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Magnesium in PDB 6z9t: Transcription Termination Intermediate Complex 5

Enzymatic activity of Transcription Termination Intermediate Complex 5

All present enzymatic activity of Transcription Termination Intermediate Complex 5:
2.7.7.6;

Other elements in 6z9t:

The structure of Transcription Termination Intermediate Complex 5 also contains other interesting chemical elements:

Fluorine (F) 15 atoms
Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Transcription Termination Intermediate Complex 5 (pdb code 6z9t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Transcription Termination Intermediate Complex 5, PDB code: 6z9t:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6z9t

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Magnesium binding site 1 out of 6 in the Transcription Termination Intermediate Complex 5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Transcription Termination Intermediate Complex 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Mg1001

b:0.9
occ:1.00
 F3 a:BEF1002 2.0 0.9 1.0
OG1 a:THR185 2.0 0.6 1.0
O a:HOH1102 2.1 1.0 1.0
O a:HOH1103 2.1 0.1 1.0
O a:HOH1101 2.3 0.2 1.0
O2B a:ADP1000 2.8 0.5 1.0
O1B a:ADP1000 2.9 0.5 1.0
BE a:BEF1002 3.1 0.9 1.0
F2 a:BEF1002 3.3 0.9 1.0
PB a:ADP1000 3.3 0.5 1.0
CB a:THR185 3.4 0.6 1.0
NZ a:LYS184 3.7 0.1 1.0
N a:THR185 4.0 0.6 1.0
O2A a:ADP1000 4.1 0.5 1.0
CG2 a:THR185 4.1 0.6 1.0
O1A a:ADP1000 4.1 0.5 1.0
CG a:LYS184 4.2 0.1 1.0
CA a:THR185 4.2 0.6 1.0
O3A a:ADP1000 4.3 0.5 1.0
PA a:ADP1000 4.3 0.5 1.0
OE1 a:GLU215 4.3 0.7 1.0
OE2 a:GLU215 4.4 0.7 1.0
CE a:LYS184 4.4 0.1 1.0
F1 a:BEF1002 4.4 0.9 1.0
O3B a:ADP1000 4.6 0.5 1.0
NH1 a:ARG212 4.6 0.0 1.0
OE2 a:GLU211 4.7 0.6 1.0
CD a:GLU215 4.7 0.7 1.0
CD a:LYS184 5.0 0.1 1.0

Magnesium binding site 2 out of 6 in 6z9t

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Magnesium binding site 2 out of 6 in the Transcription Termination Intermediate Complex 5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Transcription Termination Intermediate Complex 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg1001

b:98.4
occ:1.00
 O3B b:ADP1000 2.0 0.6 1.0
F3 b:BEF1002 2.0 1.0 1.0
OG1 b:THR185 2.0 92.3 1.0
O b:HOH1103 2.0 91.6 1.0
O b:HOH1102 2.0 0.1 1.0
O b:HOH1101 2.2 0.3 1.0
PB b:ADP1000 3.1 0.6 1.0
BE b:BEF1002 3.4 1.0 1.0
CB b:THR185 3.4 92.3 1.0
O2B b:ADP1000 3.7 0.6 1.0
O1B b:ADP1000 3.8 0.6 1.0
F2 b:BEF1002 4.0 1.0 1.0
CG2 b:THR185 4.0 92.3 1.0
OE2 b:GLU215 4.1 0.2 1.0
NZ b:LYS184 4.1 93.8 1.0
OE1 b:GLU215 4.2 0.2 1.0
N b:THR185 4.2 92.3 1.0
CA b:THR185 4.3 92.3 1.0
O3A b:ADP1000 4.4 0.6 1.0
CD b:GLU215 4.5 0.2 1.0
NH1 b:ARG212 4.5 0.8 1.0
F1 b:BEF1002 4.5 1.0 1.0
O2A b:ADP1000 4.6 0.6 1.0
CG b:LYS184 4.6 93.8 1.0
O1A b:ADP1000 4.7 0.6 1.0
OE2 b:GLU211 4.7 0.4 1.0
CE b:LYS184 4.7 93.8 1.0
PA b:ADP1000 4.8 0.6 1.0
NH2 a:ARG366 4.9 0.1 1.0

Magnesium binding site 3 out of 6 in 6z9t

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Magnesium binding site 3 out of 6 in the Transcription Termination Intermediate Complex 5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Transcription Termination Intermediate Complex 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Mg1001

b:90.4
occ:1.00
 O c:HOH1101 1.9 93.9 1.0
O3B c:ADP1000 2.0 0.0 1.0
O c:HOH1102 2.2 88.0 1.0
F3 c:BEF1002 2.2 0.3 1.0
O c:HOH1103 2.2 0.4 1.0
OG1 c:THR185 2.4 89.3 1.0
PB c:ADP1000 3.4 0.0 1.0
BE c:BEF1002 3.6 0.3 1.0
NZ c:LYS184 3.6 86.4 1.0
CB c:THR185 3.8 89.3 1.0
O2B c:ADP1000 3.9 0.0 1.0
O2A c:ADP1000 4.0 0.0 1.0
OE1 c:GLU215 4.0 95.3 1.0
F2 c:BEF1002 4.1 0.3 1.0
NH1 c:ARG212 4.1 86.2 1.0
OE2 c:GLU211 4.2 92.6 1.0
CG2 c:THR185 4.3 89.3 1.0
OE2 c:GLU215 4.3 95.3 1.0
O1A c:ADP1000 4.3 0.0 1.0
O1B c:ADP1000 4.3 0.0 1.0
O3A c:ADP1000 4.3 0.0 1.0
CE c:LYS184 4.4 86.4 1.0
PA c:ADP1000 4.4 0.0 1.0
CG c:LYS184 4.5 86.4 1.0
CD c:GLU215 4.5 95.3 1.0
N c:THR185 4.5 89.3 1.0
CA c:THR185 4.6 89.3 1.0
F1 c:BEF1002 4.7 0.3 1.0
NH2 b:ARG366 4.8 91.9 1.0

Magnesium binding site 4 out of 6 in 6z9t

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Magnesium binding site 4 out of 6 in the Transcription Termination Intermediate Complex 5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Transcription Termination Intermediate Complex 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Mg1001

b:0.1
occ:1.00
 OG1 d:THR185 2.0 0.6 1.0
F3 d:BEF1002 2.1 0.6 1.0
O d:HOH1101 2.1 0.6 1.0
O d:HOH1103 2.1 99.0 1.0
O1B d:ADP1000 2.3 0.5 1.0
O d:HOH1102 2.4 0.6 1.0
O2B d:ADP1000 2.9 0.5 1.0
PB d:ADP1000 3.1 0.5 1.0
BE d:BEF1002 3.3 0.6 1.0
CB d:THR185 3.5 0.6 1.0
F2 d:BEF1002 3.5 0.6 1.0
N d:THR185 4.0 0.6 1.0
O2A d:ADP1000 4.0 0.5 1.0
NZ d:LYS184 4.0 91.8 1.0
O1A d:ADP1000 4.1 0.5 1.0
O3A d:ADP1000 4.2 0.5 1.0
O3B d:ADP1000 4.2 0.5 1.0
CG d:LYS184 4.2 91.8 1.0
CG2 d:THR185 4.3 0.6 1.0
CA d:THR185 4.3 0.6 1.0
PA d:ADP1000 4.3 0.5 1.0
OE2 d:GLU215 4.5 0.5 1.0
F1 d:BEF1002 4.5 0.6 1.0
CE d:LYS184 4.5 91.8 1.0
OE1 d:GLU215 4.7 0.5 1.0
N d:LYS184 4.8 91.8 1.0
CD d:GLU215 4.9 0.5 1.0
NH1 d:ARG212 5.0 95.0 1.0
NH2 c:ARG366 5.0 95.7 1.0

Magnesium binding site 5 out of 6 in 6z9t

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Magnesium binding site 5 out of 6 in the Transcription Termination Intermediate Complex 5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Transcription Termination Intermediate Complex 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Mg1001

b:0.1
occ:1.00
 F3 e:BEF1002 2.0 0.5 1.0
OG1 e:THR185 2.0 0.1 1.0
O1B e:ADP1000 2.0 0.6 1.0
O e:HOH1102 2.0 0.5 1.0
O e:HOH1103 2.1 0.6 1.0
O e:HOH1101 2.4 0.0 1.0
PB e:ADP1000 3.1 0.6 1.0
O2B e:ADP1000 3.2 0.6 1.0
CB e:THR185 3.3 0.1 1.0
BE e:BEF1002 3.4 0.5 1.0
N e:THR185 3.7 0.1 1.0
F2 e:BEF1002 3.8 0.5 1.0
O3B e:ADP1000 4.1 0.6 1.0
CA e:THR185 4.1 0.1 1.0
O1A e:ADP1000 4.1 0.6 1.0
O3A e:ADP1000 4.2 0.6 1.0
CG e:LYS184 4.2 0.4 1.0
CG2 e:THR185 4.3 0.1 1.0
O2A e:ADP1000 4.3 0.6 1.0
N e:LYS184 4.3 0.4 1.0
PA e:ADP1000 4.4 0.6 1.0
NZ e:LYS184 4.5 0.4 1.0
F1 e:BEF1002 4.5 0.5 1.0
OE2 e:GLU215 4.7 0.3 1.0
C e:LYS184 4.8 0.4 1.0
CE e:LYS184 4.8 0.4 1.0
N e:GLY183 4.8 0.5 1.0
CA e:GLY183 4.9 0.5 1.0
C e:GLY183 5.0 0.5 1.0

Magnesium binding site 6 out of 6 in 6z9t

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Magnesium binding site 6 out of 6 in the Transcription Termination Intermediate Complex 5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Transcription Termination Intermediate Complex 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg1501

b:91.2
occ:1.00
 OD1 Y:ASP462 2.1 68.5 1.0
OD1 Y:ASP460 2.1 76.2 1.0
OD1 Y:ASP464 2.4 83.9 1.0
OD2 Y:ASP462 2.7 68.5 1.0
CG Y:ASP462 2.7 68.5 1.0
CG Y:ASP460 2.7 76.2 1.0
OD2 Y:ASP460 2.8 76.2 1.0
OD2 Y:ASP464 3.0 83.9 1.0
CG Y:ASP464 3.1 83.9 1.0
CB Y:ASP460 4.1 76.2 1.0
O Y:ASP460 4.1 76.2 1.0
CB Y:ASP462 4.2 68.5 1.0
N Y:ASP460 4.4 76.2 1.0
C Y:ASP460 4.5 76.2 1.0
CB Y:ASP464 4.5 83.9 1.0
CA Y:ASP460 4.6 76.2 1.0
N Y:ASP462 4.6 68.5 1.0
NH1 Y:ARG425 4.7 75.4 1.0
CA Y:ASP462 4.9 68.5 1.0
N Y:ASP464 4.9 83.9 1.0

Reference:

N.Said, T.Hilal, B.Loll, M.C.Wahl. Snapshots Along A Factor-Mediated, Elongation Complex-Dependent Path to Transcription Termination To Be Published.
Page generated: Wed Aug 13 22:01:57 2025

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