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Magnesium in PDB 6kqd: Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt

Enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt

All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt, PDB code: 6kqd was solved by Y.Zhang, L.Li, R.H.Ebright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.35 / 3.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 185.501, 104.044, 297.441, 90.00, 98.50, 90.00
R / Rfree (%) 20.7 / 25

Other elements in 6kqd:

The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt (pdb code 6kqd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt, PDB code: 6kqd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 6kqd

Go back to Magnesium Binding Sites List in 6kqd
Magnesium binding site 1 out of 7 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2001

b:80.6
occ:1.00
 OD1 B:ASP183 2.5 0.4 1.0
OD1 B:ASP193 3.0 87.0 1.0
OD1 B:ASP191 3.1 98.4 1.0
O B:ASP191 3.4 77.4 1.0
CG B:ASP183 3.7 0.6 1.0
CG B:ARG30 4.0 72.0 1.0
CG B:ASP193 4.0 74.2 1.0
C B:ASP191 4.1 85.1 1.0
OD2 B:ASP183 4.2 0.5 1.0
O B:LEU192 4.2 84.5 1.0
CG B:ASP191 4.3 94.1 1.0
OD2 B:ASP193 4.5 70.5 1.0
CA B:ASP191 4.6 87.5 1.0
C B:LEU192 4.6 79.8 1.0
CD B:ARG30 4.7 72.3 1.0
CB B:ARG30 4.8 70.1 1.0
CB B:ASP183 4.8 93.8 1.0
CA B:ARG30 4.9 75.1 1.0
CA B:ASP183 4.9 89.1 1.0
N B:GLY31 5.0 67.4 1.0
N B:LEU192 5.0 85.5 1.0

Magnesium binding site 2 out of 7 in 6kqd

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Magnesium binding site 2 out of 7 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:36.1
occ:1.00
 OD1 D:ASP739 1.9 46.7 1.0
O3' I:A3 2.1 56.4 1.0
OD1 D:ASP741 2.2 37.6 1.0
OD1 D:ASP743 2.2 39.5 1.0
OD2 D:ASP741 2.7 46.2 1.0
CG D:ASP741 2.8 42.7 1.0
CG D:ASP739 2.9 47.3 1.0
CG D:ASP743 3.0 39.4 1.0
OD2 D:ASP743 3.0 39.0 1.0
OD2 D:ASP739 3.2 51.5 1.0
C3' I:A3 3.4 54.9 1.0
O2' I:A3 3.5 56.8 1.0
C2' I:A3 3.9 56.5 1.0
C4' I:A3 4.1 54.9 1.0
CB D:ASP739 4.3 39.2 1.0
O D:ASP739 4.3 41.7 1.0
CB D:ASP741 4.3 42.6 1.0
N D:ASP739 4.3 33.8 1.0
CB D:ASP743 4.4 36.2 1.0
C D:ASP739 4.5 37.8 1.0
NH2 D:ARG704 4.5 45.8 1.0
CA D:ASP739 4.6 35.6 1.0
N D:ASP741 4.6 41.0 1.0
N D:ASP743 4.8 36.9 1.0
CA D:ASP741 4.9 37.9 1.0
CA D:ASP743 5.0 36.2 1.0

Magnesium binding site 3 out of 7 in 6kqd

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Magnesium binding site 3 out of 7 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:42.3
occ:1.00
 O D:LYS840 2.2 60.9 1.0
OD2 B:ASP168 3.2 67.0 1.0
C D:LYS840 3.4 63.6 1.0
OE2 B:GLU154 3.7 76.9 1.0
OD1 B:ASP168 3.9 76.9 1.0
CG B:ASP168 3.9 74.4 1.0
O D:LEU839 4.3 60.7 1.0
N D:TYR841 4.3 67.4 1.0
CA D:LYS840 4.3 61.8 1.0
CA D:TYR841 4.4 59.2 1.0
N D:VAL842 4.4 52.9 1.0
OE1 B:GLU64 4.5 0.6 1.0
OE2 B:GLU64 4.6 0.9 1.0
CD B:GLU154 4.7 86.5 1.0
OE1 B:GLU154 4.7 84.9 1.0
C D:TYR841 4.8 55.9 1.0
CB B:ALA153 4.9 75.2 1.0

Magnesium binding site 4 out of 7 in 6kqd

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Magnesium binding site 4 out of 7 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg2001

b:64.7
occ:1.00
 O F:TRP299 2.6 76.4 1.0
O F:GLY296 2.6 81.3 1.0
O F:ALA292 2.8 75.8 1.0
C F:ALA292 3.5 73.4 1.0
C F:TRP299 3.7 74.2 1.0
C F:GLY296 3.7 85.8 1.0
CA F:GLU293 4.0 73.2 1.0
N F:GLU293 4.0 72.4 1.0
CB F:TRP299 4.2 66.0 1.0
N F:TRP299 4.2 80.4 1.0
CA F:TRP299 4.3 70.4 1.0
O F:GLU293 4.4 76.9 1.0
CB F:ALA292 4.5 72.8 1.0
CA F:ALA292 4.5 69.7 1.0
N F:GLY296 4.5 82.9 1.0
CA F:PRO297 4.6 80.1 1.0
N F:PRO297 4.6 83.0 1.0
CA F:GLY296 4.6 81.7 1.0
C F:GLU293 4.6 69.5 1.0
N F:ASP300 4.8 72.1 1.0
C F:PRO297 5.0 83.2 1.0

Magnesium binding site 5 out of 7 in 6kqd

Go back to Magnesium Binding Sites List in 6kqd
Magnesium binding site 5 out of 7 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Mg1001

b:76.5
occ:1.00
 O K:HOH1102 2.6 77.3 1.0
O K:VAL170 2.8 87.0 1.0
O K:PHE171 3.1 76.0 1.0
O K:THR51 3.2 86.4 1.0
O K:SER172 3.2 74.6 1.0
OD2 K:ASP202 3.6 84.1 1.0
C K:PHE171 3.6 79.4 1.0
C K:SER172 3.9 76.2 1.0
C K:VAL170 3.9 82.3 1.0
CA K:PHE171 4.2 77.4 1.0
N K:SER172 4.3 82.0 1.0
C K:THR51 4.3 87.5 1.0
CA K:PRO173 4.4 74.3 1.0
N K:PRO173 4.4 76.5 1.0
N K:PHE171 4.5 75.1 1.0
CB K:ALA52 4.6 83.4 1.0
CA K:SER172 4.8 77.0 1.0
CG1 K:VAL170 4.8 87.6 1.0
CG K:ASP202 4.8 84.5 1.0
N K:THR51 4.8 84.5 1.0

Magnesium binding site 6 out of 7 in 6kqd

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Magnesium binding site 6 out of 7 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2003

b:44.1
occ:1.00
 OD1 N:ASP739 2.0 55.3 1.0
O3' S:A3 2.1 59.1 1.0
OD1 N:ASP741 2.4 41.6 1.0
OD1 N:ASP743 2.5 46.4 1.0
OD2 N:ASP743 2.8 42.6 1.0
CG N:ASP739 3.0 51.7 1.0
CG N:ASP743 3.0 46.1 1.0
OD2 N:ASP741 3.1 48.6 1.0
CG N:ASP741 3.1 48.8 1.0
OD2 N:ASP739 3.3 54.5 1.0
C3' S:A3 3.3 62.9 1.0
O2' S:A3 3.4 59.5 1.0
C2' S:A3 3.9 63.6 1.0
C4' S:A3 4.1 62.1 1.0
CB N:ASP739 4.3 44.9 1.0
N N:ASP739 4.3 41.1 1.0
CB N:ASP743 4.5 45.3 1.0
NH2 N:ARG704 4.5 54.4 1.0
O N:ASP739 4.6 49.2 1.0
CB N:ASP741 4.6 50.1 1.0
C N:ASP739 4.7 45.0 1.0
CA N:ASP739 4.7 43.7 1.0
N N:ASP741 4.9 54.8 1.0

Magnesium binding site 7 out of 7 in 6kqd

Go back to Magnesium Binding Sites List in 6kqd
Magnesium binding site 7 out of 7 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 3 Nt within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg2004

b:61.4
occ:1.00
 O N:HOH2102 2.0 62.8 1.0
O N:LYS840 2.1 71.0 1.0
C N:LYS840 3.2 71.7 1.0
O N:LEU839 3.6 66.5 1.0
OD2 L:ASP168 3.8 73.5 1.0
OE1 L:GLU64 3.9 0.6 1.0
CA N:LYS840 4.1 67.7 1.0
N N:TYR841 4.1 76.0 1.0
N N:VAL842 4.1 70.4 1.0
OE2 L:GLU154 4.3 83.0 1.0
CA N:TYR841 4.3 70.8 1.0
OE2 L:GLU64 4.3 0.5 1.0
CD L:GLU64 4.5 0.9 1.0
CG2 N:VAL842 4.6 62.0 1.0
C N:TYR841 4.6 70.7 1.0
C N:LEU839 4.6 72.6 1.0
CG L:ASP168 4.7 74.0 1.0
CB N:VAL842 4.7 67.0 1.0
OD1 L:ASP168 4.7 77.8 1.0
N N:LYS840 4.8 70.6 1.0

Reference:

L.Li, V.Molodtsov, W.Lin, R.H.Ebright, Y.Zhang. Rna Extension Drives A Stepwise Displacement of An Initiation-Factor Structural Module in Initial Transcription. Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490
DOI: 10.1073/PNAS.1920747117
Page generated: Tue Oct 1 07:33:29 2024

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