Magnesium in PDB 5vsw: X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex

All present enzymatic activity of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex:
2.7.7.6;

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex, PDB code: 5vsw was solved by K.S.Murakami, V.Molodtsov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.82 / 4.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	187.274, 205.259, 311.313, 90.00, 90.00, 90.00
R / Rfree (%)	22.1 / 25.9

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex also contains other interesting chemical elements:

Zinc

(Zn)

5 atoms

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex (pdb code 5vsw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex, PDB code: 5vsw:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2001 b:0.1 occ:1.00 OD1 D:ASP462 2.1 0.7 1.0 OD1 D:ASP460 2.2 0.1 1.0 OD1 D:ASP464 2.2 0.8 1.0 OD2 D:ASP464 2.3 0.7 1.0 OD2 D:ASP462 2.6 0.0 1.0 CG D:ASP464 2.6 0.5 1.0 CG D:ASP462 2.6 0.5 1.0 CG D:ASP460 3.2 0.6 1.0 OD2 D:ASP460 3.6 0.7 1.0 CB D:ASP462 4.1 0.8 1.0 CB D:ASP464 4.1 0.1 1.0 NH2 D:ARG425 4.4 0.7 1.0 N D:ASP462 4.4 0.2 1.0 CB D:ASP460 4.6 0.6 1.0 O D:ASP460 4.6 0.3 1.0 NH1 D:ARG425 4.6 0.7 1.0 N D:ASP460 4.6 0.0 1.0 CG M:PRO72 4.6 0.5 1.0 C D:ASP460 4.7 0.8 1.0 CA D:ASP462 4.7 0.6 1.0 N D:ASP464 4.7 0.8 1.0 OD1 M:ASP71 4.7 0.8 1.0 CB M:PRO72 4.7 0.6 1.0 CA D:ASP464 4.8 0.2 1.0 CA D:ASP460 4.8 0.4 1.0 C D:ASP462 5.0 0.4 1.0 CD M:PRO72 5.0 0.3 1.0

Magnesium binding site 2 out of 2 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase and Dksa/Ppgpp Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg2001 b:0.4 occ:1.00 OD1 J:ASP462 2.1 0.7 1.0 OD2 J:ASP464 2.2 0.6 1.0 OD1 J:ASP460 2.3 0.8 1.0 OD1 J:ASP464 2.3 0.5 1.0 OD2 J:ASP462 2.4 0.8 1.0 CG J:ASP462 2.5 0.4 1.0 CG J:ASP464 2.5 0.8 1.0 CG J:ASP460 3.3 0.3 1.0 OD2 J:ASP460 3.6 0.2 1.0 CB J:ASP462 4.0 0.6 1.0 CB J:ASP464 4.0 0.2 1.0 NH2 J:ARG425 4.3 0.2 1.0 N J:ASP462 4.4 0.9 1.0 N J:ASP464 4.6 0.8 1.0 CA J:ASP462 4.6 0.0 1.0 CB J:ASP460 4.6 0.3 1.0 O J:ASP460 4.6 0.3 1.0 CA J:ASP464 4.8 0.5 1.0 C J:ASP462 4.8 0.7 1.0 C J:ASP460 4.8 0.4 1.0 N J:ASP460 4.8 0.3 1.0 CA J:ASP460 4.9 0.2 1.0 NH1 J:ARG425 5.0 0.3 1.0

V.Molodtsov, E.Sineva, L.Zhang, X.Huang, M.Cashel, S.E.Ades, K.S.Murakami. Allosteric Effector Ppgpp Potentiates the Inhibition of Transcript Initiation By Dksa. Mol. Cell V. 69 828 2018.
ISSN: ISSN 1097-4164
PubMed: 29478808
DOI: 10.1016/J.MOLCEL.2018.01.035