Zinc in PDB 2vrt: Crystal Structure of E. Coli Rnase E Possessing M1 Rna Fragments - Catalytic Domain

The structure of Crystal Structure of E. Coli Rnase E Possessing M1 Rna Fragments - Catalytic Domain, PDB code: 2vrt was solved by D.J.Koslover, A.J.Callaghan, M.J.Marcaida, E.F.Garman, 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)	24.98 / 3.5
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93.894, 121.252, 242.228, 90.00, 99.47, 90.00
R / Rfree (%)	31.7 / 35.1

The binding sites of Zinc atom in the Crystal Structure of E. Coli Rnase E Possessing M1 Rna Fragments - Catalytic Domain (pdb code 2vrt). 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 Possessing M1 Rna Fragments - Catalytic Domain, PDB code: 2vrt:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of E. Coli Rnase E Possessing M1 Rna Fragments - 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 Possessing M1 Rna Fragments - Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1506 b:97.7 occ:1.00 SG A:CYS404 2.6 0.6 1.0 CB A:CYS404 2.8 0.6 1.0 SG B:CYS404 3.1 95.7 1.0 SG B:CYS407 3.4 0.5 1.0 SG A:CYS407 3.7 0.1 1.0 N A:CYS407 4.1 0.1 1.0 CA B:GLY411 4.2 0.7 1.0 CA A:CYS404 4.2 0.5 1.0 CB B:CYS404 4.3 99.9 1.0 N B:CYS407 4.3 0.9 1.0 N B:GLY411 4.4 1.0 1.0 O B:CYS407 4.5 0.7 1.0 CB B:ARG406 4.6 0.7 1.0 CB B:CYS407 4.7 0.4 1.0 C A:CYS404 4.8 0.5 1.0 N A:CYS404 4.8 0.7 1.0 CG B:ARG406 4.8 0.2 1.0 CA A:CYS407 4.9 0.8 1.0 CA B:CYS407 4.9 0.2 1.0 C B:GLY411 4.9 0.5 1.0 CB A:CYS407 4.9 0.5 1.0 C A:CYS407 5.0 0.7 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of E. Coli Rnase E Possessing M1 Rna Fragments - 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 Possessing M1 Rna Fragments - Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1509 b:0.7 occ:1.00 SG D:CYS407 1.8 0.6 1.0 SG D:CYS404 1.8 0.1 1.0 SG C:CYS404 2.6 0.6 1.0 CB D:CYS404 2.8 0.3 1.0 CB D:CYS407 3.1 0.2 1.0 N D:CYS407 3.2 0.9 1.0 SG C:CYS407 3.3 0.8 1.0 CB C:CYS404 3.3 0.2 1.0 CA D:CYS407 3.6 0.9 1.0 O D:CYS407 3.8 0.2 1.0 CB C:CYS407 3.9 0.1 1.0 C D:CYS407 4.1 0.1 1.0 CA D:CYS404 4.2 0.6 1.0 CB D:ARG406 4.2 0.8 1.0 O C:THR410 4.3 0.8 1.0 C D:ARG406 4.3 0.3 1.0 C D:CYS404 4.5 1.0 1.0 N D:ARG406 4.5 0.0 1.0 CA D:ARG406 4.6 0.9 1.0 CA D:GLY411 4.6 0.7 1.0 N D:GLY411 4.7 1.0 1.0 CA C:CYS404 4.7 0.4 1.0 CG D:ARG406 4.8 0.4 1.0 N C:CYS407 4.8 0.3 1.0 O D:CYS404 4.9 0.8 1.0 N D:PRO405 4.9 0.2 1.0 CA C:CYS407 5.0 0.7 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