Magnesium in PDB 8hsr: Thermus Thermophilus Rho-Engaged Rnap Elongation Complex

Enzymatic activity of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex

All present enzymatic activity of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex:
2.7.7.6;

Other elements in 8hsr:

The structure of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex also contains other interesting chemical elements:

Zinc (Zn) 2 atoms
Fluorine (F) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex (pdb code 8hsr). 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 Rho-Engaged Rnap Elongation Complex, PDB code: 8hsr:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 8hsr

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Magnesium binding site 1 out of 7 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:35.8
occ:1.00
 F1 A:BEF1002 2.0 43.0 1.0
O1B A:ADP1000 2.0 45.4 1.0
O3A A:ADP1000 2.3 45.4 1.0
OG1 A:THR191 2.5 0.7 1.0
PB A:ADP1000 2.7 45.4 1.0
BE A:BEF1002 3.0 43.0 1.0
O1A A:ADP1000 3.1 45.4 1.0
PA A:ADP1000 3.2 45.4 1.0
OE1 A:GLU217 3.4 0.7 1.0
CB A:THR191 3.5 0.7 1.0
O3B A:ADP1000 3.7 45.4 1.0
O2B A:ADP1000 3.8 45.4 1.0
F2 A:BEF1002 4.0 43.0 1.0
OE2 A:GLU221 4.0 0.7 1.0
O2A A:ADP1000 4.1 45.4 1.0
CD A:GLU217 4.1 0.7 1.0
OE2 A:GLU217 4.1 0.7 1.0
N A:THR191 4.2 0.7 1.0
F3 A:BEF1002 4.2 43.0 1.0
OE1 A:GLU221 4.3 0.7 1.0
CD A:GLU221 4.4 0.7 1.0
O5' A:ADP1000 4.5 45.4 1.0
CA A:THR191 4.5 0.7 1.0
CG2 A:THR191 4.5 0.7 1.0
NH1 A:ARG218 4.5 0.7 1.0
N A:LYS190 4.9 0.8 1.0

Magnesium binding site 2 out of 7 in 8hsr

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Magnesium binding site 2 out of 7 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:45.7
occ:1.00
 O5' B:ADP501 1.9 43.9 1.0
NH2 C:ARG373 2.3 0.8 1.0
O1A B:ADP501 2.3 43.9 1.0
PA B:ADP501 2.3 43.9 1.0
O3' B:ADP501 2.4 43.9 1.0
NE C:ARG373 2.5 0.8 1.0
C5' B:ADP501 2.5 43.9 1.0
C3' B:ADP501 2.5 43.9 1.0
O3A B:ADP501 2.6 43.9 1.0
C4' B:ADP501 2.7 43.9 1.0
CZ C:ARG373 2.8 0.8 1.0
F1 B:BEF502 3.0 40.5 1.0
OE2 B:GLU221 3.2 0.7 1.0
OG1 B:THR191 3.6 0.7 1.0
O2A B:ADP501 3.8 43.9 1.0
CD C:ARG373 3.8 0.8 1.0
NH1 B:ARG218 4.0 0.7 1.0
C2' B:ADP501 4.0 43.9 1.0
NH1 C:ARG373 4.1 0.8 1.0
O4' B:ADP501 4.1 43.9 1.0
PB B:ADP501 4.1 43.9 1.0
BE B:BEF502 4.1 40.5 1.0
OE2 B:GLU217 4.2 0.7 1.0
F3 B:BEF502 4.4 40.5 1.0
CD B:GLU221 4.4 0.7 1.0
CG2 B:THR191 4.5 0.7 1.0
O1B B:ADP501 4.6 43.9 1.0
CA B:LYS187 4.6 0.7 1.0
CG C:ARG373 4.6 0.8 1.0
F2 B:BEF502 4.6 40.5 1.0
CB B:THR191 4.7 0.7 1.0
O2' B:ADP501 4.7 43.9 1.0
O2B B:ADP501 4.7 43.9 1.0
C1' B:ADP501 4.7 43.9 1.0
O3B B:ADP501 4.9 43.9 1.0

Magnesium binding site 3 out of 7 in 8hsr

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Magnesium binding site 3 out of 7 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1003

b:31.2
occ:1.00
 OG1 C:THR191 1.9 0.7 1.0
O1A C:ADP1002 2.0 43.3 1.0
O2B C:ADP1002 2.0 43.3 1.0
O1B C:ADP1002 2.3 43.3 1.0
PB C:ADP1002 2.5 43.3 1.0
F1 C:BEF1004 2.8 40.5 1.0
OE1 C:GLU217 2.8 0.7 1.0
PA C:ADP1002 3.1 43.3 1.0
O3A C:ADP1002 3.1 43.3 1.0
CB C:THR191 3.1 0.7 1.0
F3 C:BEF1004 3.5 40.5 1.0
BE C:BEF1004 3.6 40.5 1.0
OE2 C:GLU221 3.7 0.7 1.0
CG2 C:THR191 3.8 0.7 1.0
CD C:GLU217 3.8 0.7 1.0
NH1 C:ARG218 3.8 0.7 1.0
OD2 C:ASP272 3.9 0.8 1.0
O3B C:ADP1002 3.9 43.3 1.0
O2A C:ADP1002 4.0 43.3 1.0
OE1 C:GLU221 4.0 0.7 1.0
F2 C:BEF1004 4.1 40.5 1.0
CD C:GLU221 4.1 0.7 1.0
OE2 C:GLU217 4.2 0.7 1.0
O5' C:ADP1002 4.3 43.3 1.0
CA C:THR191 4.3 0.7 1.0
N C:THR191 4.4 0.7 1.0
OD1 C:ASP272 4.5 0.8 1.0
CG C:ASP272 4.6 0.8 1.0
C5' C:ADP1002 4.8 43.3 1.0
CG C:GLU217 5.0 0.7 1.0

Magnesium binding site 4 out of 7 in 8hsr

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Magnesium binding site 4 out of 7 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:35.9
occ:1.00
 F1 D:BEF1002 1.9 43.3 1.0
O1B D:ADP1000 2.1 44.2 1.0
O2A D:ADP1000 2.4 44.2 1.0
OG1 D:THR191 2.5 0.7 1.0
O1A D:ADP1000 2.9 44.2 1.0
PA D:ADP1000 2.9 44.2 1.0
OE1 D:GLU217 3.1 0.7 1.0
BE D:BEF1002 3.4 43.3 1.0
PB D:ADP1000 3.4 44.2 1.0
OE2 D:GLU217 3.5 0.7 1.0
CD D:GLU217 3.6 0.7 1.0
O3A D:ADP1000 3.6 44.2 1.0
CB D:THR191 3.9 0.7 1.0
F3 D:BEF1002 4.1 43.3 1.0
F2 D:BEF1002 4.1 43.3 1.0
OE2 D:GLU221 4.2 0.7 1.0
O2B D:ADP1000 4.3 44.2 1.0
NH1 D:ARG218 4.4 0.7 1.0
O3B D:ADP1000 4.4 44.2 1.0
O5' D:ADP1000 4.4 44.2 1.0
OD2 D:ASP272 4.6 0.8 1.0
N D:THR191 4.6 0.7 1.0
CG2 D:THR191 4.7 0.7 1.0
CA D:THR191 4.7 0.7 1.0
CD D:GLU221 4.8 0.7 1.0
NH2 D:ARG276 4.8 0.8 1.0
CG D:GLU217 4.9 0.7 1.0
OE1 D:GLU221 4.9 0.7 1.0
OD1 D:ASP272 4.9 0.8 1.0
C5' D:ADP1000 4.9 44.2 1.0

Magnesium binding site 5 out of 7 in 8hsr

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Magnesium binding site 5 out of 7 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1001

b:37.0
occ:1.00
 O2B E:ADP1000 2.0 42.7 1.0
O2A E:ADP1000 2.3 42.7 1.0
PA E:ADP1000 2.8 42.7 1.0
O1A E:ADP1000 2.8 42.7 1.0
CG2 E:THR191 2.9 0.7 1.0
F2 E:BEF1002 3.1 44.9 1.0
PB E:ADP1000 3.1 42.7 1.0
O3A E:ADP1000 3.4 42.7 1.0
O1B E:ADP1000 3.8 42.7 1.0
F1 E:BEF1002 3.8 44.9 1.0
OG1 E:THR191 3.9 0.7 1.0
NH1 E:ARG218 4.0 0.7 1.0
CB E:THR191 4.0 0.7 1.0
BE E:BEF1002 4.0 44.9 1.0
OE1 E:GLU217 4.0 0.7 1.0
OE2 E:GLU221 4.3 0.7 1.0
O5' E:ADP1000 4.3 42.7 1.0
O3B E:ADP1000 4.4 42.7 1.0
N E:THR191 4.4 0.7 1.0
CE E:LYS190 4.5 0.8 1.0
CA E:THR191 4.8 0.7 1.0
CB E:LYS190 4.9 0.8 1.0

Magnesium binding site 6 out of 7 in 8hsr

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Magnesium binding site 6 out of 7 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1001

b:32.8
occ:1.00
 O1A F:ADP1000 1.9 44.9 1.0
O1B F:ADP1000 2.0 44.9 1.0
O3A F:ADP1000 2.4 44.9 1.0
PA F:ADP1000 2.7 44.9 1.0
PB F:ADP1000 2.7 44.9 1.0
F1 F:BEF1002 2.8 41.9 1.0
OE2 F:GLU217 3.1 0.7 1.0
O3B F:ADP1000 3.3 44.9 1.0
OG1 F:THR191 3.5 0.7 1.0
F2 F:BEF1002 3.5 41.9 1.0
BE F:BEF1002 3.7 41.9 1.0
CD F:GLU217 3.7 0.7 1.0
OE1 F:GLU217 3.7 0.7 1.0
O2A F:ADP1000 3.7 44.9 1.0
O5' F:ADP1000 3.8 44.9 1.0
C5' F:ADP1000 3.9 44.9 1.0
O2B F:ADP1000 4.0 44.9 1.0
OE2 F:GLU221 4.4 0.7 1.0
NH1 F:ARG218 4.4 0.7 1.0
CB F:THR191 4.5 0.7 1.0
F3 F:BEF1002 4.7 41.9 1.0
NH1 F:ARG276 4.9 0.8 1.0
N F:LYS187 4.9 0.7 1.0

Magnesium binding site 7 out of 7 in 8hsr

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Magnesium binding site 7 out of 7 in the Thermus Thermophilus Rho-Engaged Rnap Elongation Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Thermus Thermophilus Rho-Engaged Rnap Elongation Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg1603

b:96.7
occ:1.00
 OD1 J:ASP741 2.0 86.1 1.0
OP1 R:U29 2.0 105.0 1.0
OD1 J:ASP739 2.0 89.5 1.0
O3' R:C28 2.4 101.7 1.0
P R:U29 2.7 105.0 1.0
CG J:ASP741 2.8 86.1 1.0
CG J:ASP739 2.9 89.5 1.0
OD2 J:ASP743 2.9 86.5 1.0
OD2 J:ASP741 2.9 86.1 1.0
OD2 J:ASP739 3.1 89.5 1.0
CG J:ASP743 3.2 86.5 1.0
CB J:ASP743 3.5 86.5 1.0
C3' R:C28 3.7 101.7 1.0
OP2 R:U29 3.8 105.0 1.0
O5' R:U29 3.8 105.0 1.0
OD1 J:ASP743 3.8 86.5 1.0
O2' R:C28 3.8 101.7 1.0
CB J:ASP739 4.2 89.5 1.0
CB J:ASP741 4.2 86.1 1.0
N J:ASP743 4.3 86.5 1.0
C2' R:C28 4.3 101.7 1.0
N J:ASP739 4.3 89.5 1.0
C4' R:C28 4.3 101.7 1.0
N J:ASP741 4.4 86.1 1.0
C5' R:U29 4.5 105.0 1.0
CA J:ASP743 4.5 86.5 1.0
C J:ASP739 4.5 89.5 1.0
O J:ASP739 4.5 89.5 1.0
CA J:ASP739 4.6 89.5 1.0
CA J:ASP741 4.7 86.1 1.0
NH2 J:ARG704 4.7 81.3 1.0
C J:ASP741 4.8 86.1 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 08:15:10 2024

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