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Magnesium in PDB 4oio: Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation

Enzymatic activity of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation

All present enzymatic activity of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation, PDB code: 4oio was solved by Y.Zhang, R.H.Ebright, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.92 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 184.110, 103.780, 296.090, 90.00, 98.86, 90.00
R / Rfree (%) 20.5 / 25.6

Other elements in 4oio:

The structure of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation (pdb code 4oio). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation, PDB code: 4oio:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4oio

Go back to Magnesium Binding Sites List in 4oio
Magnesium binding site 1 out of 2 in the Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:12.7
occ:1.00
OD2 D:ASP739 2.0 20.6 1.0
O3' D:ATP2005 2.0 26.4 0.8
OD1 D:ASP743 2.1 16.6 1.0
OD2 D:ASP741 2.2 20.8 1.0
OD1 D:ASP741 2.2 27.1 1.0
CG D:ASP741 2.5 21.9 1.0
CG D:ASP739 3.0 22.3 1.0
CG D:ASP743 3.1 16.8 1.0
C3' D:ATP2005 3.2 29.8 0.8
O D:HOH2121 3.2 18.4 1.0
OD1 D:ASP739 3.5 32.9 1.0
OD2 D:ASP743 3.5 19.1 1.0
O2' D:ATP2005 3.6 31.9 0.8
C4' D:ATP2005 3.8 26.8 0.8
C2' D:ATP2005 4.0 28.8 0.8
CB D:ASP741 4.0 15.1 1.0
O D:ASP739 4.1 14.2 1.0
N D:ASP739 4.2 15.0 1.0
CB D:ASP739 4.3 18.0 1.0
C D:ASP739 4.3 12.3 1.0
CB D:ASP743 4.4 11.4 1.0
C5' D:ATP2005 4.5 33.4 0.8
CA D:ASP739 4.5 13.5 1.0
C5' D:2TM2006 4.5 47.3 1.0
N D:ASP741 4.6 12.6 1.0
C4' D:2TM2006 4.7 44.1 1.0
O D:HOH2152 4.7 27.8 1.0
N D:ASP743 4.7 13.7 1.0
CA D:ASP741 4.8 11.4 1.0
O4' D:2TM2006 4.8 43.7 1.0
NH2 D:ARG704 4.9 18.9 1.0
CA D:ASP743 4.9 13.6 1.0
O4' D:ATP2005 4.9 26.3 0.8

Magnesium binding site 2 out of 2 in 4oio

Go back to Magnesium Binding Sites List in 4oio
Magnesium binding site 2 out of 2 in the Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Thermus Thermophilus Pre-Insertion Substrate Complex For De Novo Transcription Initiation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2004

b:32.0
occ:1.00
O1B D:2TM2006 2.1 56.0 1.0
O3G D:2TM2006 2.1 55.1 1.0
OD1 D:ASP739 2.1 32.9 1.0
CG D:ASP739 3.1 22.3 1.0
OE1 C:GLU685 3.4 31.8 1.0
PB D:2TM2006 3.4 73.6 1.0
CB D:ASP739 3.5 18.0 1.0
PG D:2TM2006 3.5 64.9 1.0
O D:HOH2152 3.6 27.8 1.0
O D:HOH2166 3.6 28.7 1.0
O3B D:2TM2006 4.0 71.6 1.0
NH2 C:ARG879 4.0 34.4 1.0
C1 D:2TM2006 4.1 50.0 1.0
CD C:GLU685 4.2 31.9 1.0
OD1 C:ASP686 4.2 33.4 1.0
OD2 D:ASP739 4.2 20.6 1.0
OE2 C:GLU685 4.3 33.7 1.0
O1G D:2TM2006 4.4 39.3 1.0
O2G D:2TM2006 4.5 38.9 1.0
O2B D:2TM2006 4.6 55.0 1.0
O D:HOH2121 4.7 18.4 1.0
NH2 D:ARG1029 4.7 27.8 1.0
CA D:ASP739 5.0 13.5 1.0
NH1 D:ARG1029 5.0 24.5 1.0

Reference:

Y.Zhang, D.Degen, M.X.Ho, E.Sineva, K.Y.Ebright, Y.W.Ebright, V.Mekler, H.Vahedian-Movahed, Y.Feng, R.Yin, S.Tuske, H.Irschik, R.Jansen, S.Maffioli, S.Donadio, E.Arnold, R.H.Ebright. GE23077 Binds to the Rna Polymerase 'I' and 'I+1' Sites and Prevents the Binding of Initiating Nucleotides. Elife V. 3 02450 2014.
ISSN: ESSN 2050-084X
PubMed: 24755292
Page generated: Tue Aug 20 00:51:09 2024

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