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Magnesium in PDB 4ylo: E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna

Enzymatic activity of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna

All present enzymatic activity of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna:
2.7.7.6;

Protein crystallography data

The structure of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna, PDB code: 4ylo was solved by Y.Zuo, T.A.Steitz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.95 / 6.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 240.888, 208.174, 256.323, 90.00, 119.31, 90.00
R / Rfree (%) 22.7 / 31.4

Other elements in 4ylo:

The structure of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna also contains other interesting chemical elements:

Zinc (Zn) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna (pdb code 4ylo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna, PDB code: 4ylo:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ylo

Go back to Magnesium Binding Sites List in 4ylo
Magnesium binding site 1 out of 3 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1401

b:0.4
occ:1.00
CG C:ASP814 3.0 0.9 1.0
NH2 C:ARG678 3.2 0.5 1.0
OD1 C:ASP814 3.2 0.4 1.0
OD2 C:ASP814 3.2 0.6 1.0
OD2 D:ASP462 3.5 0.5 1.0
CB C:ASP814 3.6 0.8 1.0
NE C:ARG1106 3.6 0.9 1.0
CD C:ARG1106 4.3 0.6 1.0
CZ C:ARG678 4.3 0.3 1.0
CG C:ARG1106 4.5 0.5 1.0
NH2 C:ARG1106 4.5 0.0 1.0
CZ C:ARG1106 4.6 0.3 1.0
NH1 C:ARG678 4.6 0.0 1.0
CG D:ASP462 4.6 0.3 1.0
OD2 D:ASP460 4.7 0.1 1.0
O C:LYS1073 4.9 0.6 1.0
CG C:LYS1073 4.9 0.4 1.0

Magnesium binding site 2 out of 3 in 4ylo

Go back to Magnesium Binding Sites List in 4ylo
Magnesium binding site 2 out of 3 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg1503

b:0.1
occ:1.00
OD1 J:ASP464 1.7 0.7 1.0
OD1 J:ASP462 1.9 0.1 1.0
CG J:ASP464 2.4 0.1 1.0
OD2 J:ASP464 2.8 0.7 1.0
O J:ASP462 2.9 0.4 1.0
OD1 J:ASP460 2.9 0.5 1.0
CG J:ASP462 3.0 0.7 1.0
O J:ASP460 3.1 0.4 1.0
C J:ASP462 3.2 1.0 1.0
N J:ASP462 3.4 0.9 1.0
N J:ASP464 3.6 0.5 1.0
CB J:ASP464 3.6 0.4 1.0
C4' 6:G15 3.7 0.4 1.0
O2' 6:G15 3.7 0.7 1.0
CA J:ASP462 3.7 0.3 1.0
N J:GLY463 3.8 0.1 1.0
O3' 6:G15 3.8 0.5 1.0
CB J:ASP462 3.9 0.9 1.0
OD2 J:ASP462 3.9 0.5 1.0
CG J:ASP460 3.9 0.5 1.0
C J:ASP460 3.9 0.2 1.0
CA J:ASP464 4.0 0.3 1.0
C J:GLY463 4.1 0.3 1.0
C3' 6:G15 4.2 0.7 1.0
C J:PHE461 4.4 1.0 1.0
CA J:GLY463 4.4 0.2 1.0
OD2 J:ASP460 4.5 0.8 1.0
O4' 6:G15 4.5 0.7 1.0
C5' 6:G15 4.5 0.6 1.0
C2' 6:G15 4.5 0.0 1.0
O5' 6:G15 4.6 0.4 1.0
N J:PHE461 4.7 0.6 1.0
CA J:ASP460 4.8 0.1 1.0
O J:GLY463 4.8 1.0 1.0
CA J:PHE461 4.8 0.1 1.0
N J:ASP460 4.8 0.6 1.0
CB J:ASP460 4.9 0.5 1.0

Magnesium binding site 3 out of 3 in 4ylo

Go back to Magnesium Binding Sites List in 4ylo
Magnesium binding site 3 out of 3 in the E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Transcription Initiation Complex - 16-Bp Spacer and 4-Nt Rna within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg1503

b:0.5
occ:1.00
OD1 P:ASP460 2.0 0.7 1.0
OD1 P:ASP462 2.3 0.6 1.0
OP1 9:U16 2.4 0.9 1.0
O3' 9:G15 2.5 0.3 1.0
CG P:ASP460 2.7 0.8 1.0
OD2 P:ASP462 2.8 0.7 1.0
OD2 P:ASP460 2.9 0.2 1.0
CG P:ASP462 2.9 0.6 1.0
P 9:U16 3.0 0.3 1.0
OD2 P:ASP464 3.3 0.8 1.0
C3' 9:G15 3.7 0.6 1.0
C4' 9:G15 3.7 0.8 1.0
OD1 P:ASP464 4.0 0.9 1.0
O5' 9:U16 4.0 0.9 1.0
CG P:ASP464 4.0 0.6 1.0
C5' 9:U16 4.0 0.6 1.0
O P:ASP460 4.1 0.1 1.0
CB P:ASP460 4.2 0.4 1.0
OP2 9:U16 4.2 0.3 1.0
O2' 9:G15 4.3 0.7 1.0
C5' 9:G15 4.3 0.5 1.0
CB P:ASP462 4.4 0.1 1.0
C2' 9:G15 4.6 0.5 1.0
C P:ASP460 4.6 0.6 1.0
O5' 9:G15 4.6 0.5 1.0
CA P:ASP460 4.8 1.0 1.0
O P:ASP462 4.8 0.9 1.0
N P:ASP460 4.8 0.2 1.0
NZ O:LYS1073 5.0 0.4 1.0

Reference:

Y.Zuo, T.A.Steitz. Crystal Structures of the E. Coli Transcription Initiation Complexes with A Complete Bubble. Mol.Cell V. 58 534 2015.
ISSN: ISSN 1097-2765
PubMed: 25866247
DOI: 10.1016/J.MOLCEL.2015.03.010
Page generated: Sat Sep 28 23:22:19 2024

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