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Magnesium in PDB 6z9p: Transcription Termination Intermediate Complex 1

Enzymatic activity of Transcription Termination Intermediate Complex 1

All present enzymatic activity of Transcription Termination Intermediate Complex 1:
2.7.7.6;

Other elements in 6z9p:

The structure of Transcription Termination Intermediate Complex 1 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 1 (pdb code 6z9p). 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 1, PDB code: 6z9p:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6z9p

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Mg1001

b:0.5
occ:1.00
 O3B b:ADP1000 2.0 0.9 1.0
O b:HOH1101 2.1 0.7 1.0
O b:HOH1103 2.1 0.1 1.0
O b:HOH1102 2.1 0.6 1.0
OG1 b:THR185 2.4 0.5 1.0
F3 a:BEF501 2.6 0.5 1.0
PB b:ADP1000 3.3 0.9 1.0
BE a:BEF501 3.5 0.5 1.0
O2B b:ADP1000 3.6 0.9 1.0
O1A b:ADP1000 3.7 0.9 1.0
CB b:THR185 3.8 0.5 1.0
N b:THR185 3.8 0.5 1.0
PA b:ADP1000 4.2 0.9 1.0
O2A b:ADP1000 4.2 0.9 1.0
CA b:THR185 4.2 0.5 1.0
O3A b:ADP1000 4.2 0.9 1.0
NH2 a:ARG366 4.3 0.7 1.0
CB b:LYS184 4.4 0.1 1.0
O1B b:ADP1000 4.4 0.9 1.0
F2 a:BEF501 4.5 0.5 1.0
C b:LYS184 4.6 0.1 1.0
F1 a:BEF501 4.7 0.5 1.0
CG2 b:THR185 4.7 0.5 1.0
OE1 b:GLU215 4.8 0.5 1.0
N b:LYS184 4.8 0.1 1.0
CA b:LYS184 4.9 0.1 1.0
OD2 b:ASP265 4.9 0.1 1.0
CE b:LYS184 4.9 0.1 1.0
OD1 b:ASP265 5.0 0.1 1.0

Magnesium binding site 2 out of 6 in 6z9p

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Magnesium binding site 2 out of 6 in the Transcription Termination Intermediate Complex 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
c:Mg1001

b:0.1
occ:1.00
 O2B c:ADP1000 2.0 0.6 1.0
O c:HOH1102 2.0 0.1 1.0
O c:HOH1101 2.1 0.8 1.0
F3 b:BEF1002 2.2 0.4 1.0
O c:HOH1103 2.2 0.2 1.0
OG1 c:THR185 2.4 0.5 1.0
PB c:ADP1000 3.3 0.6 1.0
BE b:BEF1002 3.3 0.4 1.0
O3B c:ADP1000 3.6 0.6 1.0
NH2 b:ARG366 3.7 0.7 1.0
CB c:THR185 3.8 0.5 1.0
N c:THR185 3.8 0.5 1.0
O2A c:ADP1000 3.8 0.6 1.0
O3A c:ADP1000 3.8 0.6 1.0
PA c:ADP1000 4.1 0.6 1.0
O1A c:ADP1000 4.2 0.6 1.0
CA c:THR185 4.3 0.5 1.0
F1 b:BEF1002 4.3 0.4 1.0
F2 b:BEF1002 4.3 0.4 1.0
CB c:LYS184 4.4 0.2 1.0
O1B c:ADP1000 4.5 0.6 1.0
CZ b:ARG366 4.6 0.7 1.0
N c:LYS184 4.7 0.2 1.0
C c:LYS184 4.7 0.2 1.0
CG2 c:THR185 4.8 0.5 1.0
CA c:LYS184 4.8 0.2 1.0
OE1 c:GLU215 4.9 0.8 1.0
NH1 b:ARG366 4.9 0.7 1.0
CE c:LYS184 5.0 0.2 1.0

Magnesium binding site 3 out of 6 in 6z9p

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Magnesium binding site 3 out of 6 in the Transcription Termination Intermediate Complex 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
d:Mg1001

b:0.0
occ:1.00
 O d:HOH1101 2.1 0.1 1.0
O d:HOH1103 2.1 0.2 1.0
O2B d:ADP1000 2.1 0.2 1.0
O d:HOH1102 2.1 0.3 1.0
OG1 d:THR185 2.5 0.5 1.0
F3 c:BEF1002 2.6 0.1 1.0
PB d:ADP1000 3.6 0.2 1.0
N d:THR185 3.6 0.5 1.0
CB d:THR185 3.8 0.5 1.0
BE c:BEF1002 3.8 0.1 1.0
O1A d:ADP1000 3.9 0.2 1.0
O2A d:ADP1000 4.0 0.2 1.0
CA d:THR185 4.0 0.5 1.0
CB d:LYS184 4.0 0.4 1.0
PA d:ADP1000 4.2 0.2 1.0
O3B d:ADP1000 4.3 0.2 1.0
O3A d:ADP1000 4.3 0.2 1.0
C d:LYS184 4.3 0.4 1.0
OD2 d:ASP265 4.4 0.7 1.0
OD1 d:ASP265 4.4 0.7 1.0
O1B d:ADP1000 4.5 0.2 1.0
F2 c:BEF1002 4.6 0.1 1.0
CA d:LYS184 4.6 0.4 1.0
CE d:LYS184 4.6 0.4 1.0
CG2 d:THR185 4.7 0.5 1.0
CG d:ASP265 4.7 0.7 1.0
N d:LYS184 4.7 0.4 1.0
NH2 c:ARG366 4.8 0.4 1.0
F1 c:BEF1002 4.9 0.1 1.0
OE1 d:GLU215 5.0 1.0 1.0

Magnesium binding site 4 out of 6 in 6z9p

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Magnesium binding site 4 out of 6 in the Transcription Termination Intermediate Complex 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
e:Mg502

b:0.7
occ:1.00
 O1B e:ADP501 2.0 0.2 1.0
O e:HOH1102 2.1 0.0 1.0
O e:HOH1101 2.2 0.3 1.0
F3 e:BEF503 2.3 0.0 1.0
O e:HOH1103 2.4 0.2 1.0
OG1 e:THR185 2.8 0.8 1.0
PB e:ADP501 3.1 0.2 1.0
O2B e:ADP501 3.3 0.2 1.0
O2A e:ADP501 3.6 0.2 1.0
BE e:BEF503 3.6 0.0 1.0
O1A e:ADP501 4.0 0.2 1.0
PA e:ADP501 4.0 0.2 1.0
O3A e:ADP501 4.0 0.2 1.0
NH2 d:ARG366 4.0 0.2 1.0
N e:THR185 4.1 0.8 1.0
CB e:THR185 4.1 0.8 1.0
O3B e:ADP501 4.3 0.2 1.0
CB e:LYS184 4.4 0.3 1.0
F1 e:BEF503 4.5 0.0 1.0
CA e:THR185 4.5 0.8 1.0
F2 e:BEF503 4.7 0.0 1.0
CE e:LYS184 4.7 0.3 1.0
CZ d:ARG366 4.8 0.2 1.0
N e:LYS184 4.8 0.3 1.0
C e:LYS184 4.8 0.3 1.0
NZ e:LYS184 4.9 0.3 1.0
CA e:LYS184 4.9 0.3 1.0
NH1 d:ARG366 5.0 0.2 1.0
OD1 e:ASP265 5.0 0.9 1.0

Magnesium binding site 5 out of 6 in 6z9p

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
f:Mg1001

b:0.8
occ:1.00
 F3 e:BEF504 2.1 0.6 1.0
O f:HOH1102 2.1 1.0 1.0
O f:HOH1101 2.2 0.6 1.0
O2B f:ADP1000 2.2 0.0 1.0
O1B f:ADP1000 2.5 0.0 1.0
O f:HOH1103 2.6 0.9 1.0
PB f:ADP1000 2.8 0.0 1.0
OG1 f:THR185 2.8 0.9 1.0
BE e:BEF504 3.3 0.6 1.0
F2 e:BEF504 3.7 0.6 1.0
O1A f:ADP1000 3.7 0.0 1.0
O3B f:ADP1000 3.9 0.0 1.0
O3A f:ADP1000 4.0 0.0 1.0
N f:THR185 4.1 0.9 1.0
CB f:THR185 4.2 0.9 1.0
PA f:ADP1000 4.2 0.0 1.0
CB f:LYS184 4.3 0.9 1.0
NH2 e:ARG366 4.5 1.0 1.0
O2A f:ADP1000 4.5 0.0 1.0
F1 e:BEF504 4.6 0.6 1.0
CA f:THR185 4.6 0.9 1.0
CE f:LYS184 4.6 0.9 1.0
N f:LYS184 4.8 0.9 1.0
NZ f:LYS184 4.8 0.9 1.0
C f:LYS184 4.8 0.9 1.0
CA f:LYS184 4.9 0.9 1.0
OD1 f:ASP265 5.0 0.6 1.0

Magnesium binding site 6 out of 6 in 6z9p

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


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg1501

b:67.5
occ:1.00
 OD1 Y:ASP460 2.0 54.1 1.0
O3' R:C99 2.0 66.5 1.0
OD1 Y:ASP464 2.1 56.4 1.0
OD1 Y:ASP462 2.1 57.9 1.0
OD2 Y:ASP464 2.5 56.4 1.0
CG Y:ASP464 2.6 56.4 1.0
CG Y:ASP462 2.9 57.9 1.0
CG Y:ASP460 3.1 54.1 1.0
OD2 Y:ASP462 3.2 57.9 1.0
C3' R:C99 3.3 66.5 1.0
OD2 Y:ASP460 3.6 54.1 1.0
O2' R:C99 3.6 66.5 1.0
C4' R:C99 3.8 66.5 1.0
O Y:ASP460 3.9 54.1 1.0
C2' R:C99 4.0 66.5 1.0
N Y:ASP460 4.0 54.1 1.0
CB Y:ASP464 4.1 56.4 1.0
C Y:ASP460 4.3 54.1 1.0
CB Y:ASP462 4.3 57.9 1.0
CB Y:ASP460 4.3 54.1 1.0
C5' R:C99 4.4 66.5 1.0
CA Y:ASP460 4.4 54.1 1.0
N Y:ASP462 4.5 57.9 1.0
N Y:ASP464 4.5 56.4 1.0
NH1 Y:ARG425 4.7 47.4 1.0
CA Y:ASP464 4.7 56.4 1.0
CA Y:ASP462 4.8 57.9 1.0
C Y:ALA459 4.8 49.6 1.0
C Y:ASP462 4.9 57.9 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 Oct 2 02:13:06 2024

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