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

Go back to Magnesium Binding Sites List in 7mlj
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

Go back to Magnesium Binding Sites List in 7mlj
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

Go back to Magnesium Binding Sites List in 7mlj
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

Go back to Magnesium Binding Sites List in 7mlj
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

Go back to Magnesium Binding Sites List in 7mlj
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: Wed Apr 5 13:20:58 2023

Last articles

Mg in 4Y52
Mg in 4Y30
Mg in 4Y2V
Mg in 4Y2X
Mg in 4Y2Y
Mg in 4Y2U
Mg in 4Y2T
Mg in 4Y2Q
Mg in 4Y2R
Mg in 4Y2S
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy