Zinc in PDB 4lk1: Crystal Structure Analysis of the E.Coli Holoenzyme

All present enzymatic activity of Crystal Structure Analysis of the E.Coli Holoenzyme:
2.7.7.6;

The structure of Crystal Structure Analysis of the E.Coli Holoenzyme, PDB code: 4lk1 was solved by B.Bae, S.A.Darst, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.78 / 3.84
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	186.675, 206.392, 308.836, 90.00, 90.00, 90.00
R / Rfree (%)	22.4 / 27.2

The structure of Crystal Structure Analysis of the E.Coli Holoenzyme also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Zinc atom in the Crystal Structure Analysis of the E.Coli Holoenzyme (pdb code 4lk1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure Analysis of the E.Coli Holoenzyme, PDB code: 4lk1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure Analysis of the E.Coli Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure Analysis of the E.Coli Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1502 b:0.6 occ:1.00 SG D:CYS72 2.2 80.4 1.0 SG D:CYS85 2.3 62.6 1.0 SG D:CYS70 2.3 81.5 1.0 CB D:CYS85 3.1 70.4 1.0 SG D:CYS88 3.4 0.0 1.0 CB D:CYS72 3.5 80.8 1.0 O D:CYS88 3.8 0.9 1.0 CB D:CYS70 3.9 85.2 1.0 CB D:LYS74 4.0 89.9 1.0 N D:CYS72 4.0 0.7 1.0 CB D:LYS87 4.0 0.9 1.0 N D:CYS88 4.0 0.7 1.0 CA D:CYS72 4.2 0.0 1.0 N D:LYS74 4.3 0.6 1.0 N D:GLY73 4.4 0.3 1.0 CA D:CYS85 4.6 99.9 1.0 C D:CYS72 4.7 0.2 1.0 N D:LYS87 4.7 0.2 1.0 C D:CYS88 4.7 0.6 1.0 CB D:CYS88 4.7 0.4 1.0 CA D:CYS88 4.8 0.1 1.0 CA D:LYS87 4.8 0.3 1.0 CA D:LYS74 4.8 96.1 1.0 N D:LEU71 4.8 92.6 1.0 C D:LYS87 4.9 0.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure Analysis of the E.Coli Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure Analysis of the E.Coli Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1503 b:0.7 occ:1.00 SG D:CYS814 2.3 62.8 1.0 SG D:CYS895 2.3 0.2 1.0 SG D:CYS888 2.3 65.7 1.0 SG D:CYS898 2.4 0.1 1.0 CB D:CYS898 2.7 66.3 1.0 CB D:CYS888 3.0 89.4 1.0 CB D:CYS814 3.5 76.4 1.0 CA D:CYS888 3.5 85.9 1.0 CB D:CYS895 3.8 79.8 1.0 CA D:CYS898 3.9 85.1 1.0 N D:CYS898 4.1 90.6 1.0 NH2 D:ARG883 4.2 0.4 1.0 N D:ASP889 4.2 59.0 1.0 C D:CYS888 4.3 74.8 1.0 N D:CYS814 4.3 69.7 1.0 N D:CYS895 4.4 67.8 1.0 CA D:CYS814 4.5 70.7 1.0 O D:CYS895 4.5 73.5 1.0 CG2 D:THR816 4.5 86.7 1.0 CA D:CYS895 4.6 85.8 1.0 N D:CYS888 4.7 84.3 1.0 C D:CYS895 4.9 65.3 1.0

Zinc binding site 3 out of 4 in the Crystal Structure Analysis of the E.Coli Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure Analysis of the E.Coli Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1502 b:0.9 occ:1.00 SG J:CYS85 2.2 70.2 1.0 SG J:CYS72 2.2 0.7 1.0 SG J:CYS70 2.3 0.1 1.0 CB J:CYS85 3.1 60.6 1.0 SG J:CYS88 3.4 0.7 1.0 CB J:CYS72 3.5 0.3 1.0 O J:CYS88 3.8 85.2 1.0 CB J:CYS70 3.9 0.2 1.0 CB J:LYS74 4.0 0.1 1.0 N J:CYS72 4.0 0.0 1.0 CB J:LYS87 4.0 89.1 1.0 N J:CYS88 4.0 0.9 1.0 CA J:CYS72 4.2 0.9 1.0 N J:LYS74 4.3 0.0 1.0 N J:GLY73 4.4 0.3 1.0 CA J:CYS85 4.6 84.9 1.0 C J:CYS72 4.7 0.1 1.0 N J:LYS87 4.7 0.7 1.0 C J:CYS88 4.7 99.6 1.0 CB J:CYS88 4.8 0.3 1.0 CA J:CYS88 4.8 0.2 1.0 CA J:LYS74 4.8 0.3 1.0 CA J:LYS87 4.8 0.6 1.0 N J:LEU71 4.8 0.6 1.0 C J:LYS87 4.9 0.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure Analysis of the E.Coli Holoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure Analysis of the E.Coli Holoenzyme within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1503 b:37.1 occ:1.00 SG J:CYS814 2.3 83.5 1.0 SG J:CYS895 2.3 52.9 1.0 SG J:CYS888 2.4 73.1 1.0 SG J:CYS898 2.4 88.6 1.0 CB J:CYS898 2.7 63.5 1.0 CB J:CYS888 3.0 87.8 1.0 CB J:CYS814 3.5 75.3 1.0 CA J:CYS888 3.5 50.5 1.0 CB J:CYS895 3.8 89.5 1.0 CA J:CYS898 3.9 78.4 1.0 N J:CYS898 4.1 78.1 1.0 NH2 J:ARG883 4.2 98.2 1.0 N J:ASP889 4.2 73.8 1.0 C J:CYS888 4.3 72.7 1.0 N J:CYS814 4.4 81.1 1.0 N J:CYS895 4.4 95.0 1.0 O J:CYS895 4.5 86.6 1.0 CA J:CYS814 4.5 83.6 1.0 CG2 J:THR816 4.5 97.2 1.0 CA J:CYS895 4.6 92.9 1.0 N J:CYS888 4.7 27.3 1.0 C J:CYS895 4.9 82.9 1.0

B.Bae, E.Davis, D.Brown, E.A.Campbell, S.Wigneshweraraj, S.A.Darst. Phage T7 GP2 Inhibition of Escherichia Coli Rna Polymerase Involves Misappropriation of Sigma 70 Domain 1.1. Proc.Natl.Acad.Sci.Usa V. 110 19772 2013.
ISSN: ISSN 0027-8424
PubMed: 24218560
DOI: 10.1073/PNAS.1314576110