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:
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
Go back to
Magnesium Binding Sites List in 8hsj
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
Go back to
Magnesium Binding Sites List in 8hsj
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
Go back to
Magnesium Binding Sites List in 8hsj
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
Go back to
Magnesium Binding Sites List in 8hsj
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
Go back to
Magnesium Binding Sites List in 8hsj
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
Go back to
Magnesium Binding Sites List in 8hsj
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 Jul 28 01:29:35 2023
|
