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Magnesium in PDB 7rdq: Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna

Enzymatic activity of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna

All present enzymatic activity of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna:
2.7.7.6;

Other elements in 7rdq:

The structure of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna (pdb code 7rdq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna, PDB code: 7rdq:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7rdq

Go back to Magnesium Binding Sites List in 7rdq
Magnesium binding site 1 out of 5 in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:58.6
occ:1.00
 O B:ASP191 3.0 51.4 1.0
C B:ASP191 3.2 51.4 1.0
OD1 B:ASP193 3.3 38.7 1.0
CG B:ASP183 3.5 46.4 1.0
OD2 B:ASP183 3.5 46.4 1.0
CA B:ASP191 3.5 51.4 1.0
OD1 B:ASP183 3.6 46.4 1.0
O B:LEU192 3.6 44.0 1.0
CB B:ASP191 4.0 51.4 1.0
N B:LEU192 4.0 44.0 1.0
C B:LEU192 4.1 44.0 1.0
CB B:ASP183 4.2 46.4 1.0
CG B:ARG30 4.5 36.2 1.0
CD B:ARG30 4.5 36.2 1.0
CA B:LEU192 4.6 44.0 1.0
CG B:ASP193 4.6 38.7 1.0
CA B:ASP183 4.6 46.4 1.0
O B:THR190 4.8 55.5 1.0
N B:ASP191 4.8 51.4 1.0
CB B:ARG30 4.9 36.2 1.0
N B:ASP193 4.9 38.7 1.0

Magnesium binding site 2 out of 5 in 7rdq

Go back to Magnesium Binding Sites List in 7rdq
Magnesium binding site 2 out of 5 in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:18.3
occ:1.00
 O3' I:G11 2.2 25.4 1.0
OD1 D:ASP739 2.2 16.8 1.0
OD1 D:ASP743 2.7 20.1 1.0
OD1 D:ASP741 3.0 18.8 1.0
OD2 D:ASP743 3.1 20.1 1.0
CG D:ASP739 3.1 16.8 1.0
CG D:ASP743 3.2 20.1 1.0
OD2 D:ASP739 3.3 16.8 1.0
C3' I:G11 3.6 25.4 1.0
CG D:ASP741 3.8 18.8 1.0
OD2 D:ASP741 3.8 18.8 1.0
O2' I:G11 4.0 25.4 1.0
C2' I:G11 4.2 25.4 1.0
NH2 D:ARG704 4.3 17.0 1.0
N D:ASP739 4.4 16.8 1.0
CB D:ASP739 4.5 16.8 1.0
C4' I:G11 4.6 25.4 1.0
CB D:ASP743 4.7 20.1 1.0
CA D:ASP739 4.8 16.8 1.0
O D:ASP739 5.0 16.8 1.0
C D:ASP739 5.0 16.8 1.0

Magnesium binding site 3 out of 5 in 7rdq

Go back to Magnesium Binding Sites List in 7rdq
Magnesium binding site 3 out of 5 in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:37.2
occ:1.00
 O D:LYS840 2.1 33.5 1.0
C D:LYS840 3.2 33.5 1.0
CA D:LYS840 3.8 33.5 1.0
OD1 B:ASP168 4.1 37.6 1.0
O D:LEU839 4.2 37.1 1.0
N D:TYR841 4.3 30.3 1.0
CG D:LYS840 4.4 33.5 1.0
CB D:LYS840 4.7 33.5 1.0
CA D:TYR841 4.7 30.3 1.0
N D:LYS840 4.9 33.5 1.0
C D:LEU839 5.0 37.1 1.0

Magnesium binding site 4 out of 5 in 7rdq

Go back to Magnesium Binding Sites List in 7rdq
Magnesium binding site 4 out of 5 in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:43.7
occ:1.00
 O D:ILE900 2.4 28.1 1.0
O D:TRP897 2.4 38.7 1.0
O D:GLU898 2.9 36.5 1.0
C D:GLU898 3.3 36.5 1.0
C D:TRP897 3.5 38.7 1.0
CA D:GLU898 3.6 36.5 1.0
C D:ILE900 3.6 28.1 1.0
N D:ILE900 4.0 28.1 1.0
N D:GLU898 4.0 36.5 1.0
N D:LEU899 4.3 29.1 1.0
C D:LEU899 4.4 29.1 1.0
CA D:ILE900 4.4 28.1 1.0
N D:GLN901 4.6 29.8 1.0
O D:LEU899 4.8 29.1 1.0
CA D:TRP897 4.8 38.7 1.0
CA D:GLN901 4.8 29.8 1.0
CA D:LEU899 4.9 29.1 1.0
CB D:GLU898 4.9 36.5 1.0

Magnesium binding site 5 out of 5 in 7rdq

Go back to Magnesium Binding Sites List in 7rdq
Magnesium binding site 5 out of 5 in the Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Cryo-Em Structure of Thermus Thermophilus Reiterative Transcription Complex with 11NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:48.5
occ:1.00
 OE1 F:GLU293 3.5 62.0 1.0
N F:GLU293 3.6 62.0 1.0
CA F:GLU293 3.8 62.0 1.0
CB F:ALA292 3.9 55.9 1.0
O F:TRP299 3.9 49.5 1.0
O F:GLU289 3.9 59.2 1.0
C F:ALA292 3.9 55.9 1.0
CB F:GLU293 4.1 62.0 1.0
O F:ALA292 4.3 55.9 1.0
CG F:GLU289 4.5 59.2 1.0
CA F:ALA292 4.5 55.9 1.0
CD F:GLU293 4.6 62.0 1.0
CA F:ASP300 4.7 51.2 1.0
C F:GLU289 4.9 59.2 1.0
C F:TRP299 4.9 49.5 1.0
CG F:GLU293 4.9 62.0 1.0

Reference:

Y.Liu, L.Yu, C.Pukhrambam, J.T.Winkelman, E.Firlar, J.T.Kaelber, Y.Zhang, B.E.Nickels, R.H.Ebright. Structural and Mechanistic Basis of Reiterative Transcription Initiation. Proc.Natl.Acad.Sci.Usa V. 119 2022.
ISSN: ESSN 1091-6490
PubMed: 35082149
DOI: 10.1073/PNAS.2115746119
Page generated: Thu Oct 3 07:48:57 2024

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