Magnesium in PDB 7eh2: Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer

Enzymatic activity of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer

All present enzymatic activity of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer:
2.7.7.6;

Protein crystallography data

The structure of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer, PDB code: 7eh2 was solved by L.Li, Y.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 97.82 / 3.34
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 184.85, 104.2, 296.65, 90, 98.42, 90
R / Rfree (%) 20.1 / 24.8

Other elements in 7eh2:

The structure of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer (pdb code 7eh2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer, PDB code: 7eh2:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 7eh2

Go back to Magnesium Binding Sites List in 7eh2
Magnesium binding site 1 out of 3 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg2003

b:54.3
occ:1.00
O3' I:G2 1.8 60.2 0.8
OD1 D:ASP739 2.0 63.0 1.0
OD1 D:ASP741 2.1 56.0 1.0
OD1 D:ASP743 2.1 59.8 1.0
CG D:ASP739 2.8 60.8 1.0
OD2 D:ASP739 2.9 65.9 1.0
CG D:ASP743 3.0 54.3 1.0
CG D:ASP741 3.0 57.9 1.0
OD2 D:ASP743 3.1 54.5 1.0
OD2 D:ASP741 3.2 65.8 1.0
C3' I:G2 3.2 63.6 0.8
C4' I:G2 3.8 69.6 0.8
O2' I:G2 3.9 65.0 0.8
C2' I:G2 4.1 68.3 0.8
CB D:ASP739 4.2 48.2 1.0
C5' I:G2 4.2 72.3 0.8
CB D:ASP743 4.4 53.0 1.0
CB D:ASP741 4.4 58.6 1.0
N D:ASP741 4.5 58.6 1.0
N D:ASP739 4.5 51.8 1.0
NH2 D:ARG704 4.5 60.2 1.0
N D:ASP743 4.6 59.2 1.0
C D:ASP739 4.6 52.8 1.0
CA D:ASP739 4.7 50.8 1.0
CA D:ASP741 4.8 58.9 1.0
O D:ASP739 4.8 58.9 1.0
C D:ASP741 4.8 61.2 1.0
CA D:ASP743 4.8 57.6 1.0

Magnesium binding site 2 out of 3 in 7eh2

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Magnesium binding site 2 out of 3 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Mg401

b:77.4
occ:1.00
OD2 L:ASP168 2.2 86.5 1.0
O N:LYS840 2.4 82.9 1.0
CG L:ASP168 3.2 82.8 1.0
OD1 L:ASP168 3.4 82.4 1.0
C N:LYS840 3.6 82.8 1.0
OE2 L:GLU154 3.8 101.5 1.0
N N:VAL842 4.3 80.3 1.0
CA N:TYR841 4.3 81.1 1.0
OE1 L:GLU154 4.4 113.9 1.0
N N:TYR841 4.4 87.4 1.0
CD L:GLU154 4.5 114.8 1.0
CB L:ASP168 4.5 77.1 1.0
O N:LEU839 4.6 79.1 1.0
CA N:LYS840 4.6 83.0 1.0
OE1 L:GLU64 4.7 117.9 1.0
C N:TYR841 4.8 82.5 1.0
NZ L:LYS83 4.8 83.6 1.0
OE2 L:GLU64 5.0 121.2 1.0

Magnesium binding site 3 out of 3 in 7eh2

Go back to Magnesium Binding Sites List in 7eh2
Magnesium binding site 3 out of 3 in the Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Thermus Thermophilus Transcription Initiation Complex Containing A Template-Strand Pyrimidine at Position Tss-2 and Gpg Rna Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mg1603

b:61.0
occ:1.00
O3' R:G2 1.8 71.0 0.8
OD1 N:ASP739 2.0 69.4 1.0
OD1 N:ASP741 2.1 64.9 1.0
OD1 N:ASP743 2.1 66.5 1.0
CG N:ASP743 2.9 64.2 1.0
CG N:ASP739 2.9 69.2 1.0
CG N:ASP741 2.9 67.1 1.0
OD2 N:ASP743 3.0 65.5 1.0
OD2 N:ASP741 3.1 69.4 1.0
OD2 N:ASP739 3.2 70.0 1.0
C3' R:G2 3.2 74.3 0.8
C4' R:G2 4.0 76.0 0.8
O2' R:G2 4.0 76.8 0.8
C2' R:G2 4.1 78.8 0.8
CB N:ASP739 4.3 56.4 1.0
NH2 N:ARG704 4.3 64.6 1.0
CB N:ASP743 4.3 63.5 1.0
CB N:ASP741 4.4 62.6 1.0
N N:ASP739 4.4 63.3 1.0
C5' R:G2 4.4 75.4 0.8
N N:ASP741 4.5 65.5 1.0
C N:ASP739 4.6 62.9 1.0
O N:ASP739 4.6 65.5 1.0
N N:ASP743 4.7 65.8 1.0
CA N:ASP739 4.7 58.4 1.0
CA N:ASP741 4.8 62.1 1.0
CA N:ASP743 4.9 69.9 1.0
C N:ASP741 4.9 65.5 1.0

Reference:

K.S.Skalenko, L.Li, Y.Zhang, I.O.Vvedenskaya, J.T.Winkelman, A.L.Cope, D.M.Taylor, P.Shah, R.H.Ebright, J.B.Kinney, Y.Zhang, B.E.Nickels. Promoter-Sequence Determinants and Structural Basis of Primer-Dependent Transcription Initiation in Escherichia Coli . Proc.Natl.Acad.Sci.Usa V. 118 2021.
ISSN: ESSN 1091-6490
PubMed: 34187896
DOI: 10.1073/PNAS.2106388118
Page generated: Sat Aug 21 16:23:59 2021

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