Magnesium in PDB 6byu: X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex

All present enzymatic activity of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex:
2.7.7.6;

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex, PDB code: 6byu 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)	30.00 / 3.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	186.254, 203.656, 308.322, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 31.1

The structure of X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp Complex (pdb code 6byu). 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 (Rpob- H526Y) and Ppapp Complex, PDB code: 6byu:
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 (Rpob- H526Y) and Ppapp 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 (Rpob- H526Y) and Ppapp Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg2001 b:47.5 occ:1.00 OD2 D:ASP464 2.3 75.9 1.0 OD1 D:ASP462 2.3 0.1 1.0 OD2 D:ASP462 2.3 0.2 1.0 OD1 D:ASP460 2.4 1.0 1.0 OD1 D:ASP464 2.5 84.7 1.0 CG D:ASP462 2.6 98.7 1.0 CG D:ASP464 2.7 78.4 1.0 CB D:ASP460 3.0 79.7 1.0 CG D:ASP460 3.1 0.9 1.0 CA D:ASP460 3.9 72.9 1.0 N D:ASP460 4.0 73.4 1.0 CB D:ASP462 4.0 89.4 1.0 CB D:ASP464 4.2 69.0 1.0 N D:ASP462 4.2 98.6 1.0 OD2 D:ASP460 4.3 0.1 1.0 C D:ASP460 4.3 72.2 1.0 CA D:ASP462 4.6 86.4 1.0 NH1 D:ARG425 4.6 78.1 1.0 O D:ASP460 4.6 77.4 1.0 N D:ASP464 4.7 72.0 1.0 N D:PHE461 4.7 83.5 1.0 C D:ASP462 4.8 85.7 1.0 CA D:ASP464 5.0 72.5 1.0

Magnesium binding site 2 out of 2 in the X-Ray Crystal Structure of Escherichia Coli Rna Polymerase (Rpob- H526Y) and Ppapp 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 (Rpob- H526Y) and Ppapp Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg2001 b:81.1 occ:1.00 OD2 J:ASP464 2.3 0.8 1.0 OD1 J:ASP464 2.3 0.4 1.0 OD2 J:ASP462 2.3 0.0 1.0 OD1 J:ASP462 2.4 0.4 1.0 OD1 J:ASP460 2.5 0.1 1.0 CG J:ASP464 2.6 0.9 1.0 CG J:ASP462 2.6 0.6 1.0 CB J:ASP460 3.2 0.0 1.0 CG J:ASP460 3.2 0.8 1.0 N J:ASP460 4.0 0.3 1.0 CA J:ASP460 4.1 0.9 1.0 CB J:ASP462 4.1 0.7 1.0 CB J:ASP464 4.1 0.6 1.0 OD2 J:ASP460 4.4 0.5 1.0 N J:ASP462 4.4 1.0 1.0 C J:ASP460 4.4 0.7 1.0 NH1 J:ARG425 4.5 0.6 1.0 N J:ASP464 4.7 0.9 1.0 CA J:ASP462 4.7 0.5 1.0 O J:ASP460 4.7 0.1 1.0 C J:ASP462 4.9 0.1 1.0 CA J:ASP464 4.9 0.6 1.0 N J:PHE461 4.9 0.3 1.0

B.Bruhn-Olszewska, V.Molodtsov, M.Sobala, M.Dylewski, K.S.Murakami, M.Cashel, K.Potrykus. Structure-Function Comparisons of (P)Ppapp Vs (P)Ppgpp For Escherichia Coli Rna Polymerase Binding Sites and For Rrnb P1 Promoter Regulatory Responses in Vitro. Biochim. Biophys. Acta V.1861 731 2018.
ISSN: ISSN 0006-3002
PubMed: 30012465
DOI: 10.1016/J.BBAGRM.2018.07.005