Magnesium in PDB 8e3h: Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part

Other elements in 8e3h:

The structure of Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part also contains other interesting chemical elements:

Fluorine (F) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part (pdb code 8e3h). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part, PDB code: 8e3h:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 8e3h

Go back to Magnesium Binding Sites List in 8e3h
Magnesium binding site 1 out of 6 in the Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Mg1001

b:157.0
occ:1.00
 F3 e:BEF1002 1.9 157.0 1.0
O2B e:ADP1000 2.2 188.5 1.0
BE e:BEF1002 3.2 164.8 1.0
PB e:ADP1000 3.3 191.2 1.0
OG1 e:THR185 3.3 21.8 1.0
O1B e:ADP1000 3.3 168.3 1.0
CE e:LYS184 3.3 23.4 1.0
NZ e:LYS184 3.5 23.4 1.0
F2 e:BEF1002 3.8 177.2 1.0
CB e:LYS184 3.9 23.4 1.0
O1A e:ADP1000 3.9 210.7 1.0
N e:THR185 4.1 21.8 1.0
F1 e:BEF1002 4.3 172.7 1.0
OD2 e:ASP265 4.4 21.4 1.0
O3B e:ADP1000 4.4 178.7 1.0
O3A e:ADP1000 4.4 230.8 1.0
CD e:LYS184 4.5 23.4 1.0
PA e:ADP1000 4.5 227.2 1.0
NH2 f:ARG366 4.5 25.5 1.0
CB e:THR185 4.5 21.8 1.0
C e:LYS184 4.6 23.4 1.0
CA e:THR185 4.6 21.8 1.0
CG e:LYS184 4.7 23.4 1.0
CA e:LYS184 4.7 23.4 1.0
O2A e:ADP1000 4.8 197.9 1.0
OD1 e:ASP265 4.9 21.4 1.0

Magnesium binding site 2 out of 6 in 8e3h

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Magnesium binding site 2 out of 6 in the Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Mg1001

b:157.0
occ:1.00
 F3 f:BEF1002 1.8 157.0 1.0
O1B f:ADP1000 2.2 188.5 1.0
BE f:BEF1002 3.2 164.8 1.0
PB f:ADP1000 3.3 191.2 1.0
OG1 f:THR185 3.3 21.8 1.0
O2B f:ADP1000 3.3 168.3 1.0
CE f:LYS184 3.3 23.4 1.0
NZ f:LYS184 3.5 23.4 1.0
F2 f:BEF1002 3.8 177.2 1.0
CB f:LYS184 3.9 23.4 1.0
O1A f:ADP1000 3.9 210.7 1.0
N f:THR185 4.1 21.8 1.0
F1 f:BEF1002 4.3 172.7 1.0
OD2 f:ASP265 4.4 21.4 1.0
O3B f:ADP1000 4.4 178.7 1.0
O3A f:ADP1000 4.4 230.8 1.0
CD f:LYS184 4.5 23.4 1.0
PA f:ADP1000 4.5 227.2 1.0
CB f:THR185 4.5 21.8 1.0
NH2 a:ARG366 4.6 25.5 1.0
C f:LYS184 4.6 23.4 1.0
CA f:THR185 4.6 21.8 1.0
CG f:LYS184 4.7 23.4 1.0
CA f:LYS184 4.7 23.4 1.0
O2A f:ADP1000 4.8 197.9 1.0
OD1 f:ASP265 4.9 21.4 1.0

Magnesium binding site 3 out of 6 in 8e3h

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Magnesium binding site 3 out of 6 in the Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Mg1001

b:157.0
occ:1.00
 F3 c:BEF1002 1.8 157.0 1.0
O3B c:ADP1000 2.2 188.5 1.0
BE c:BEF1002 3.2 164.8 1.0
PB c:ADP1000 3.3 191.2 1.0
OG1 c:THR185 3.3 21.8 1.0
O2B c:ADP1000 3.3 168.3 1.0
CE c:LYS184 3.3 23.4 1.0
NZ c:LYS184 3.5 23.4 1.0
F2 c:BEF1002 3.8 177.2 1.0
CB c:LYS184 3.9 23.4 1.0
O1A c:ADP1000 3.9 210.7 1.0
N c:THR185 4.1 21.8 1.0
F1 c:BEF1002 4.3 172.7 1.0
OD2 c:ASP265 4.4 21.4 1.0
O1B c:ADP1000 4.4 178.7 1.0
O3A c:ADP1000 4.4 230.8 1.0
CD c:LYS184 4.5 23.4 1.0
PA c:ADP1000 4.5 227.2 1.0
CB c:THR185 4.5 21.8 1.0
NH2 d:ARG366 4.6 25.5 1.0
C c:LYS184 4.6 23.4 1.0
CA c:THR185 4.6 21.8 1.0
CG c:LYS184 4.7 23.4 1.0
CA c:LYS184 4.7 23.4 1.0
O2A c:ADP1000 4.8 197.9 1.0
OD1 c:ASP265 4.9 21.4 1.0

Magnesium binding site 4 out of 6 in 8e3h

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Magnesium binding site 4 out of 6 in the Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg1001

b:157.0
occ:1.00
 F3 b:BEF1002 1.8 157.0 1.0
O1B b:ADP1000 2.2 188.5 1.0
BE b:BEF1002 3.2 164.8 1.0
PB b:ADP1000 3.3 191.2 1.0
OG1 b:THR185 3.3 21.8 1.0
O2B b:ADP1000 3.3 168.3 1.0
CE b:LYS184 3.3 23.4 1.0
NZ b:LYS184 3.5 23.4 1.0
F2 b:BEF1002 3.8 177.2 1.0
CB b:LYS184 3.9 23.4 1.0
O2A b:ADP1000 3.9 210.7 1.0
N b:THR185 4.1 21.8 1.0
F1 b:BEF1002 4.3 172.7 1.0
OD2 b:ASP265 4.4 21.4 1.0
O3B b:ADP1000 4.4 178.7 1.0
O3A b:ADP1000 4.4 230.8 1.0
OE2 b:GLU211 4.4 24.4 1.0
CD b:LYS184 4.5 23.4 1.0
PA b:ADP1000 4.5 227.2 1.0
CB b:THR185 4.5 21.8 1.0
NH2 c:ARG366 4.6 25.5 1.0
C b:LYS184 4.6 23.4 1.0
CA b:THR185 4.6 21.8 1.0
CG b:LYS184 4.7 23.4 1.0
CA b:LYS184 4.7 23.4 1.0
O1A b:ADP1000 4.8 197.9 1.0
OD1 b:ASP265 4.9 21.4 1.0

Magnesium binding site 5 out of 6 in 8e3h

Go back to Magnesium Binding Sites List in 8e3h
Magnesium binding site 5 out of 6 in the Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1001

b:157.0
occ:1.00
 F3 a:BEF1002 1.9 157.0 1.0
O1B a:ADP1000 2.2 188.5 1.0
BE a:BEF1002 3.2 164.8 1.0
PB a:ADP1000 3.3 191.2 1.0
OG1 a:THR185 3.3 21.8 1.0
O2B a:ADP1000 3.3 168.3 1.0
CE a:LYS184 3.3 23.4 1.0
NZ a:LYS184 3.5 23.4 1.0
F2 a:BEF1002 3.8 177.2 1.0
CB a:LYS184 3.9 23.4 1.0
O2A a:ADP1000 3.9 210.7 1.0
N a:THR185 4.1 21.8 1.0
F1 a:BEF1002 4.3 172.7 1.0
OD2 a:ASP265 4.4 21.4 1.0
O3B a:ADP1000 4.4 178.7 1.0
O3A a:ADP1000 4.4 230.8 1.0
OE2 a:GLU211 4.4 24.4 1.0
CD a:LYS184 4.5 23.4 1.0
PA a:ADP1000 4.5 227.2 1.0
CB a:THR185 4.5 21.8 1.0
NH2 b:ARG366 4.6 25.5 1.0
C a:LYS184 4.6 23.4 1.0
CA a:THR185 4.6 21.8 1.0
CG a:LYS184 4.7 23.4 1.0
CA a:LYS184 4.7 23.4 1.0
O1A a:ADP1000 4.8 197.9 1.0
OD1 a:ASP265 4.9 21.4 1.0

Magnesium binding site 6 out of 6 in 8e3h

Go back to Magnesium Binding Sites List in 8e3h
Magnesium binding site 6 out of 6 in the Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Escherichia Coli Rho-Dependent Transcription Pre-Termination Complex Containing 18 Nt Long Rna Spacer, Mg-Adp-BEF3, and Nusg; Rho Hexamer Part within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Mg1001

b:157.0
occ:1.00
 F3 d:BEF1002 1.8 157.0 1.0
O2B d:ADP1000 2.2 188.5 1.0
BE d:BEF1002 3.2 164.8 1.0
PB d:ADP1000 3.3 191.2 1.0
OG1 d:THR185 3.3 21.8 1.0
O1B d:ADP1000 3.3 168.3 1.0
CE d:LYS184 3.3 23.4 1.0
NZ d:LYS184 3.5 23.4 1.0
F2 d:BEF1002 3.8 177.2 1.0
CB d:LYS184 3.9 23.4 1.0
O1A d:ADP1000 3.9 210.7 1.0
N d:THR185 4.1 21.8 1.0
F1 d:BEF1002 4.3 172.7 1.0
OD2 d:ASP265 4.4 21.4 1.0
O3B d:ADP1000 4.4 178.7 1.0
O3A d:ADP1000 4.4 230.8 1.0
NH2 e:ARG366 4.4 25.5 1.0
OE2 d:GLU211 4.4 24.4 1.0
CD d:LYS184 4.5 23.4 1.0
PA d:ADP1000 4.5 227.2 1.0
CB d:THR185 4.5 21.8 1.0
C d:LYS184 4.6 23.4 1.0
CA d:THR185 4.6 21.8 1.0
CG d:LYS184 4.7 23.4 1.0
CA d:LYS184 4.7 23.4 1.0
O2A d:ADP1000 4.8 197.9 1.0
OD1 d:ASP265 4.9 21.4 1.0

Reference:

V.Molodtsov, C.Wang, E.Firlar, J.T.Kaelber, R.H.Ebright. Structural Basis of Rho-Dependent Transcription Termination Biorxiv 2022.
DOI: 10.1101/2022.08.29.505764
Page generated: Fri Oct 4 01:01:36 2024

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