Zinc in PDB 4yfk: Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.

All present enzymatic activity of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.:
2.7.7.6;

The structure of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8., PDB code: 4yfk 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)	29.97 / 3.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	186.105, 206.438, 307.993, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.2

The structure of Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8. also contains other interesting chemical elements:

Magnesium

(Mg)

4 atoms

The binding sites of Zinc atom in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8. (pdb code 4yfk). 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 Squaramide Compound 8., PDB code: 4yfk:
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 Squaramide Compound 8.


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 Squaramide Compound 8. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2002 b:0.6 occ:1.00 SG D:CYS85 2.0 0.8 1.0 SG D:CYS70 2.2 0.5 1.0 SG D:CYS72 2.3 0.0 1.0 CB D:CYS85 3.1 0.6 1.0 CB D:CYS72 3.3 0.1 1.0 SG D:CYS88 3.3 0.9 1.0 N D:CYS72 3.8 0.1 1.0 CB D:CYS70 3.9 0.6 1.0 CB D:LYS87 4.0 0.4 1.0 O D:CYS88 4.0 0.2 1.0 N D:CYS88 4.0 0.2 1.0 CA D:CYS72 4.1 0.8 1.0 N D:GLY73 4.4 0.7 1.0 CB D:LYS74 4.4 0.3 1.0 CA D:CYS85 4.4 0.3 1.0 N D:LYS87 4.5 0.9 1.0 N D:LEU71 4.5 0.4 1.0 C D:CYS85 4.6 0.3 1.0 N D:LYS74 4.6 0.7 1.0 CA D:LYS87 4.7 0.7 1.0 C D:CYS72 4.7 0.4 1.0 CD1 D:TYR75 4.8 0.6 1.0 CB D:CYS88 4.8 0.5 1.0 CA D:CYS88 4.8 0.7 1.0 C D:CYS88 4.8 0.2 1.0 O D:CYS85 4.9 0.8 1.0 C D:LYS87 4.9 0.7 1.0 C D:LEU71 4.9 0.1 1.0 CA D:CYS70 4.9 0.3 1.0 C D:CYS70 4.9 0.7 1.0

Zinc binding site 2 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.


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 Squaramide Compound 8. within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn2003 b:0.1 occ:1.00 SG D:CYS895 2.0 0.0 1.0 SG D:CYS898 2.1 0.3 1.0 SG D:CYS888 2.1 0.1 1.0 SG D:CYS814 2.2 0.0 1.0 CB D:CYS888 2.9 0.2 1.0 CB D:CYS898 3.1 0.3 1.0 CB D:CYS814 3.2 0.2 1.0 CB D:CYS895 3.3 0.1 1.0 CA D:CYS888 3.5 0.8 1.0 NH2 D:ARG883 3.9 0.3 1.0 N D:ASP889 4.1 1.0 1.0 N D:CYS895 4.1 0.0 1.0 N D:CYS898 4.1 0.1 1.0 N D:CYS814 4.1 0.6 1.0 C D:CYS888 4.2 0.5 1.0 CA D:CYS895 4.2 0.3 1.0 CA D:CYS898 4.2 0.9 1.0 CA D:CYS814 4.3 1.0 1.0 O D:CYS895 4.4 0.3 1.0 CG2 D:THR816 4.5 0.2 1.0 N D:THR890 4.6 0.0 1.0 C D:CYS895 4.7 0.2 1.0 N D:CYS888 4.7 0.5 1.0 CZ D:ARG883 4.9 0.1 1.0 CB D:THR890 4.9 0.7 1.0 NE D:ARG883 5.0 0.8 1.0

Zinc binding site 3 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.


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 Squaramide Compound 8. within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn2002 b:0.3 occ:1.00 SG J:CYS70 2.1 0.3 1.0 SG J:CYS85 2.2 0.7 1.0 SG J:CYS72 2.3 0.6 1.0 CB J:CYS85 2.5 0.3 1.0 CB J:CYS70 3.3 0.4 1.0 CB J:CYS72 3.6 0.6 1.0 SG J:CYS88 3.9 0.5 1.0 N J:CYS72 3.9 0.6 1.0 CA J:CYS85 4.0 0.6 1.0 O J:CYS88 4.1 0.4 1.0 N J:GLY73 4.1 0.5 1.0 CA J:CYS72 4.2 0.2 1.0 N J:LYS74 4.4 0.6 1.0 CB J:LYS74 4.4 0.4 1.0 CB J:LYS87 4.4 1.0 1.0 N J:CYS88 4.5 0.3 1.0 C J:CYS85 4.6 0.8 1.0 C J:CYS72 4.6 0.8 1.0 CD1 J:TYR75 4.6 0.3 1.0 N J:LEU71 4.6 0.8 1.0 CA J:CYS70 4.6 0.6 1.0 C J:CYS70 4.7 0.0 1.0 N J:CYS85 4.9 0.0 1.0 N J:LYS87 4.9 0.5 1.0 N J:TYR75 5.0 1.0 1.0 C J:LEU71 5.0 0.6 1.0 CA J:LYS74 5.0 0.5 1.0

Zinc binding site 4 out of 4 in the Escherichia Coli Rna Polymerase in Complex with Squaramide Compound 8.


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 Squaramide Compound 8. within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn2003 b:0.1 occ:1.00 SG J:CYS895 2.0 0.7 1.0 SG J:CYS814 2.4 0.9 1.0 SG J:CYS898 2.4 0.1 1.0 SG J:CYS888 2.5 0.0 1.0 CB J:CYS898 2.6 0.6 1.0 CB J:CYS888 3.3 0.7 1.0 CB J:CYS895 3.6 0.9 1.0 NH2 J:ARG883 3.7 0.5 1.0 CA J:CYS898 3.7 0.8 1.0 CB J:CYS814 3.8 0.5 1.0 N J:CYS898 3.8 0.2 1.0 CA J:CYS888 3.8 0.2 1.0 CG2 J:THR816 4.2 0.3 1.0 N J:CYS814 4.4 0.0 1.0 N J:ASP889 4.4 0.3 1.0 OG1 J:THR890 4.4 0.3 1.0 N J:CYS895 4.4 0.6 1.0 CA J:CYS895 4.5 0.5 1.0 O J:CYS895 4.5 0.4 1.0 C J:CYS888 4.6 0.0 1.0 CZ J:ARG883 4.6 0.9 1.0 CA J:CYS814 4.7 0.7 1.0 NE J:ARG883 4.7 0.3 1.0 C J:CYS895 4.8 0.1 1.0 OD1 J:ASP813 4.9 0.8 1.0 N J:THR890 4.9 0.8 1.0 N J:CYS888 4.9 0.1 1.0 C J:HIS897 5.0 0.6 1.0 C J:CYS898 5.0 0.2 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.