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

Go back to Magnesium Binding Sites List in 7eh2
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

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy