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Magnesium in PDB 7mlj: Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G Rna

Enzymatic activity of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G Rna

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G Rna:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G Rna, PDB code: 7mlj 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) 46.21 / 3.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 186.309, 104.656, 298.413, 90, 98.12, 90
R / Rfree (%) 26.5 / 28.3

Other elements in 7mlj:

The structure of Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G 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 4NT Oligo-G Rna (pdb code 7mlj). 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 4NT Oligo-G Rna, PDB code: 7mlj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7mlj

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Magnesium binding site 1 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT 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 Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:139.3
occ:1.00
 OD1 B:ASP183 2.2 150.8 1.0
OD1 B:ASP193 2.5 141.2 1.0
O B:ASP191 3.1 144.1 1.0
CG B:ASP183 3.4 151.6 1.0
OD1 B:ASP191 3.5 156.0 1.0
O B:LEU192 3.5 141.6 1.0
C B:ASP191 3.7 150.8 1.0
CG B:ASP193 3.7 129.2 1.0
C B:LEU192 3.9 142.8 1.0
OD2 B:ASP183 4.1 149.9 1.0
CG B:ARG30 4.3 135.6 1.0
CA B:ASP191 4.4 156.4 1.0
CA B:ASP183 4.4 144.9 1.0
N B:LEU192 4.4 149.5 1.0
N B:ASP193 4.4 142.3 1.0
CB B:ASP183 4.4 147.3 1.0
OD2 B:ASP193 4.5 122.2 1.0
CA B:ASP193 4.5 133.1 1.0
CG B:ASP191 4.5 152.0 1.0
CA B:LEU192 4.6 143.6 1.0
CB B:ASP193 4.8 128.7 1.0
CA B:ARG30 4.9 137.5 1.0
CB B:ASP191 4.9 153.3 1.0
CB B:ARG30 5.0 136.6 1.0
N B:ASP183 5.0 143.5 1.0

Magnesium binding site 2 out of 5 in 7mlj

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Magnesium binding site 2 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT 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 Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2002

b:92.5
occ:1.00
 O D:LYS840 2.2 130.1 1.0
OD2 B:ASP168 3.4 119.2 1.0
C D:LYS840 3.5 136.7 1.0
OE2 B:GLU154 3.5 141.2 1.0
OD1 B:ASP168 3.5 122.2 1.0
CG B:ASP168 3.9 121.9 1.0
CD B:GLU154 4.3 147.7 1.0
N D:TYR841 4.4 140.9 1.0
CA D:LYS840 4.4 132.0 1.0
OE1 B:GLU154 4.4 149.8 1.0
CA D:TYR841 4.4 137.8 1.0
CB B:ALA153 4.6 142.6 1.0
O D:LEU839 4.7 123.5 1.0
OE2 B:GLU64 4.7 172.9 1.0
N D:VAL842 4.8 137.9 1.0
CG D:LYS840 4.9 138.5 1.0
OE1 B:GLU64 5.0 182.1 1.0

Magnesium binding site 3 out of 5 in 7mlj

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Magnesium binding site 3 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT 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 Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:98.6
occ:1.00
 OD1 D:ASP739 2.0 117.0 1.0
O3' I:G4 2.0 126.4 1.0
OD1 D:ASP743 2.5 102.2 1.0
OD1 D:ASP741 2.7 103.4 1.0
OD2 D:ASP743 2.8 95.3 1.0
CG D:ASP739 2.9 109.7 1.0
CG D:ASP743 3.0 101.0 1.0
OD2 D:ASP739 3.2 114.9 1.0
C3' I:G4 3.3 141.2 1.0
OD2 D:ASP741 3.4 114.3 1.0
O2' I:G4 3.4 133.0 1.0
CG D:ASP741 3.4 106.5 1.0
C2' I:G4 3.8 141.5 1.0
C4' I:G4 4.1 146.0 1.0
N D:ASP739 4.2 104.3 1.0
CB D:ASP739 4.3 96.8 1.0
NH2 D:ARG704 4.3 101.3 1.0
CB D:ASP743 4.5 100.9 1.0
CA D:ASP739 4.7 96.6 1.0
O D:ASP739 4.7 105.2 1.0
C D:ASP739 4.8 92.9 1.0
C5' I:G4 4.9 148.2 1.0
CB D:ASP741 4.9 99.1 1.0

Magnesium binding site 4 out of 5 in 7mlj

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Magnesium binding site 4 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT 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 Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:149.4
occ:1.00
 O D:TRP897 2.8 144.8 1.0
O D:ILE900 2.8 145.5 1.0
O D:GLU898 3.4 124.1 1.0
C D:GLU898 3.9 134.2 1.0
C D:TRP897 4.0 143.8 1.0
C D:ILE900 4.0 136.9 1.0
CA D:GLU898 4.1 139.1 1.0
N D:ILE900 4.5 140.8 1.0
N D:GLU898 4.5 139.2 1.0
NE1 D:TRP897 4.7 163.1 1.0
CD1 D:TRP897 4.7 159.5 1.0
CA D:ILE900 4.8 137.6 1.0
N D:LEU899 4.8 139.6 1.0
C D:LEU899 4.9 137.7 1.0

Magnesium binding site 5 out of 5 in 7mlj

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Magnesium binding site 5 out of 5 in the Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT 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 Crystal Structure of Thermus Thermophilus Reiterative Transcription Complex with 4NT Oligo-G Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:147.6
occ:1.00
 O F:TRP299 2.0 154.9 1.0
O F:ALA292 2.6 156.4 1.0
O F:GLY296 2.6 178.5 1.0
C F:TRP299 3.2 159.9 1.0
C F:ALA292 3.3 163.3 1.0
C F:GLY296 3.8 180.7 1.0
CA F:TRP299 3.8 164.7 1.0
CB F:TRP299 3.9 157.0 1.0
N F:TRP299 3.9 168.9 1.0
N F:GLU293 4.0 165.1 1.0
CB F:ALA292 4.0 160.4 1.0
CA F:ALA292 4.1 161.0 1.0
CA F:GLU293 4.1 163.3 1.0
N F:ASP300 4.3 159.5 1.0
N F:GLY296 4.5 174.1 1.0
CA F:ASP300 4.6 167.3 1.0
CA F:GLY296 4.6 180.4 1.0
N F:PRO297 4.7 177.1 1.0
CA F:PRO297 4.7 176.5 1.0
O F:GLU293 4.8 162.2 1.0
C F:GLU293 4.8 160.6 1.0
C F:PRO297 4.9 172.1 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 01:01:10 2024

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