Magnesium in PDB 8w8n: Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State

Enzymatic activity of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State

All present enzymatic activity of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State, PDB code: 8w8n was solved by L.Li, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.86 / 2.69
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.422, 103.704, 295.444, 90, 98.67, 90
R / Rfree (%) 21.2 / 26

Other elements in 8w8n:

The structure of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State (pdb code 8w8n). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State, PDB code: 8w8n:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8w8n

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Magnesium binding site 1 out of 6 in the Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:60.5
occ:1.00
 OD1 B:ASP183 2.2 68.8 1.0
OD1 B:ASP191 2.2 67.7 1.0
OD1 B:ASP193 2.3 68.0 1.0
O B:ASP191 3.1 58.1 1.0
CG B:ASP183 3.4 66.1 1.0
CG B:ASP191 3.4 73.4 1.0
CG B:ASP193 3.5 54.6 1.0
O B:LEU192 3.7 46.3 1.0
C B:ASP191 3.8 60.5 1.0
OD2 B:ASP193 4.1 47.2 1.0
C B:LEU192 4.1 45.4 1.0
OD2 B:ASP183 4.2 72.3 1.0
OD2 B:ASP191 4.3 75.3 1.0
CA B:ASP191 4.3 64.8 1.0
CB B:ASP183 4.3 52.5 1.0
CB B:ASP191 4.3 66.5 1.0
CA B:ASP183 4.4 47.8 1.0
CG B:ARG30 4.4 41.8 1.0
N B:ASP193 4.6 42.7 1.0
CA B:ASP193 4.6 41.0 1.0
N B:LEU192 4.6 55.2 1.0
CB B:ASP193 4.6 35.5 1.0
CA B:LEU192 4.8 45.7 1.0
CA B:ARG30 5.0 37.4 1.0

Magnesium binding site 2 out of 6 in 8w8n

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Magnesium binding site 2 out of 6 in the Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1603

b:18.4
occ:1.00
 O3' I:G7 1.8 34.1 0.7
OD1 D:ASP739 1.9 21.7 1.0
OP1 I:U8 2.0 40.6 0.6
OD1 D:ASP743 2.1 22.9 1.0
OD1 D:ASP741 2.1 21.1 1.0
P I:U8 2.1 57.4 0.6
OP2 I:U8 2.7 44.2 0.6
CG D:ASP743 2.9 18.7 1.0
OD2 D:ASP743 2.9 15.7 1.0
CG D:ASP739 2.9 23.0 1.0
CG D:ASP741 3.0 24.5 1.0
C3' I:G7 3.2 32.8 0.9
OD2 D:ASP741 3.2 37.8 1.0
OD2 D:ASP739 3.3 32.9 1.0
O5' I:U8 3.6 43.7 0.6
C4' I:G7 3.7 34.7 0.8
O2' I:G7 4.1 32.1 0.9
C5' I:G7 4.1 35.0 0.7
C2' I:G7 4.2 32.7 1.0
O D:ASP739 4.2 14.8 1.0
CB D:ASP739 4.3 21.6 1.0
CB D:ASP743 4.3 14.3 1.0
N D:ASP739 4.4 13.6 1.0
C D:ASP739 4.4 15.9 1.0
CB D:ASP741 4.4 15.6 1.0
N D:ASP741 4.4 19.2 1.0
C5' I:U8 4.5 35.8 0.6
CA D:ASP739 4.6 14.5 1.0
N D:ASP743 4.6 17.9 1.0
CA D:ASP741 4.8 11.3 1.0
C D:ASP741 4.8 12.4 1.0
CA D:ASP743 4.9 14.3 1.0
NH2 D:ARG704 4.9 26.5 1.0
O D:ASP741 4.9 19.8 1.0
O5' I:G7 4.9 42.9 0.8

Magnesium binding site 3 out of 6 in 8w8n

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Magnesium binding site 3 out of 6 in the Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1604

b:33.1
occ:1.00
 O D:LYS840 2.0 37.2 1.0
C D:LYS840 3.2 37.1 1.0
OE1 B:GLU154 3.6 59.8 1.0
OD2 B:ASP168 3.8 43.6 1.0
N D:TYR841 4.0 35.1 1.0
OD1 B:ASP168 4.0 45.7 1.0
OE2 B:GLU154 4.1 51.5 1.0
CA D:LYS840 4.1 33.5 1.0
CA D:TYR841 4.2 28.1 1.0
O D:LEU839 4.2 39.8 1.0
CD B:GLU154 4.3 57.0 1.0
CG B:ASP168 4.3 43.4 1.0
N D:VAL842 4.5 31.6 1.0
C D:TYR841 4.8 33.4 1.0
OE2 B:GLU64 4.8 77.0 1.0
CG D:LYS840 4.9 26.6 1.0

Magnesium binding site 4 out of 6 in 8w8n

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Magnesium binding site 4 out of 6 in the Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1605

b:41.9
occ:1.00
 O D:TRP897 2.5 35.1 1.0
O D:ILE900 2.6 50.1 1.0
C D:TRP897 3.7 34.6 1.0
O D:GLU898 3.8 41.2 1.0
C D:ILE900 3.8 33.3 1.0
C D:GLU898 4.0 40.4 1.0
CA D:GLU898 4.1 33.4 1.0
N D:ILE900 4.4 35.0 1.0
N D:GLU898 4.4 30.1 1.0
CA D:ILE900 4.6 27.5 1.0
CD1 D:TRP897 4.6 46.5 1.0
NE1 D:TRP897 4.6 57.9 1.0
N D:LEU899 4.7 33.4 1.0
C D:LEU899 4.8 32.9 1.0
N D:GLN901 4.8 26.2 1.0
CA D:TRP897 4.8 35.5 1.0
CG D:TRP897 4.8 48.0 1.0
CE2 D:TRP897 4.9 56.7 1.0
CA D:GLN901 5.0 28.0 1.0
CD2 D:TRP897 5.0 49.7 1.0

Magnesium binding site 5 out of 6 in 8w8n

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Magnesium binding site 5 out of 6 in the Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg501

b:41.3
occ:1.00
 O F:GLY296 2.4 51.3 1.0
O F:ALA292 2.4 50.1 1.0
O F:TRP299 3.0 43.1 1.0
C F:ALA292 3.4 48.1 1.0
C F:GLY296 3.4 52.0 1.0
CA F:GLU293 3.9 44.0 1.0
O F:GLU293 3.9 40.6 1.0
N F:GLU293 3.9 45.3 1.0
N F:GLY296 4.0 44.6 1.0
C F:TRP299 4.1 45.6 1.0
CA F:GLY296 4.1 44.1 1.0
C F:GLU293 4.2 39.2 1.0
N F:PRO297 4.4 54.8 1.0
CA F:ALA292 4.4 39.9 1.0
CB F:TRP299 4.5 43.2 1.0
N F:TRP299 4.5 51.6 1.0
CA F:PRO297 4.6 54.3 1.0
CA F:TRP299 4.6 42.3 1.0
CB F:ALA292 4.6 39.2 1.0

Magnesium binding site 6 out of 6 in 8w8n

Go back to Magnesium Binding Sites List in 8w8n
Magnesium binding site 6 out of 6 in the Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermus Thermophilus Initiation Transcription Complex in the Pre- Translocated State within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg502

b:43.2
occ:1.00
 OD2 F:ASP326 2.0 48.5 1.0
O6 G:DG18 2.3 40.8 1.0
O G:HOH102 3.1 36.3 1.0
CG F:ASP326 3.3 48.7 1.0
C6 G:DG18 3.6 41.7 1.0
O G:HOH101 4.1 30.2 1.0
OD1 F:ASP326 4.1 44.8 1.0
CB F:ASP326 4.2 49.8 1.0
N7 G:DA17 4.2 46.4 1.0
OE1 F:GLU324 4.3 45.8 1.0
N6 G:DA17 4.4 37.7 1.0
O6 G:DG19 4.4 48.2 1.0
N1 G:DG19 4.4 46.0 1.0
N1 G:DG18 4.5 41.3 1.0
C5 G:DG18 4.6 42.2 1.0
OP2 G:DC16 4.8 45.5 1.0
C6 G:DG19 4.8 44.0 1.0
N7 G:DG18 4.8 35.3 1.0
C5 G:DA17 4.8 41.8 1.0
O F:ASP326 4.9 56.1 1.0
C6 G:DA17 4.9 40.1 1.0

Reference:

I.C.Nova, J.M.Craig, A.Mazumder, A.H.Laszlo, I.M.Derrington, M.T.Noakes, H.Brinkerhoff, S.Yang, H.Vahedian-Movahed, L.Li, Y.Zhang, J.L.Bowman, J.R.Huang, J.W.Mount, R.H.Ebright, J.H.Gundlach. Nanopore Tweezers Show Fractional-Nucleotide Translocation in Sequence-Dependent Pausing By Rna Polymerase. Proc.Natl.Acad.Sci.Usa V. 121 17121 2024.
ISSN: ESSN 1091-6490
PubMed: 38990947
DOI: 10.1073/PNAS.2321017121
Page generated: Fri Oct 4 22:40:03 2024

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