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Magnesium in PDB 7mli: Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna

Enzymatic activity of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna, PDB code: 7mli was solved by Y.Liu, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.96 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 187.076, 103.883, 298.739, 90, 97.95, 90
R / Rfree (%) 24.3 / 29.2

Other elements in 7mli:

The structure of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 5 in 7mli

Go back to Magnesium Binding Sites List in 7mli
Magnesium binding site 1 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:153.3
occ:1.00
 OD1 B:ASP193 2.3 143.2 1.0
OD1 B:ASP183 2.4 152.1 1.0
O B:ASP191 3.1 144.8 1.0
CG B:ASP193 3.6 97.3 1.0
OD1 B:ASP191 3.6 154.5 1.0
CG B:ASP183 3.6 163.0 1.0
O B:LEU192 3.7 120.9 1.0
C B:ASP191 3.9 149.4 1.0
CG B:ARG30 4.1 150.7 1.0
C B:LEU192 4.1 139.6 1.0
OD2 B:ASP193 4.2 108.1 1.0
OD2 B:ASP183 4.3 165.3 1.0
N B:ASP193 4.5 140.4 1.0
CA B:ASP193 4.6 107.1 1.0
CA B:ASP191 4.6 140.0 1.0
CG B:ASP191 4.6 159.3 1.0
CA B:ASP183 4.7 127.0 1.0
CB B:ASP193 4.7 98.4 1.0
N B:LEU192 4.7 139.0 1.0
CA B:ARG30 4.7 139.1 1.0
CB B:ASP183 4.7 151.6 1.0
CB B:ARG30 4.7 145.9 1.0
N B:GLY31 4.8 121.7 1.0
CA B:LEU192 4.8 131.8 1.0
CD B:ARG30 5.0 138.4 1.0

Magnesium binding site 2 out of 5 in 7mli

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Magnesium binding site 2 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:87.7
occ:1.00
 O3' I:C5 1.9 99.2 1.0
OD1 D:ASP739 1.9 109.3 1.0
OD1 D:ASP741 2.2 79.5 1.0
OD1 D:ASP743 2.5 106.5 1.0
CG D:ASP739 2.7 97.7 1.0
OD2 D:ASP741 2.9 111.3 1.0
OD2 D:ASP739 2.9 98.9 1.0
CG D:ASP741 2.9 87.7 1.0
OD2 D:ASP743 3.2 79.5 1.0
CG D:ASP743 3.3 97.8 1.0
C3' I:C5 3.3 117.5 1.0
C4' I:C5 4.0 121.8 1.0
CB D:ASP739 4.1 79.5 1.0
O2' I:C5 4.1 153.3 1.0
C2' I:C5 4.2 143.8 1.0
CB D:ASP741 4.3 79.5 1.0
C5' I:C5 4.4 133.0 1.0
N D:ASP739 4.4 82.8 1.0
C D:ASP739 4.6 89.6 1.0
N D:ASP741 4.6 109.0 1.0
O D:ASP739 4.6 114.1 1.0
CA D:ASP739 4.6 93.5 1.0
CB D:ASP743 4.7 109.9 1.0
NH2 D:ARG704 4.9 86.5 1.0
CA D:ASP741 4.9 92.0 1.0
O5' I:C5 5.0 149.7 1.0

Magnesium binding site 3 out of 5 in 7mli

Go back to Magnesium Binding Sites List in 7mli
Magnesium binding site 3 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:79.5
occ:1.00
 O D:LYS840 2.3 114.5 1.0
C D:LYS840 3.5 122.5 1.0
OE2 B:GLU154 3.5 147.4 1.0
OD2 B:ASP168 3.8 79.5 1.0
OD1 B:ASP168 4.0 110.8 1.0
CG B:ASP168 4.3 117.3 1.0
N D:TYR841 4.4 141.4 1.0
CA D:TYR841 4.4 118.9 1.0
CA D:LYS840 4.4 103.7 1.0
CD B:GLU154 4.5 151.3 1.0
OE1 B:GLU154 4.6 130.9 1.0
N D:VAL842 4.6 128.6 1.0
O D:LEU839 4.7 79.5 1.0
OE2 B:GLU64 4.8 184.9 1.0
OE1 B:GLU64 5.0 147.7 1.0

Magnesium binding site 4 out of 5 in 7mli

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Magnesium binding site 4 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:141.5
occ:1.00
 O D:TRP897 2.8 136.1 1.0
O D:ILE900 2.9 150.8 1.0
O D:GLU898 3.4 111.7 1.0
C D:GLU898 3.9 120.4 1.0
C D:TRP897 4.0 123.5 1.0
CA D:GLU898 4.1 119.9 1.0
C D:ILE900 4.1 120.8 1.0
N D:ILE900 4.5 129.1 1.0
N D:GLU898 4.5 101.4 1.0
NE1 D:TRP897 4.7 147.6 1.0
CD1 D:TRP897 4.8 146.2 1.0
CA D:ILE900 4.8 114.6 1.0
N D:LEU899 4.8 128.2 1.0
C D:LEU899 4.9 104.8 1.0

Magnesium binding site 5 out of 5 in 7mli

Go back to Magnesium Binding Sites List in 7mli
Magnesium binding site 5 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 5NT Oligo-C Rna


Mono view


Stereo pair view

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

b:133.9
occ:1.00
 O F:TRP299 2.1 144.4 1.0
O F:GLY296 2.6 194.3 1.0
O F:ALA292 2.7 145.2 1.0
C F:TRP299 3.2 155.7 1.0
C F:ALA292 3.4 173.0 1.0
C F:GLY296 3.7 204.2 1.0
CA F:TRP299 3.9 169.6 1.0
N F:TRP299 3.9 177.7 1.0
CB F:TRP299 3.9 155.5 1.0
N F:GLU293 4.0 183.8 1.0
CB F:ALA292 4.1 167.6 1.0
CA F:GLU293 4.1 168.1 1.0
CA F:ALA292 4.2 170.6 1.0
N F:ASP300 4.4 162.0 1.0
N F:GLY296 4.4 200.1 1.0
CA F:GLY296 4.5 207.4 1.0
N F:PRO297 4.6 196.8 1.0
CA F:PRO297 4.6 185.0 1.0
CA F:ASP300 4.7 170.8 1.0
O F:GLU293 4.8 153.9 1.0
C F:GLU293 4.8 159.0 1.0
C F:PRO297 4.9 177.0 1.0
N F:GLY298 4.9 169.1 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 01:01:09 2024

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