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Magnesium in PDB 4xlq: Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter

Enzymatic activity of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter

All present enzymatic activity of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter:
2.7.7.6;

Protein crystallography data

The structure of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter, PDB code: 4xlq was solved by B.Bae, S.A.Darst, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.81 / 4.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 288.230, 288.230, 535.250, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 28.1

Other elements in 4xlq:

The structure of Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter (pdb code 4xlq). 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 T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter, PDB code: 4xlq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4xlq

Go back to Magnesium Binding Sites List in 4xlq
Magnesium binding site 1 out of 2 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter


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 T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:0.8
occ:1.00
 OD2 D:ASP741 2.1 0.0 1.0
OD1 D:ASP743 2.2 0.2 1.0
OD2 D:ASP743 2.3 0.3 1.0
OD1 D:ASP739 2.3 0.8 1.0
OD1 D:ASP741 2.4 0.6 1.0
CG D:ASP743 2.4 0.2 1.0
CG D:ASP741 2.5 0.1 1.0
CG D:ASP739 3.4 0.7 1.0
OD2 D:ASP739 3.7 0.9 1.0
CB D:ASP743 3.8 0.4 1.0
CB D:ASP741 3.9 0.9 1.0
O D:ASP739 4.1 0.8 1.0
CA D:ASP743 4.4 0.9 1.0
N D:ASP743 4.4 0.5 1.0
N D:ASP741 4.6 0.3 1.0
N D:ASP739 4.7 0.9 1.0
CA D:ASP741 4.7 0.9 1.0
CB D:ASP739 4.8 0.0 1.0
NH2 D:ARG704 4.8 0.2 1.0
C D:ASP739 4.8 0.9 1.0

Magnesium binding site 2 out of 2 in 4xlq

Go back to Magnesium Binding Sites List in 4xlq
Magnesium binding site 2 out of 2 in the Crystal Structure of T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter


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 T.Aquaticus Transcription Initiation Complex Containing Upstream Fork (-11 Base-Paired) Promoter within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg2003

b:0.2
occ:1.00
 OD2 J:ASP741 2.0 0.1 1.0
OD2 J:ASP743 2.0 0.8 1.0
OD1 J:ASP743 2.1 0.3 1.0
CG J:ASP743 2.1 0.4 1.0
OD1 J:ASP739 2.2 0.7 1.0
CG J:ASP741 2.5 0.2 1.0
OD1 J:ASP741 2.6 0.9 1.0
CG J:ASP739 3.3 0.8 1.0
CB J:ASP743 3.5 0.1 1.0
O J:ASP739 3.8 0.4 1.0
OD2 J:ASP739 3.8 0.4 1.0
CB J:ASP741 3.9 0.5 1.0
CA J:ASP743 4.1 1.0 1.0
N J:ASP743 4.2 0.5 1.0
N J:ASP739 4.4 0.6 1.0
N J:ASP741 4.4 0.8 1.0
C J:ASP739 4.5 0.7 1.0
CB J:ASP739 4.6 0.3 1.0
CA J:ASP741 4.7 1.0 1.0
NH2 J:ARG704 4.8 0.8 1.0
CA J:ASP739 4.8 0.6 1.0
NH1 J:ARG704 5.0 0.8 1.0
C J:ASP741 5.0 0.7 1.0

Reference:

B.Bae, A.Feklistov, A.Lass-Napiorkowska, R.Landick, S.A.Darst. Structure of A Bacterial Rna Polymerase Holoenzyme Open Promoter Complex. Elife V. 4 2015.
ISSN: ESSN 2050-084X
PubMed: 26349032
DOI: 10.7554/ELIFE.08504
Page generated: Mon Dec 14 19:47:14 2020

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