Zinc in PDB 6zvh: EDF1-Ribosome Complex

All present enzymatic activity of EDF1-Ribosome Complex:
4.2.99.18;

The structure of EDF1-Ribosome Complex also contains other interesting chemical elements:

Magnesium

(Mg)

30 atoms

The binding sites of Zinc atom in the EDF1-Ribosome Complex (pdb code 6zvh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the EDF1-Ribosome Complex, PDB code: 6zvh:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of EDF1-Ribosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ a:Zn201 b:37.8 occ:1.00 SG a:CYS77 2.3 22.2 1.0 SG a:CYS26 2.3 24.2 1.0 SG a:CYS74 2.3 21.9 1.0 SG a:CYS23 2.3 24.3 1.0 CB a:CYS77 3.2 22.2 1.0 CB a:CYS23 3.3 24.3 1.0 CB a:CYS26 3.4 24.2 1.0 CB a:CYS74 3.5 21.9 1.0 OD1 a:ASN25 3.8 26.6 1.0 N a:CYS74 4.0 21.9 1.0 N a:CYS26 4.0 24.2 1.0 CA a:CYS26 4.2 24.2 1.0 N a:CYS77 4.3 22.2 1.0 CA a:CYS74 4.3 21.9 1.0 CA a:CYS77 4.3 22.2 1.0 CB a:ARG28 4.5 22.2 1.0 CA a:CYS23 4.7 24.3 1.0 CG a:ASN25 4.8 26.6 1.0 C a:CYS26 4.8 24.2 1.0 N a:ARG28 4.9 22.2 1.0 N a:ALA27 4.9 23.0 1.0 C a:ASN25 4.9 26.6 1.0 C a:CYS74 5.0 21.9 1.0

Zinc binding site 2 out of 3 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of EDF1-Ribosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ d:Zn101 b:73.5 occ:1.00 N d:PHE43 2.2 27.2 1.0 C d:CYS42 2.3 28.2 1.0 CE d:MET38 2.5 30.4 1.0 CB d:CYS42 2.6 28.2 1.0 CB d:MET38 2.7 30.4 1.0 O d:CYS42 2.8 28.2 1.0 CA d:PHE43 2.8 27.2 1.0 CA d:CYS42 3.0 28.2 1.0 O d:CYS39 3.2 28.2 1.0 SD d:MET38 3.2 30.4 1.0 CG d:MET38 3.4 30.4 1.0 CB d:PHE43 3.5 27.2 1.0 N d:CYS42 3.8 28.2 1.0 CA d:MET38 3.8 30.4 1.0 N d:CYS39 4.1 28.2 1.0 C d:MET38 4.1 30.4 1.0 C d:PHE43 4.2 27.2 1.0 C d:CYS39 4.3 28.2 1.0 SG d:CYS42 4.4 28.2 1.0 CG2 d:VAL23 4.6 30.9 1.0 CD2 d:TYR46 4.7 28.6 1.0 CG d:PHE43 4.7 27.2 1.0 SG d:CYS21 4.8 31.7 1.0 C d:GLN41 4.8 24.5 1.0 CA d:CYS39 4.8 28.2 1.0 O d:MET38 4.8 30.4 1.0 O d:PHE43 4.9 27.2 1.0 N d:ARG44 4.9 25.1 1.0 CD1 d:PHE43 5.0 27.2 1.0

Zinc binding site 3 out of 3 in the EDF1-Ribosome Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of EDF1-Ribosome Complex within 5.0Å range: probe atom residue distance (Å) B Occ f:Zn200 b:0.8 occ:1.00 SG f:CYS144 2.3 0.1 1.0 SG f:CYS126 2.3 0.5 1.0 SG f:CYS141 2.3 98.4 1.0 CB f:CYS144 2.7 0.1 1.0 OG f:SER123 2.9 0.9 1.0 N f:CYS144 3.0 0.1 1.0 CA f:CYS144 3.4 0.1 1.0 CB f:CYS141 3.9 98.4 1.0 CB f:LYS143 3.9 96.9 1.0 SG f:CYS121 3.9 0.6 1.0 CB f:SER123 3.9 0.9 1.0 CB f:CYS126 4.0 0.5 1.0 C f:LYS143 4.1 96.9 1.0 CB f:CYS121 4.2 0.6 1.0 CA f:LYS143 4.4 96.9 1.0 CG2 f:VAL130 4.5 0.1 1.0 N f:LYS143 4.5 96.9 1.0 C f:CYS144 4.6 0.1 1.0 OE1 f:GLU125 4.9 0.9 1.0 N f:CYS145 5.0 97.7 1.0

N.K.Sinha, A.Ordureau, K.Best, J.A.Saba, B.Zinshteyn, E.Sundaramoorthy, A.Fulzele, D.M.Garshott, T.Denk, M.Thoms, J.A.Paulo, W.Harper, E.J.Bennett, R.Beckmann, R.Green. EDF1 Coordinates Cellular Responses to Ribosome Collisions. Elife V. 9 2020.
ISSN: ESSN 2050-084X
PubMed: 32744497
DOI: 10.7554/ELIFE.58828