Zinc in PDB 2vmk: Crystal Structure of E. Coli Rnase E Apoprotein - Catalytic Domain

The structure of Crystal Structure of E. Coli Rnase E Apoprotein - Catalytic Domain, PDB code: 2vmk was solved by D.J.Koslover, A.J.Callaghan, M.J.Marcaida, M.Martick, W.G.Scott, B.F.Luisi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.84 / 3.3
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	73.241, 75.571, 109.370, 94.95, 102.03, 91.77
R / Rfree (%)	26.7 / 29.3

The binding sites of Zinc atom in the Crystal Structure of E. Coli Rnase E Apoprotein - Catalytic Domain (pdb code 2vmk). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of E. Coli Rnase E Apoprotein - Catalytic Domain, PDB code: 2vmk:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of E. Coli Rnase E Apoprotein - Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of E. Coli Rnase E Apoprotein - Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1514 b:58.1 occ:0.50 SG B:CYS404 2.1 81.1 1.0 SG B:CYS407 2.2 85.6 1.0 SG A:CYS407 2.3 75.5 1.0 CB B:CYS407 2.7 65.0 1.0 SG A:CYS404 2.7 77.7 1.0 CB B:CYS404 2.9 69.4 1.0 CB A:CYS407 3.1 80.7 1.0 CB A:CYS404 3.4 78.3 1.0 N B:CYS407 3.4 68.1 1.0 CA B:CYS407 3.6 70.7 1.0 N A:CYS407 4.0 82.4 1.0 CB B:ARG406 4.1 75.0 1.0 C B:ARG406 4.1 64.8 1.0 CA A:CYS407 4.1 80.6 1.0 CA B:CYS404 4.3 73.9 1.0 O A:THR410 4.5 0.5 1.0 CA B:ARG406 4.5 65.3 1.0 C B:CYS404 4.5 78.1 1.0 N B:ARG406 4.6 72.3 1.0 N B:GLY411 4.7 67.4 1.0 CA A:GLY411 4.7 92.5 1.0 O B:CYS404 4.8 79.1 1.0 CA A:CYS404 4.8 77.8 1.0 C B:CYS407 4.8 70.8 1.0 CA B:GLY411 4.9 61.8 1.0 O B:ARG406 5.0 65.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of E. Coli Rnase E Apoprotein - Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of E. Coli Rnase E Apoprotein - Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1516 b:64.5 occ:0.50 SG C:CYS407 2.0 77.7 1.0 SG D:CYS407 2.1 77.1 1.0 SG D:CYS404 2.2 80.3 1.0 SG C:CYS404 2.3 70.2 1.0 CB D:CYS404 3.1 79.6 1.0 CB C:CYS404 3.2 70.9 1.0 CB C:CYS407 3.5 77.4 1.0 N D:CYS407 3.6 75.2 1.0 CB D:CYS407 3.8 67.0 1.0 N C:CYS407 3.8 83.8 1.0 CB D:ARG406 3.9 76.0 1.0 CA C:CYS407 4.3 82.7 1.0 CA D:CYS407 4.4 80.7 1.0 O C:THR410 4.4 96.0 1.0 C D:ARG406 4.5 70.9 1.0 CA D:CYS404 4.5 76.2 1.0 CA D:GLY411 4.6 91.9 1.0 CA C:CYS404 4.6 76.0 1.0 CA D:ARG406 4.6 72.9 1.0 CB C:ARG406 4.6 79.7 1.0 C C:ARG406 4.6 82.8 1.0 N D:GLY411 4.6 90.5 1.0 N D:ARG406 4.6 75.5 1.0 O C:CYS404 4.7 85.4 1.0 N C:ARG406 4.7 80.0 1.0 C C:CYS404 4.8 78.2 1.0 CA C:ARG406 4.9 78.8 1.0 C D:CYS404 4.9 79.6 1.0 CG D:ARG406 5.0 84.4 1.0

D.J.Koslover, A.J.Callaghan, M.J.Marcaida, E.F.Garman, M.Martick, W.G.Scott, B.F.Luisi. The Crystal Structure of the Escherichia Coli Rnase E Apoprotein and A Mechanism For Rna Degradation. Structure V. 16 1238 2008.
ISSN: ISSN 0969-2126
PubMed: 18682225
DOI: 10.1016/J.STR.2008.04.017