Magnesium in PDB 6kqh: Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt
Enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt
All present enzymatic activity of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt:
2.7.7.6;
Protein crystallography data
The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt, PDB code: 6kqh
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)
|
39.82 /
3.18
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
183.007,
103.566,
294.935,
90.00,
99.20,
90.00
|
R / Rfree (%)
|
20.3 /
24.7
|
Other elements in 6kqh:
The structure of Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt also contains other interesting chemical elements:
Magnesium Binding Sites:
The binding sites of Magnesium atom in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt
(pdb code 6kqh). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the
Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt, PDB code: 6kqh:
Jump to Magnesium binding site number:
1;
2;
3;
4;
Magnesium binding site 1 out
of 4 in 6kqh
Go back to
Magnesium Binding Sites List in 6kqh
Magnesium binding site 1 out
of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt
![](/pictures/MG/pdb/kq/6kqh-MG-sphere_01.jpg) Mono view
![](/pictures/MG/pdb/kq/6kqh-MG-sphere_01_stereo.jpg) 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 7 Nt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2001
b:73.4
occ:1.00
|
O
|
B:ASP191
|
2.4
|
81.0
|
1.0
|
OD1
|
B:ASP183
|
2.7
|
83.2
|
1.0
|
OD1
|
B:ASP193
|
3.1
|
74.1
|
1.0
|
C
|
B:ASP191
|
3.3
|
82.5
|
1.0
|
CG
|
B:ASP183
|
3.7
|
78.3
|
1.0
|
CA
|
B:ASP191
|
3.8
|
90.3
|
1.0
|
CG
|
B:ARG30
|
4.0
|
59.0
|
1.0
|
O
|
B:LEU192
|
4.0
|
66.7
|
1.0
|
CB
|
B:ASP191
|
4.1
|
95.0
|
1.0
|
O
|
B:HOH2101
|
4.2
|
73.3
|
1.0
|
OD2
|
B:ASP183
|
4.2
|
81.8
|
1.0
|
N
|
B:LEU192
|
4.3
|
79.4
|
1.0
|
C
|
B:LEU192
|
4.3
|
70.4
|
1.0
|
CG
|
B:ASP193
|
4.4
|
62.4
|
1.0
|
CB
|
B:ARG30
|
4.6
|
62.3
|
1.0
|
CD
|
B:ARG30
|
4.8
|
60.1
|
1.0
|
CA
|
B:LEU192
|
4.8
|
71.7
|
1.0
|
CA
|
B:ARG30
|
4.8
|
60.7
|
1.0
|
CB
|
B:ASP183
|
4.8
|
72.6
|
1.0
|
N
|
B:ASP193
|
4.9
|
65.3
|
1.0
|
|
Magnesium binding site 2 out
of 4 in 6kqh
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Magnesium Binding Sites List in 6kqh
Magnesium binding site 2 out
of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt
![](/pictures/MG/pdb/kq/6kqh-MG-sphere_02.jpg) Mono view
![](/pictures/MG/pdb/kq/6kqh-MG-sphere_02_stereo.jpg) 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 7 Nt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg2002
b:45.3
occ:1.00
|
O
|
B:HOH2108
|
2.0
|
45.3
|
1.0
|
O
|
B:HOH2106
|
2.1
|
47.5
|
1.0
|
O
|
D:HOH2108
|
2.5
|
44.7
|
1.0
|
O
|
D:LYS840
|
2.6
|
32.7
|
1.0
|
OD2
|
B:ASP168
|
3.4
|
48.0
|
1.0
|
OD1
|
B:ASP168
|
3.6
|
49.3
|
1.0
|
C
|
D:LYS840
|
3.8
|
41.5
|
1.0
|
OE1
|
B:GLU154
|
3.8
|
57.9
|
1.0
|
CG
|
B:ASP168
|
3.9
|
47.3
|
1.0
|
OE2
|
B:GLU154
|
4.3
|
59.4
|
1.0
|
OE1
|
B:GLU64
|
4.3
|
75.7
|
1.0
|
OE2
|
B:GLU64
|
4.3
|
70.2
|
1.0
|
CB
|
B:ALA153
|
4.3
|
48.9
|
1.0
|
CD
|
B:GLU154
|
4.5
|
62.3
|
1.0
|
CA
|
D:LYS840
|
4.5
|
42.6
|
1.0
|
O
|
D:LEU839
|
4.6
|
47.0
|
1.0
|
N
|
D:TYR841
|
4.7
|
49.6
|
1.0
|
CD
|
B:GLU64
|
4.7
|
78.0
|
1.0
|
CA
|
D:TYR841
|
4.8
|
42.6
|
1.0
|
N
|
D:VAL842
|
4.9
|
42.3
|
1.0
|
|
Magnesium binding site 3 out
of 4 in 6kqh
Go back to
Magnesium Binding Sites List in 6kqh
Magnesium binding site 3 out
of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt
![](/pictures/MG/pdb/kq/6kqh-MG-sphere_03.jpg) Mono view
![](/pictures/MG/pdb/kq/6kqh-MG-sphere_03_stereo.jpg) 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 7 Nt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Mg2003
b:23.7
occ:1.00
|
OD1
|
D:ASP739
|
2.0
|
31.2
|
1.0
|
O
|
D:HOH2124
|
2.0
|
29.8
|
1.0
|
OD1
|
D:ASP741
|
2.0
|
30.9
|
1.0
|
OD1
|
D:ASP743
|
2.2
|
28.9
|
1.0
|
O
|
D:HOH2119
|
2.4
|
26.7
|
1.0
|
O3'
|
I:A7
|
2.6
|
37.4
|
1.0
|
CG
|
D:ASP741
|
2.8
|
31.8
|
1.0
|
OD2
|
D:ASP741
|
2.9
|
34.0
|
1.0
|
CG
|
D:ASP739
|
2.9
|
33.2
|
1.0
|
CG
|
D:ASP743
|
3.0
|
27.9
|
1.0
|
OD2
|
D:ASP743
|
3.1
|
25.5
|
1.0
|
OD2
|
D:ASP739
|
3.2
|
30.7
|
1.0
|
C5'
|
I:A7
|
3.5
|
34.1
|
1.0
|
C3'
|
I:A7
|
3.5
|
36.3
|
1.0
|
C4'
|
I:A7
|
3.8
|
33.6
|
1.0
|
CB
|
D:ASP741
|
4.2
|
27.5
|
1.0
|
CB
|
D:ASP739
|
4.3
|
29.1
|
1.0
|
O5'
|
I:A7
|
4.4
|
42.2
|
1.0
|
CB
|
D:ASP743
|
4.4
|
25.0
|
1.0
|
N
|
D:ASP739
|
4.5
|
25.1
|
1.0
|
N
|
D:ASP741
|
4.5
|
27.0
|
1.0
|
O
|
D:ASP739
|
4.5
|
30.9
|
1.0
|
N
|
D:ASP743
|
4.5
|
26.2
|
1.0
|
C
|
D:ASP739
|
4.6
|
28.2
|
1.0
|
CA
|
D:ASP739
|
4.7
|
23.4
|
1.0
|
CA
|
D:ASP741
|
4.7
|
24.6
|
1.0
|
NH2
|
D:ARG704
|
4.8
|
25.1
|
1.0
|
C
|
D:ASP741
|
4.8
|
31.4
|
1.0
|
CA
|
D:ASP743
|
4.8
|
27.7
|
1.0
|
C2'
|
I:A7
|
4.9
|
40.4
|
1.0
|
N
|
D:GLY742
|
4.9
|
28.3
|
1.0
|
|
Magnesium binding site 4 out
of 4 in 6kqh
Go back to
Magnesium Binding Sites List in 6kqh
Magnesium binding site 4 out
of 4 in the Thermus Thermophilus Initial Transcription Complex Comprising Sigma A and 5'-Oh Rna of 7 Nt
![](/pictures/MG/pdb/kq/6kqh-MG-sphere_04.jpg) Mono view
![](/pictures/MG/pdb/kq/6kqh-MG-sphere_04_stereo.jpg) 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 7 Nt within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Mg2001
b:70.6
occ:1.00
|
O
|
F:ALA292
|
2.4
|
73.3
|
1.0
|
O
|
F:GLY296
|
2.5
|
76.3
|
1.0
|
O
|
F:TRP299
|
3.1
|
61.6
|
1.0
|
C
|
F:GLY296
|
3.4
|
81.8
|
1.0
|
C
|
F:ALA292
|
3.4
|
70.5
|
1.0
|
CA
|
F:GLU293
|
3.7
|
66.2
|
1.0
|
N
|
F:GLU293
|
3.9
|
70.6
|
1.0
|
N
|
F:GLY296
|
4.0
|
78.7
|
1.0
|
CA
|
F:GLY296
|
4.0
|
82.8
|
1.0
|
O
|
F:GLU293
|
4.1
|
63.3
|
1.0
|
C
|
F:GLU293
|
4.2
|
59.4
|
1.0
|
C
|
F:TRP299
|
4.2
|
65.9
|
1.0
|
N
|
F:PRO297
|
4.3
|
76.2
|
1.0
|
CA
|
F:PRO297
|
4.5
|
73.3
|
1.0
|
CB
|
F:TRP299
|
4.5
|
63.2
|
1.0
|
CA
|
F:ALA292
|
4.5
|
68.3
|
1.0
|
N
|
F:TRP299
|
4.6
|
67.1
|
1.0
|
CA
|
F:TRP299
|
4.7
|
66.2
|
1.0
|
CB
|
F:ALA292
|
4.8
|
68.8
|
1.0
|
CB
|
F:GLU293
|
5.0
|
77.4
|
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: Mon Dec 14 23:09:08 2020
|