protein crystallography data

The structure of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8), PDB code: 5e18 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) 38.35 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 185.917, 103.241, 298.404, 90.00, 97.93, 90.00
R / Rfree (%) 23.8 / 28.4

Other elements in 5e18:

The structure of T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) 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 Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) (pdb code 5e18). 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 Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8), PDB code: 5e18:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5e18

Go back to Magnesium Binding Sites List in 5e18
Magnesium binding site 1 out of 4 in the T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)


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 Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:0.6
occ:1.00
OD2 B:ASP183 2.1 0.8 1.0
O B:ASP191 2.5 0.3 1.0
CG B:ASP183 3.3 0.5 1.0
C B:ASP191 3.3 0.3 1.0
OD1 B:ASP193 3.6 0.4 1.0
CA B:ASP191 3.8 0.2 1.0
OD1 B:ASP183 4.0 0.8 1.0
CB B:ASP191 4.1 0.3 1.0
O B:LEU192 4.3 0.4 1.0
CB B:ASP183 4.4 0.8 1.0
N B:LEU192 4.4 0.5 1.0
CG B:ARG30 4.5 96.6 1.0
C B:LEU192 4.6 0.6 1.0
CG B:ASP193 4.6 98.7 1.0
CA B:ASP183 4.9 0.8 1.0
CA B:LEU192 5.0 0.8 1.0

Magnesium binding site 2 out of 4 in 5e18

Go back to Magnesium Binding Sites List in 5e18
Magnesium binding site 2 out of 4 in the T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)


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 Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:53.6
occ:1.00
OD1 D:ASP741 2.0 67.2 1.0
OD1 D:ASP739 2.1 66.6 1.0
OD1 D:ASP743 2.1 60.0 1.0
OD2 D:ASP743 2.4 66.8 1.0
O3' I:A7 2.4 76.4 1.0
CG D:ASP743 2.6 62.5 1.0
CG D:ASP741 2.8 72.9 1.0
OD2 D:ASP741 3.0 77.9 1.0
CG D:ASP739 3.0 67.2 1.0
OD2 D:ASP739 3.3 75.0 1.0
C3' I:A7 3.5 73.1 1.0
C5' I:A7 3.7 76.0 1.0
C4' I:A7 3.8 71.8 1.0
CB D:ASP743 4.1 60.4 1.0
CB D:ASP741 4.1 69.1 1.0
NH2 D:ARG704 4.2 65.5 1.0
N D:ASP739 4.3 55.8 1.0
N D:ASP741 4.4 69.0 1.0
O D:ASP739 4.4 59.2 1.0
CB D:ASP739 4.4 65.3 1.0
C D:ASP739 4.6 56.5 1.0
CA D:ASP739 4.7 61.2 1.0
N D:ASP743 4.8 64.7 1.0
CA D:ASP743 4.8 65.4 1.0
C2' I:A7 4.8 71.3 1.0
CA D:ASP741 4.8 63.0 1.0
O5' I:A7 4.8 79.6 1.0
CZ D:ARG704 5.0 68.3 1.0

Magnesium binding site 3 out of 4 in 5e18

Go back to Magnesium Binding Sites List in 5e18
Magnesium binding site 3 out of 4 in the T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)


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 Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:65.2
occ:1.00
O D:LYS840 2.1 77.4 1.0
C D:LYS840 3.2 79.0 1.0
OD2 B:ASP168 3.5 87.7 1.0
OE1 B:GLU154 3.7 93.8 1.0
OD1 B:ASP168 3.8 82.7 1.0
CG B:ASP168 4.1 84.1 1.0
CA D:LYS840 4.1 72.3 1.0
N D:TYR841 4.2 84.5 1.0
O D:LEU839 4.3 75.8 1.0
CA D:TYR841 4.3 77.8 1.0
OE2 B:GLU64 4.5 0.9 1.0
CD B:GLU154 4.6 94.3 1.0
N D:VAL842 4.7 70.7 1.0
OE1 B:GLU64 4.7 0.5 1.0
CB B:ALA153 4.8 95.2 1.0
OE2 B:GLU154 4.8 96.2 1.0
CG D:LYS840 5.0 72.8 1.0
C D:TYR841 5.0 73.8 1.0

Magnesium binding site 4 out of 4 in 5e18

Go back to Magnesium Binding Sites List in 5e18
Magnesium binding site 4 out of 4 in the T. Thermophilus Transcription Initiation Complex Having A Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8)


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 Yyy Discriminator Sequence and A Nontemplate-Strand Length Corresponding to Tss Selection at Position 8 (Rpo-Ccc-8) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:0.3
occ:1.00
O F:ALA292 2.0 0.5 1.0
O F:TRP299 2.1 0.1 1.0
O F:GLY296 2.1 0.1 1.0
CB F:TRP299 2.6 0.6 1.0
C F:TRP299 2.9 1.0 1.0
C F:ALA292 3.0 0.2 1.0
CA F:TRP299 3.1 0.5 1.0
C F:GLY296 3.3 0.1 1.0
N F:TRP299 3.4 0.3 1.0
N F:GLY296 3.7 0.5 1.0
CA F:ALA292 3.8 0.0 1.0
CG F:TRP299 3.9 0.1 1.0
CB F:ALA292 4.0 0.2 1.0
N F:GLU293 4.0 0.2 1.0
CA F:GLY296 4.1 0.3 1.0
N F:ASP300 4.2 0.6 1.0
C F:MET295 4.2 0.3 1.0
CB F:MET295 4.3 0.8 1.0
CA F:GLU293 4.3 0.6 1.0
N F:PRO297 4.4 0.9 1.0
CD1 F:TRP299 4.4 0.3 1.0
O F:GLU293 4.6 0.2 1.0
C F:GLU293 4.6 0.2 1.0
CA F:MET295 4.6 0.6 1.0
N F:MET295 4.6 1.0 1.0
CA F:PRO297 4.7 0.6 1.0
C F:PRO297 4.7 0.6 1.0
C F:GLY298 4.7 0.9 1.0
N F:GLY298 4.8 0.0 1.0
CA F:ASP300 4.8 1.0 1.0
O F:MET295 4.9 0.1 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 20:13:30 2020

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