Atomistry » Magnesium » PDB 8hio-8huj » 8hsr
Atomistry »
  Magnesium »
    PDB 8hio-8huj »
      8hsr »

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

Go back to Magnesium Binding Sites List in 8hsr
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

Go back to Magnesium Binding Sites List in 8hsr
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

Go back to Magnesium Binding Sites List in 8hsr
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

Go back to Magnesium Binding Sites List in 8hsr
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

Go back to Magnesium Binding Sites List in 8hsr
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

Go back to Magnesium Binding Sites List in 8hsr
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

Go back to Magnesium Binding Sites List in 8hsr
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy