Zinc in PDB 4yfx: Escherichia Coli Rna Polymerase in Complex with Myxopyronin B

All present enzymatic activity of Escherichia Coli Rna Polymerase in Complex with Myxopyronin B:
2.7.7.6;

The structure of Escherichia Coli Rna Polymerase in Complex with Myxopyronin B, PDB code: 4yfx was solved by V.Molodtsov, P.R.Fleming, C.J.Eyermann, A.D.Ferguson, M.A.Foulk, D.C.Mckinney, C.E.Masse, E.T.Buurman, K.S.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.95 / 3.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	188.520, 205.177, 310.140, 90.00, 90.00, 90.00
R / Rfree (%)	23.6 / 30

The structure of Escherichia Coli Rna Polymerase in Complex with Myxopyronin B also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Escherichia Coli Rna Polymerase in Complex with Myxopyronin B (pdb code 4yfx). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Escherichia Coli Rna Polymerase in Complex with Myxopyronin B, PDB code: 4yfx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Myxopyronin B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Escherichia Coli Rna Polymerase in Complex with Myxopyronin B within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.1 occ:1.00 SG D:CYS85 2.1 1.0 1.0 SG D:CYS70 2.1 0.6 1.0 SG D:CYS88 2.2 0.2 1.0 SG D:CYS72 2.3 0.7 1.0 CB D:CYS85 2.3 0.1 1.0 CB D:CYS72 3.1 0.5 1.0 N D:CYS72 3.2 0.3 1.0 CB D:CYS70 3.2 0.6 1.0 CA D:CYS72 3.6 0.8 1.0 N D:GLY73 3.6 0.5 1.0 CA D:CYS85 3.7 0.5 1.0 N D:LEU71 3.9 0.8 1.0 CB D:CYS88 3.9 0.4 1.0 N D:CYS88 4.0 0.1 1.0 C D:CYS72 4.1 0.0 1.0 O D:CYS88 4.1 0.7 1.0 C D:LEU71 4.3 0.9 1.0 CA D:CYS70 4.3 0.6 1.0 N D:LYS74 4.3 0.3 1.0 C D:CYS70 4.3 0.7 1.0 CA D:CYS88 4.4 0.2 1.0 CD1 D:TYR75 4.5 0.7 1.0 C D:CYS85 4.5 0.1 1.0 CA D:LEU71 4.6 0.8 1.0 N D:CYS85 4.7 0.3 1.0 CA D:GLY73 4.7 0.9 1.0 CB D:LYS87 4.7 0.9 1.0 C D:CYS88 4.7 0.5 1.0 CE1 D:TYR75 4.8 0.4 1.0 CB D:LYS74 4.9 0.8 1.0 N D:LYS87 4.9 0.3 1.0 C D:GLY73 5.0 0.8 1.0

Zinc binding site 2 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Myxopyronin B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Escherichia Coli Rna Polymerase in Complex with Myxopyronin B within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2003 b:0.9 occ:1.00 SG D:CYS895 2.1 0.0 1.0 SG D:CYS888 2.1 0.4 1.0 SG D:CYS814 2.2 0.2 1.0 SG D:CYS898 2.2 0.2 1.0 CB D:CYS898 2.4 0.4 1.0 NH2 D:ARG883 2.5 0.6 1.0 CB D:CYS888 2.9 0.0 1.0 CB D:CYS895 2.9 0.7 1.0 CB D:CYS814 3.1 0.5 1.0 CA D:CYS888 3.3 0.9 1.0 CA D:CYS898 3.5 0.8 1.0 N D:CYS898 3.6 0.4 1.0 N D:ASP889 3.7 0.8 1.0 CZ D:ARG883 3.7 0.6 1.0 N D:CYS895 3.8 0.2 1.0 C D:CYS888 3.8 0.9 1.0 CA D:CYS895 3.9 1.0 1.0 N D:CYS814 3.9 0.6 1.0 CA D:CYS814 4.1 0.2 1.0 NE D:ARG883 4.2 0.9 1.0 N D:THR890 4.3 0.3 1.0 C D:CYS895 4.5 0.8 1.0 O D:CYS895 4.5 0.5 1.0 N D:CYS888 4.5 0.2 1.0 CG2 D:THR890 4.7 0.1 1.0 C D:CYS898 4.8 0.8 1.0 CB D:THR890 4.8 0.2 1.0 NH1 D:ARG883 4.8 0.6 1.0 O D:CYS888 4.8 0.1 1.0 C D:HIS897 4.8 0.8 1.0 CA D:ASP889 5.0 0.4 1.0 N D:GLY815 5.0 0.7 1.0 CG2 D:THR816 5.0 0.8 1.0 C D:CYS814 5.0 0.2 1.0

Zinc binding site 3 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Myxopyronin B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Escherichia Coli Rna Polymerase in Complex with Myxopyronin B within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn2002 b:0.7 occ:1.00 SG J:CYS88 2.1 0.8 1.0 SG J:CYS85 2.1 0.0 1.0 SG J:CYS70 2.1 0.5 1.0 SG J:CYS72 2.2 1.0 1.0 CB J:CYS72 2.7 0.9 1.0 CB J:CYS85 2.7 0.7 1.0 N J:CYS72 2.9 0.4 1.0 N J:CYS88 3.2 0.9 1.0 CA J:CYS72 3.3 0.1 1.0 CB J:CYS88 3.4 0.9 1.0 N J:GLY73 3.7 0.2 1.0 CB J:CYS70 3.7 0.5 1.0 O J:CYS88 3.7 0.7 1.0 CA J:CYS88 3.8 0.0 1.0 CB J:LYS87 3.9 0.4 1.0 N J:LEU71 3.9 0.9 1.0 C J:CYS72 4.0 0.8 1.0 C J:LEU71 4.0 0.1 1.0 CA J:CYS85 4.2 0.9 1.0 C J:CYS88 4.2 0.1 1.0 C J:LYS87 4.3 0.4 1.0 C J:CYS70 4.4 0.7 1.0 CA J:LEU71 4.5 0.6 1.0 CA J:LYS87 4.5 0.2 1.0 N J:LYS87 4.5 0.3 1.0 N J:LYS74 4.6 0.8 1.0 CA J:CYS70 4.6 0.0 1.0 C J:CYS85 4.7 0.3 1.0 CB J:LEU71 4.9 0.2 1.0 CA J:GLY73 4.9 0.2 1.0 CG J:LYS87 5.0 0.4 1.0

Zinc binding site 4 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Myxopyronin B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Escherichia Coli Rna Polymerase in Complex with Myxopyronin B within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn2003 b:0.5 occ:1.00 SG J:CYS895 2.1 0.1 1.0 SG J:CYS898 2.1 0.7 1.0 SG J:CYS888 2.2 0.5 1.0 CB J:CYS898 2.3 0.8 1.0 CB J:CYS888 2.6 0.5 1.0 SG J:CYS814 2.9 0.1 1.0 CA J:CYS888 3.5 0.3 1.0 CB J:CYS895 3.5 0.6 1.0 CA J:CYS898 3.5 0.2 1.0 NH2 J:ARG883 3.6 0.5 1.0 N J:CYS898 3.6 1.0 1.0 CB J:CYS814 4.0 0.9 1.0 OG1 J:THR890 4.1 0.4 1.0 O J:CYS895 4.1 0.5 1.0 N J:CYS895 4.1 0.4 1.0 N J:ASP889 4.1 0.1 1.0 C J:CYS888 4.2 0.4 1.0 CA J:CYS895 4.2 0.1 1.0 C J:CYS895 4.5 0.1 1.0 N J:CYS888 4.6 0.6 1.0 CZ J:ARG883 4.6 0.3 1.0 CG2 J:THR816 4.6 0.9 1.0 N J:THR890 4.7 0.8 1.0 N J:CYS814 4.7 0.3 1.0 C J:CYS898 4.7 0.4 1.0 NE J:ARG883 4.9 0.2 1.0 CB J:THR890 4.9 0.9 1.0 OD1 J:ASP813 4.9 0.7 1.0 C J:HIS897 4.9 0.4 1.0

V.Molodtsov, P.R.Fleming, C.J.Eyermann, A.D.Ferguson, M.A.Foulk, D.C.Mckinney, C.E.Masse, E.T.Buurman, K.S.Murakami. X-Ray Crystal Structures of Escherichia Coli Rna Polymerase with Switch Region Binding Inhibitors Enable Rational Design of Squaramides with An Improved Fraction Unbound to Human Plasma Protein To Be Published.