Atomistry » Magnesium » PDB 7rb1-7rix » 7rdq
Atomistry »
  Magnesium »
    PDB 7rb1-7rix »
      7rdq »

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

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