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Magnesium in PDB 4q5s: Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna

Enzymatic activity of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna

All present enzymatic activity of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna, PDB code: 4q5s was solved by K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.98 / 3.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 187.089, 102.075, 297.263, 90.00, 98.14, 90.00
R / Rfree (%) 26.9 / 29.4

Other elements in 4q5s:

The structure of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna (pdb code 4q5s). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna, PDB code: 4q5s:

Magnesium binding site 1 out of 1 in 4q5s

Go back to Magnesium Binding Sites List in 4q5s
Magnesium binding site 1 out of 1 in the Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Rna Polymerase Initially Transcribing Complex Containing 6-Mer Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2001

b:24.2
occ:1.00
OD1 D:ASP739 1.9 42.2 1.0
OD1 D:ASP743 2.1 44.0 1.0
O3' I:A5 2.1 67.8 1.0
OD1 D:ASP741 2.2 49.4 1.0
OP1 I:C6 2.6 83.3 1.0
CG D:ASP743 2.8 42.6 1.0
OD2 D:ASP743 2.9 40.5 1.0
CG D:ASP739 2.9 41.3 1.0
P I:C6 3.0 83.5 1.0
CG D:ASP741 3.1 49.4 1.0
OD2 D:ASP739 3.2 41.5 1.0
C3' I:A5 3.2 64.0 1.0
OD2 D:ASP741 3.3 48.4 1.0
O2' I:A5 3.5 65.8 1.0
C4' I:A5 3.6 62.9 1.0
C5' I:C6 3.7 69.8 1.0
O5' I:C6 3.8 76.1 1.0
C2' I:A5 4.0 66.7 1.0
OP2 I:C6 4.2 71.7 1.0
CB D:ASP739 4.2 39.9 1.0
C5' I:A5 4.3 58.7 1.0
CB D:ASP743 4.3 44.0 1.0
N D:ASP741 4.4 55.1 1.0
N D:ASP739 4.4 37.1 1.0
CB D:ASP741 4.5 55.8 1.0
C D:ASP739 4.6 42.2 1.0
NH2 D:ARG704 4.6 36.4 1.0
CA D:ASP739 4.6 39.5 1.0
N D:ASP743 4.7 52.6 1.0
O D:ASP739 4.7 41.9 1.0
O4' I:A5 4.8 62.1 1.0
CA D:ASP743 4.8 46.2 1.0
CA D:ASP741 4.8 59.7 1.0
O5' I:A5 4.9 58.2 1.0
C D:ASP741 4.9 62.2 1.0
N D:PHE740 5.0 45.3 1.0

Reference:

R.S.Basu, B.A.Warner, V.Molodtsov, D.Pupov, D.Esyunina, C.Fernandez-Tornero, A.Kulbachinskiy, K.S.Murakami. Structural Basis of Transcription Initiation By Bacterial Rna Polymerase Holoenzyme. J.Biol.Chem. V. 289 24549 2014.
ISSN: ISSN 0021-9258
PubMed: 24973216
DOI: 10.1074/JBC.M114.584037
Page generated: Mon Dec 14 19:21:49 2020

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