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Magnesium in PDB 8hsj: Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3

Other elements in 8hsj:

The structure of Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3 also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3 (pdb code 8hsj). 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 Transcription Termination Factor Rho Bound with Adp-BEF3, PDB code: 8hsj:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8hsj

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Magnesium binding site 1 out of 6 in the Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1001

b:178.4
occ:1.00
 O1A A:ADP1000 1.9 178.3 1.0
O3' A:ADP1000 2.0 178.3 1.0
C3' A:ADP1000 2.3 178.3 1.0
O5' A:ADP1000 2.6 178.3 1.0
PA A:ADP1000 2.7 178.3 1.0
OE2 A:GLU221 2.7 163.7 1.0
C5' A:ADP1000 3.0 178.3 1.0
OG1 A:THR191 3.0 168.6 1.0
NH1 A:ARG218 3.0 160.6 1.0
C4' A:ADP1000 3.0 178.3 1.0
O3A A:ADP1000 3.5 178.3 1.0
CD A:GLU221 3.6 163.7 1.0
C2' A:ADP1000 3.7 178.3 1.0
NH2 B:ARG373 3.7 163.8 1.0
CB A:THR191 3.7 168.6 1.0
OE1 A:GLU221 3.9 163.7 1.0
O2A A:ADP1000 4.1 178.3 1.0
CZ A:ARG218 4.2 160.6 1.0
O2' A:ADP1000 4.3 178.3 1.0
O4' A:ADP1000 4.3 178.3 1.0
OE2 A:GLU217 4.4 159.6 1.0
NE B:ARG373 4.5 163.8 1.0
CZ B:ARG373 4.5 163.8 1.0
N A:THR191 4.6 168.6 1.0
C1' A:ADP1000 4.7 178.3 1.0
CG2 A:THR191 4.7 168.6 1.0
PB A:ADP1000 4.7 178.3 1.0
O2B A:ADP1000 4.7 178.3 1.0
NH2 A:ARG218 4.7 160.6 1.0
CG A:GLU221 4.8 163.7 1.0
CA A:THR191 4.8 168.6 1.0

Magnesium binding site 2 out of 6 in 8hsj

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Magnesium binding site 2 out of 6 in the Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1001

b:146.9
occ:1.00
 F1 B:BEF1002 2.3 163.1 1.0
N B:LYS190 2.4 160.8 1.0
CB B:LYS190 2.5 160.8 1.0
O2A B:ADP1000 2.6 169.3 1.0
BE B:BEF1002 2.6 163.1 1.0
C5' B:ADP1000 2.6 169.3 1.0
CA B:LYS190 2.8 160.8 1.0
N B:THR191 3.0 160.5 1.0
NZ B:LYS190 3.1 160.8 1.0
O4' B:ADP1000 3.2 169.3 1.0
F2 B:BEF1002 3.3 163.1 1.0
C B:LYS190 3.4 160.8 1.0
C4' B:ADP1000 3.4 169.3 1.0
O5' B:ADP1000 3.5 169.3 1.0
PA B:ADP1000 3.5 169.3 1.0
C B:GLY189 3.6 162.4 1.0
CG B:LYS190 3.6 160.8 1.0
N B:GLY189 3.8 162.4 1.0
CE B:LYS190 3.8 160.8 1.0
OG1 B:THR191 3.8 160.5 1.0
C8 B:ADP1000 3.9 169.3 1.0
F3 B:BEF1002 4.0 163.1 1.0
CA B:GLY189 4.1 162.4 1.0
CD B:LYS190 4.2 160.8 1.0
C3' B:ADP1000 4.2 169.3 1.0
CA B:THR191 4.3 160.5 1.0
C1' B:ADP1000 4.3 169.3 1.0
O1A B:ADP1000 4.3 169.3 1.0
N9 B:ADP1000 4.4 169.3 1.0
CB B:THR191 4.4 160.5 1.0
N B:ALA188 4.5 173.3 1.0
O B:GLY189 4.6 162.4 1.0
O B:LYS190 4.6 160.8 1.0
C B:ALA188 4.7 173.3 1.0
C2' B:ADP1000 4.8 169.3 1.0
O3A B:ADP1000 4.8 169.3 1.0
O2B B:ADP1000 4.9 169.3 1.0
N7 B:ADP1000 4.9 169.3 1.0

Magnesium binding site 3 out of 6 in 8hsj

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Magnesium binding site 3 out of 6 in the Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1001

b:177.0
occ:1.00
 OE1 C:GLU217 1.8 159.7 1.0
O5' C:ADP1000 1.8 175.2 1.0
C5' C:ADP1000 2.2 175.2 1.0
O1A C:ADP1000 2.3 175.2 1.0
OE2 C:GLU221 2.3 159.8 1.0
PA C:ADP1000 2.4 175.2 1.0
NH1 C:ARG218 2.7 157.6 1.0
OG1 C:THR191 2.9 162.2 1.0
CD C:GLU217 3.0 159.7 1.0
O3A C:ADP1000 3.0 175.2 1.0
CD C:GLU221 3.0 159.8 1.0
OE1 C:GLU221 3.3 159.8 1.0
C4' C:ADP1000 3.4 175.2 1.0
OE2 C:GLU217 3.6 159.7 1.0
O2A C:ADP1000 3.8 175.2 1.0
CB C:THR191 3.9 162.2 1.0
C3' C:ADP1000 4.0 175.2 1.0
CZ C:ARG218 4.0 157.6 1.0
CG C:GLU217 4.1 159.7 1.0
OD2 C:ASP272 4.3 161.8 1.0
O3' C:ADP1000 4.3 175.2 1.0
CG C:GLU221 4.3 159.8 1.0
PB C:ADP1000 4.4 175.2 1.0
BE C:BEF1002 4.4 161.4 1.0
CG2 C:THR191 4.5 162.2 1.0
O4' C:ADP1000 4.5 175.2 1.0
O1B C:ADP1000 4.7 175.2 1.0
NH2 C:ARG218 4.7 157.6 1.0
O3B C:ADP1000 4.8 175.2 1.0
NE C:ARG218 4.9 157.6 1.0
CB C:GLU217 4.9 159.7 1.0
CD C:ARG218 4.9 157.6 1.0
CG C:ARG218 5.0 157.6 1.0

Magnesium binding site 4 out of 6 in 8hsj

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Magnesium binding site 4 out of 6 in the Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1001

b:170.7
occ:1.00
 O1A D:ADP1000 1.8 169.0 1.0
O2B D:ADP1000 2.1 169.0 1.0
OE1 D:GLU217 2.1 165.0 1.0
O3A D:ADP1000 2.3 169.0 1.0
PB D:ADP1000 2.4 169.0 1.0
O1B D:ADP1000 2.5 169.0 1.0
PA D:ADP1000 2.5 169.0 1.0
CD D:GLU217 2.9 165.0 1.0
F2 D:BEF1002 2.9 165.7 1.0
NH1 D:ARG218 3.1 160.0 1.0
OE2 D:GLU217 3.1 165.0 1.0
O2A D:ADP1000 3.5 169.0 1.0
OE2 D:GLU221 3.5 162.7 1.0
O5' D:ADP1000 3.8 169.0 1.0
OG1 D:THR191 3.8 165.1 1.0
O3B D:ADP1000 3.9 169.0 1.0
C5' D:ADP1000 4.0 169.0 1.0
OE1 D:GLU221 4.2 162.7 1.0
CD D:GLU221 4.3 162.7 1.0
CZ D:ARG218 4.3 160.0 1.0
CG D:GLU217 4.3 165.0 1.0
OD2 D:ASP272 4.4 165.8 1.0
BE D:BEF1002 4.5 165.7 1.0
OD1 D:ASP272 4.5 165.8 1.0
O3' D:ADP1000 4.7 169.0 1.0
C3' D:ADP1000 4.7 169.0 1.0
NH2 D:ARG218 4.8 160.0 1.0
CB D:THR191 4.9 165.1 1.0
CG D:ASP272 4.9 165.8 1.0
C4' D:ADP1000 4.9 169.0 1.0

Magnesium binding site 5 out of 6 in 8hsj

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Magnesium binding site 5 out of 6 in the Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1001

b:151.0
occ:1.00
 O5' E:ADP1000 1.8 169.2 1.0
F1 E:BEF1002 1.9 161.2 1.0
O4' E:ADP1000 2.1 169.2 1.0
BE E:BEF1002 2.5 161.2 1.0
C8 E:ADP1000 2.6 169.2 1.0
C5' E:ADP1000 2.8 169.2 1.0
OG1 E:THR191 2.8 158.9 1.0
NZ E:LYS190 2.9 157.6 1.0
C4' E:ADP1000 2.9 169.2 1.0
PA E:ADP1000 3.0 169.2 1.0
O2A E:ADP1000 3.2 169.2 1.0
C1' E:ADP1000 3.2 169.2 1.0
N9 E:ADP1000 3.3 169.2 1.0
F3 E:BEF1002 3.4 161.2 1.0
O3A E:ADP1000 3.6 169.2 1.0
N7 E:ADP1000 3.8 169.2 1.0
N E:THR191 3.8 158.9 1.0
F2 E:BEF1002 3.9 161.2 1.0
CB E:LYS190 3.9 157.6 1.0
C3' E:ADP1000 4.0 169.2 1.0
N E:LYS190 4.1 157.6 1.0
C2' E:ADP1000 4.2 169.2 1.0
CB E:THR191 4.2 158.9 1.0
O1A E:ADP1000 4.2 169.2 1.0
CE E:LYS190 4.3 157.6 1.0
N E:LYS187 4.4 158.3 1.0
CA E:LYS190 4.4 157.6 1.0
CA E:LYS187 4.5 158.3 1.0
C4 E:ADP1000 4.5 169.2 1.0
C E:LYS190 4.6 157.6 1.0
CA E:THR191 4.7 158.9 1.0
O3B E:ADP1000 4.7 169.2 1.0
N E:ALA188 4.7 169.5 1.0
CG E:LYS190 4.7 157.6 1.0
C5 E:ADP1000 4.8 169.2 1.0
PB E:ADP1000 4.8 169.2 1.0
CD E:LYS190 4.9 157.6 1.0
NH2 F:ARG373 4.9 161.1 1.0
N E:GLY189 4.9 162.6 1.0

Magnesium binding site 6 out of 6 in 8hsj

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Magnesium binding site 6 out of 6 in the Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Thermus Thermophilus Transcription Termination Factor Rho Bound with Adp-BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1001

b:178.3
occ:1.00
 O1A F:ADP1000 1.9 178.6 1.0
O3' F:ADP1000 2.0 178.6 1.0
C3' F:ADP1000 2.2 178.6 1.0
O5' F:ADP1000 2.3 178.6 1.0
PA F:ADP1000 2.5 178.6 1.0
C5' F:ADP1000 2.6 178.6 1.0
OE2 F:GLU221 2.7 165.6 1.0
C4' F:ADP1000 2.8 178.6 1.0
NH1 F:ARG218 2.9 163.9 1.0
OG1 F:THR191 3.0 168.6 1.0
O3A F:ADP1000 3.3 178.6 1.0
C2' F:ADP1000 3.6 178.6 1.0
O2A F:ADP1000 3.9 178.6 1.0
CD F:GLU221 3.9 165.6 1.0
NH2 A:ARG373 3.9 167.3 1.0
CZ F:ARG218 4.0 163.9 1.0
CB F:THR191 4.0 168.6 1.0
O4' F:ADP1000 4.0 178.6 1.0
O2' F:ADP1000 4.3 178.6 1.0
NE A:ARG373 4.3 167.3 1.0
OE1 F:GLU217 4.4 163.1 1.0
NH2 F:ARG218 4.5 163.9 1.0
C1' F:ADP1000 4.5 178.6 1.0
OE1 F:GLU221 4.6 165.6 1.0
CZ A:ARG373 4.6 167.3 1.0
PB F:ADP1000 4.7 178.6 1.0
O1B F:ADP1000 4.7 178.6 1.0
N F:THR191 4.8 168.6 1.0
CG F:GLU221 4.9 165.6 1.0
CG2 F:THR191 4.9 168.6 1.0
NE F:ARG218 4.9 163.9 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 08:14:20 2024

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