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Magnesium in PDB 7mlb: Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna

Enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT Rna, PDB code: 7mlb 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) 44.62 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 186.172, 104.266, 299.017, 90, 97.95, 90
R / Rfree (%) 23.3 / 27

Other elements in 7mlb:

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

Magnesium binding site 1 out of 5 in 7mlb

Go back to Magnesium Binding Sites List in 7mlb
Magnesium binding site 1 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT 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 Transcription Initiation Complex with 5NT Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:169.4
occ:1.00
 OD1 B:ASP183 2.4 184.3 1.0
OD1 B:ASP193 2.5 149.1 1.0
O B:ASP191 3.2 123.5 1.0
OD1 B:ASP191 3.5 169.0 1.0
CG B:ASP183 3.6 182.3 1.0
CG B:ASP193 3.7 127.0 1.0
O B:LEU192 3.9 144.5 1.0
C B:ASP191 4.0 138.8 1.0
CG B:ARG30 4.0 142.7 1.0
OD2 B:ASP183 4.2 190.6 1.0
OD2 B:ASP193 4.3 129.8 1.0
C B:LEU192 4.3 151.2 1.0
CG B:ASP191 4.7 164.8 1.0
N B:ASP193 4.7 144.5 1.0
CA B:ASP193 4.7 113.8 1.0
CA B:ASP183 4.7 151.6 1.0
CA B:ASP191 4.7 163.6 1.0
CA B:ARG30 4.7 134.0 1.0
N B:GLY31 4.7 124.0 1.0
CB B:ASP183 4.7 157.7 1.0
CB B:ARG30 4.8 141.2 1.0
CB B:ASP193 4.8 126.2 1.0
N B:LEU192 4.8 127.5 1.0
CD B:ARG30 4.9 133.6 1.0

Magnesium binding site 2 out of 5 in 7mlb

Go back to Magnesium Binding Sites List in 7mlb
Magnesium binding site 2 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT 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 Transcription Initiation Complex with 5NT Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:86.9
occ:1.00
 O3' I:A5 1.9 105.2 1.0
OD1 D:ASP739 1.9 113.2 1.0
OD1 D:ASP741 2.2 111.2 1.0
OD1 D:ASP743 2.5 112.7 1.0
CG D:ASP739 2.7 114.5 1.0
OD2 D:ASP741 2.9 104.4 1.0
OD2 D:ASP739 2.9 132.4 1.0
CG D:ASP741 2.9 101.1 1.0
OD2 D:ASP743 3.3 86.9 1.0
CG D:ASP743 3.3 97.3 1.0
C3' I:A5 3.3 113.6 1.0
C4' I:A5 3.9 101.6 1.0
O2' I:A5 4.1 147.2 1.0
CB D:ASP739 4.1 86.9 1.0
C2' I:A5 4.2 125.5 1.0
CB D:ASP741 4.4 102.2 1.0
C5' I:A5 4.4 111.5 1.0
N D:ASP739 4.5 104.7 1.0
C D:ASP739 4.6 93.9 1.0
O D:ASP739 4.6 134.3 1.0
N D:ASP741 4.6 102.2 1.0
CA D:ASP739 4.6 86.9 1.0
CB D:ASP743 4.7 116.6 1.0
NH2 D:ARG704 4.9 92.0 1.0
CA D:ASP741 4.9 96.7 1.0

Magnesium binding site 3 out of 5 in 7mlb

Go back to Magnesium Binding Sites List in 7mlb
Magnesium binding site 3 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT 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 Transcription Initiation Complex with 5NT Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:86.9
occ:1.00
 O D:LYS840 2.2 110.3 1.0
C D:LYS840 3.4 119.1 1.0
OE2 B:GLU154 3.6 153.7 1.0
OD2 B:ASP168 3.8 126.3 1.0
OD1 B:ASP168 4.1 118.1 1.0
CA D:LYS840 4.3 114.2 1.0
N D:TYR841 4.4 126.5 1.0
CG B:ASP168 4.4 125.7 1.0
CA D:TYR841 4.5 116.8 1.0
OE2 B:GLU64 4.5 196.2 1.0
O D:LEU839 4.5 97.8 1.0
CD B:GLU154 4.6 162.2 1.0
OE1 B:GLU154 4.7 160.8 1.0
N D:VAL842 4.7 126.2 1.0
OE1 B:GLU64 4.8 173.4 1.0
CG D:LYS840 4.9 109.8 1.0

Magnesium binding site 4 out of 5 in 7mlb

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Magnesium binding site 4 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT 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 Transcription Initiation Complex with 5NT Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2005

b:112.0
occ:1.00
 O D:TRP897 2.7 123.5 1.0
O D:ILE900 3.0 141.5 1.0
O D:GLU898 3.3 143.2 1.0
C D:GLU898 3.9 127.7 1.0
C D:TRP897 3.9 126.6 1.0
CA D:GLU898 4.0 119.4 1.0
C D:ILE900 4.1 111.4 1.0
N D:GLU898 4.4 114.6 1.0
N D:ILE900 4.6 117.2 1.0
CD1 D:TRP897 4.6 156.1 1.0
NE1 D:TRP897 4.6 150.5 1.0
N D:LEU899 4.8 128.9 1.0
CA D:ILE900 4.9 110.8 1.0
C D:LEU899 4.9 108.8 1.0
CE2 D:TRP897 5.0 143.4 1.0
CG D:TRP897 5.0 154.3 1.0

Magnesium binding site 5 out of 5 in 7mlb

Go back to Magnesium Binding Sites List in 7mlb
Magnesium binding site 5 out of 5 in the Crystal Structure of Thermus Thermophilus Transcription Initiation Complex with 5NT 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 Transcription Initiation Complex with 5NT Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:132.6
occ:1.00
 O F:TRP299 2.1 155.5 1.0
O F:ALA292 2.5 143.9 1.0
O F:GLY296 2.6 186.5 1.0
C F:ALA292 3.2 164.5 1.0
C F:TRP299 3.3 157.2 1.0
C F:GLY296 3.7 181.4 1.0
N F:GLU293 3.9 168.0 1.0
CB F:TRP299 3.9 137.4 1.0
CA F:TRP299 3.9 147.8 1.0
N F:TRP299 4.0 153.6 1.0
CB F:ALA292 4.0 158.2 1.0
CA F:GLU293 4.0 153.9 1.0
CA F:ALA292 4.1 166.0 1.0
N F:ASP300 4.3 165.7 1.0
N F:GLY296 4.4 181.0 1.0
CA F:GLY296 4.6 177.3 1.0
N F:PRO297 4.7 164.9 1.0
C F:GLU293 4.7 146.4 1.0
CA F:ASP300 4.7 152.5 1.0
O F:GLU293 4.7 160.2 1.0
CA F:PRO297 4.7 163.3 1.0
C F:PRO297 5.0 168.1 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 01:01:08 2024

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