Magnesium in PDB 8hsl: Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer

Enzymatic activity of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer:
2.7.7.6;

Other elements in 8hsl:

The structure of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer also contains other interesting chemical elements:

Fluorine (F) 18 atoms
Zinc (Zn) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer (pdb code 8hsl). 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 Rna Polymerase Bound with An Inverted Rho Hexamer, PDB code: 8hsl:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8hsl

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Magnesium binding site 1 out of 7 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg1602

b:27.1
occ:1.00
 OD1 J:ASP739 1.9 51.9 1.0
OD2 J:ASP741 1.9 53.5 1.0
CG J:ASP741 2.2 55.5 1.0
OD1 J:ASP741 2.2 56.1 1.0
OD2 J:ASP743 2.5 58.3 1.0
CG J:ASP739 2.6 52.4 1.0
OD2 J:ASP739 2.8 55.2 1.0
CG J:ASP743 3.2 58.8 1.0
CB J:ASP741 3.5 57.0 1.0
OD1 J:ASP743 3.6 58.0 1.0
CB J:ASP739 4.0 52.3 1.0
N J:ASP739 4.0 53.0 1.0
N J:ASP741 4.1 59.6 1.0
CB J:ASP743 4.2 58.2 1.0
CA J:ASP741 4.3 58.4 1.0
CA J:ASP739 4.3 54.2 1.0
C J:ASP739 4.4 54.8 1.0
O J:ASP739 4.5 56.9 1.0
C J:ASP741 4.8 58.0 1.0
N J:ASP743 4.8 56.9 1.0
N J:PHE740 4.9 56.7 1.0
N J:GLY742 5.0 58.5 1.0

Magnesium binding site 2 out of 7 in 8hsl

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Magnesium binding site 2 out of 7 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:58.3
occ:1.00
 OG1 A:THR191 1.8 0.7 1.0
F3 A:BEF1002 1.8 37.7 1.0
O2B A:ADP1000 1.9 59.6 1.0
NZ A:LYS190 2.3 0.8 1.0
PB A:ADP1000 3.1 67.0 1.0
CB A:THR191 3.2 0.7 1.0
BE A:BEF1002 3.3 57.7 1.0
O3B A:ADP1000 3.5 60.5 1.0
O3A A:ADP1000 3.5 51.0 1.0
CE A:LYS190 3.5 0.8 1.0
NH1 A:ARG218 3.8 0.7 1.0
CG2 A:THR191 4.0 0.7 1.0
F2 A:BEF1002 4.0 67.0 1.0
N A:THR191 4.0 0.7 1.0
O2A A:ADP1000 4.0 70.2 1.0
CA A:THR191 4.1 0.7 1.0
OD2 A:ASP272 4.1 0.8 1.0
PA A:ADP1000 4.2 51.2 1.0
F1 A:BEF1002 4.3 74.4 1.0
O1B A:ADP1000 4.4 56.9 1.0
OE1 A:GLU221 4.4 0.7 1.0
OE2 A:GLU221 4.4 0.7 1.0
O1A A:ADP1000 4.4 47.3 1.0
OE1 A:GLU217 4.4 0.7 1.0
NH2 B:ARG373 4.6 0.8 1.0
CD A:GLU221 4.8 0.7 1.0
OD1 A:ASP272 4.8 0.8 1.0
CD A:LYS190 4.8 0.8 1.0
CG A:ASP272 4.9 0.8 1.0
CZ A:ARG218 4.9 0.7 1.0
CB A:LYS190 5.0 0.8 1.0

Magnesium binding site 3 out of 7 in 8hsl

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Magnesium binding site 3 out of 7 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:95.1
occ:1.00
 O2B B:ADP1000 1.8 88.8 1.0
OG1 B:THR191 2.0 0.7 1.0
F3 B:BEF1002 2.3 91.9 1.0
NZ B:LYS190 2.4 0.8 1.0
OE2 B:GLU217 2.7 0.7 1.0
PB B:ADP1000 3.3 107.9 1.0
CB B:THR191 3.4 0.7 1.0
CE B:LYS190 3.5 0.8 1.0
CD B:GLU217 3.5 0.7 1.0
BE B:BEF1002 3.6 85.5 1.0
NH1 B:ARG218 3.7 0.7 1.0
OD2 B:ASP272 3.8 0.8 1.0
O3A B:ADP1000 3.9 111.3 1.0
OE1 B:GLU217 3.9 0.7 1.0
F2 B:BEF1002 4.0 83.2 1.0
OE1 B:GLU221 4.0 0.7 1.0
CG2 B:THR191 4.1 0.7 1.0
CG B:LYS190 4.2 0.8 1.0
O3B B:ADP1000 4.2 93.1 1.0
O1B B:ADP1000 4.3 94.3 1.0
OE2 B:GLU221 4.4 0.7 1.0
CD B:LYS190 4.4 0.8 1.0
N B:THR191 4.4 0.7 1.0
CA B:THR191 4.4 0.7 1.0
OD1 B:ASP272 4.4 0.8 1.0
CG B:ASP272 4.5 0.8 1.0
CD B:GLU221 4.6 0.7 1.0
CG B:GLU217 4.6 0.7 1.0
O1A B:ADP1000 4.7 107.8 1.0
PA B:ADP1000 4.7 115.9 1.0
F1 B:BEF1002 4.8 70.8 1.0
O2A B:ADP1000 4.9 89.7 1.0
CZ B:ARG218 4.9 0.7 1.0

Magnesium binding site 4 out of 7 in 8hsl

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Magnesium binding site 4 out of 7 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:72.5
occ:1.00
 OG1 C:THR191 1.9 0.7 1.0
O2B C:ADP1000 1.9 91.8 1.0
F3 C:BEF1002 2.3 74.8 1.0
O2A C:ADP1000 2.9 72.2 1.0
PB C:ADP1000 3.0 88.2 1.0
O3A C:ADP1000 3.2 77.3 1.0
CB C:THR191 3.3 0.7 1.0
BE C:BEF1002 3.4 71.5 1.0
PA C:ADP1000 3.6 67.3 1.0
O1B C:ADP1000 3.7 75.8 1.0
F2 C:BEF1002 3.7 66.6 1.0
N C:THR191 4.0 0.7 1.0
NH1 C:ARG218 4.0 0.7 1.0
CG2 C:THR191 4.1 0.7 1.0
CA C:THR191 4.1 0.7 1.0
OD2 C:ASP272 4.2 0.8 1.0
O3B C:ADP1000 4.3 71.5 1.0
OE2 C:GLU221 4.3 0.7 1.0
O1A C:ADP1000 4.4 62.4 1.0
OD1 C:ASP272 4.4 0.8 1.0
OE1 C:GLU217 4.5 0.7 1.0
OE1 C:GLU221 4.6 0.7 1.0
F1 C:BEF1002 4.7 77.2 1.0
CG C:ASP272 4.8 0.8 1.0
NZ C:LYS190 4.8 0.8 1.0
CD C:GLU221 4.8 0.7 1.0
CB C:LYS190 4.9 0.8 1.0
CD C:GLU217 4.9 0.7 1.0
O5' C:ADP1000 4.9 70.9 1.0

Magnesium binding site 5 out of 7 in 8hsl

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Magnesium binding site 5 out of 7 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:37.8
occ:1.00
 O2B D:ADP1000 1.9 48.6 1.0
F3 D:BEF1002 1.9 28.4 1.0
OG1 D:THR191 2.1 0.7 1.0
NZ D:LYS190 3.0 0.8 1.0
O1A D:ADP1000 3.0 21.2 1.0
PB D:ADP1000 3.1 32.0 1.0
CB D:THR191 3.4 0.7 1.0
BE D:BEF1002 3.4 30.6 1.0
CE D:LYS190 3.4 0.8 1.0
NH1 D:ARG218 3.4 0.7 1.0
O3A D:ADP1000 3.5 21.0 1.0
O1B D:ADP1000 3.6 28.6 1.0
PA D:ADP1000 3.8 24.4 1.0
OE2 D:GLU221 3.8 0.7 1.0
F2 D:BEF1002 3.9 38.3 1.0
N D:THR191 4.1 0.7 1.0
OE1 D:GLU217 4.2 0.7 1.0
CD D:LYS190 4.2 0.8 1.0
CG2 D:THR191 4.3 0.7 1.0
CA D:THR191 4.3 0.7 1.0
O2A D:ADP1000 4.4 23.6 1.0
OE1 D:GLU221 4.4 0.7 1.0
CZ D:ARG218 4.4 0.7 1.0
O3B D:ADP1000 4.4 27.7 1.0
F1 D:BEF1002 4.5 26.2 1.0
CD D:GLU221 4.5 0.7 1.0
NH2 D:ARG218 4.6 0.7 1.0
OD2 D:ASP272 4.7 0.8 1.0
NH2 E:ARG373 4.9 0.8 1.0
CB D:LYS190 4.9 0.8 1.0

Magnesium binding site 6 out of 7 in 8hsl

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Magnesium binding site 6 out of 7 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1001

b:25.8
occ:1.00
 O2B E:ADP1000 1.9 31.6 1.0
F2 E:BEF1002 2.1 45.3 1.0
F3 E:BEF1002 2.5 29.5 1.0
BE E:BEF1002 2.8 32.3 1.0
PB E:ADP1000 2.9 25.1 1.0
OG1 E:THR191 2.9 0.7 1.0
O1B E:ADP1000 3.2 27.5 1.0
O3A E:ADP1000 3.4 32.5 1.0
NZ E:LYS190 3.8 0.8 1.0
O1A E:ADP1000 4.1 22.3 1.0
F1 E:BEF1002 4.1 25.0 1.0
NH1 E:ARG218 4.2 0.7 1.0
O3B E:ADP1000 4.3 23.5 1.0
CB E:THR191 4.3 0.7 1.0
PA E:ADP1000 4.3 23.6 1.0
CE E:LYS190 4.5 0.8 1.0
N E:THR191 4.6 0.7 1.0
CD E:LYS190 4.6 0.8 1.0
CB E:LYS190 4.7 0.8 1.0
OE1 E:GLU217 4.8 0.7 1.0
O2A E:ADP1000 4.8 17.6 1.0
N E:LYS187 4.9 0.7 1.0
NH2 E:ARG218 4.9 0.7 1.0
OE2 E:GLU221 5.0 0.7 1.0
OD1 E:ASP272 5.0 0.8 1.0

Magnesium binding site 7 out of 7 in 8hsl

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Magnesium binding site 7 out of 7 in the Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thermus Thermophilus Rna Polymerase Bound with An Inverted Rho Hexamer within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1001

b:45.5
occ:1.00
 O2B F:ADP1000 1.8 48.7 1.0
F3 F:BEF1002 2.2 26.9 1.0
OG1 F:THR191 2.3 0.7 1.0
PB F:ADP1000 2.7 32.8 1.0
O3A F:ADP1000 2.8 54.5 1.0
NH1 F:ARG218 2.9 0.7 1.0
NZ F:LYS190 3.2 0.8 1.0
O1B F:ADP1000 3.2 32.5 1.0
BE F:BEF1002 3.3 37.9 1.0
CB F:THR191 3.5 0.7 1.0
OE2 F:GLU221 3.5 0.7 1.0
OE1 F:GLU221 3.9 0.7 1.0
CZ F:ARG218 4.0 0.7 1.0
CG2 F:THR191 4.1 0.7 1.0
CD F:GLU221 4.1 0.7 1.0
O3B F:ADP1000 4.1 33.3 1.0
CE F:LYS190 4.1 0.8 1.0
OE1 F:GLU217 4.1 0.7 1.0
F2 F:BEF1002 4.2 47.5 1.0
PA F:ADP1000 4.2 36.0 1.0
NH2 F:ARG218 4.3 0.7 1.0
F1 F:BEF1002 4.4 32.8 1.0
OD2 F:ASP272 4.6 0.8 1.0
CA F:THR191 4.6 0.7 1.0
CG F:LYS190 4.7 0.8 1.0
O2A F:ADP1000 4.7 34.5 1.0
N F:THR191 4.7 0.7 1.0
O1A F:ADP1000 4.7 53.8 1.0
NH2 A:ARG373 4.8 0.8 1.0
CD F:GLU217 4.9 0.7 1.0

Reference:

Y.Murayama, H.Ehara, M.Aoki, M.Goto, T.Yokoyama, S.I.Sekine. Structural Basis of the Transcription Termination Factor Rho Engagement with Transcribing Rna Polymerase From Thermus Thermophilus. Sci Adv V. 9 E7093 2023.
ISSN: ESSN 2375-2548
PubMed: 36753546
DOI: 10.1126/SCIADV.ADE7093
Page generated: Fri Oct 4 08:14:37 2024

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