Zinc in PDB 6sw9: IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi

The structure of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi also contains other interesting chemical elements:

Magnesium

(Mg)

34 atoms

The binding sites of Zinc atom in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi (pdb code 6sw9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi, PDB code: 6sw9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:0.3 occ:1.00 CB C:CYS55 1.7 0.8 1.0 SG C:CYS55 2.3 0.8 1.0 SG C:CYS35 2.3 95.0 1.0 SG C:CYS32 2.4 87.7 1.0 SG C:CYS58 2.4 0.3 1.0 CB C:CYS58 2.9 0.3 1.0 CA C:CYS55 3.1 0.8 1.0 CB C:CYS35 3.7 95.0 1.0 N C:CYS55 3.7 0.8 1.0 CB C:CYS32 3.8 87.7 1.0 O C:PRO33 3.9 86.5 1.0 N C:CYS58 3.9 0.3 1.0 CA C:CYS58 4.0 0.3 1.0 CE3 C:TRP60 4.1 96.6 1.0 C C:CYS55 4.2 0.8 1.0 CZ3 C:TRP60 4.6 96.6 1.0 O C:TRP60 4.6 96.6 1.0 O C:CYS55 4.6 0.8 1.0 C C:CYS58 4.8 0.3 1.0 OE2 C:GLU37 4.9 90.2 1.0 CA C:CYS35 4.9 95.0 1.0 N C:PRO56 4.9 0.5 1.0 N C:CYS35 5.0 95.0 1.0

Zinc binding site 2 out of 6 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:0.0 occ:1.00 CB C:CYS17 1.4 74.2 1.0 N C:CYS17 1.8 74.2 1.0 CA C:CYS17 1.9 74.2 1.0 SG C:CYS17 2.3 74.2 1.0 SG C:CYS43 2.3 63.8 1.0 SG C:CYS14 2.3 64.7 1.0 SG C:CYS46 2.3 64.1 1.0 OG C:SER16 2.6 64.4 1.0 CB C:CYS46 2.8 64.1 1.0 C C:SER16 3.1 64.4 1.0 C C:CYS17 3.1 74.2 1.0 CB C:CYS14 3.4 64.7 1.0 N C:GLY18 3.4 80.8 1.0 CB C:SER16 3.8 64.4 1.0 CA C:SER16 3.8 64.4 1.0 O C:SER16 4.0 64.4 1.0 N C:SER16 4.0 64.4 1.0 CB C:CYS43 4.1 63.8 1.0 CA C:CYS46 4.1 64.1 1.0 O C:CYS17 4.2 74.2 1.0 N C:CYS43 4.7 63.8 1.0 CA C:CYS14 4.8 64.7 1.0 CA C:GLY18 4.8 80.8 1.0 N C:CYS46 4.9 64.1 1.0 N C:ARG19 5.0 66.7 1.0 CA C:CYS43 5.0 63.8 1.0

Zinc binding site 3 out of 6 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:90.9 occ:1.00 NE2 F:HIS139 2.1 48.2 1.0 SG F:CYS128 2.3 42.9 1.0 SG F:CYS135 2.3 48.8 1.0 CB F:CYS128 2.3 42.9 1.0 SG F:CYS133 2.3 45.7 1.0 CD2 F:HIS139 2.5 48.2 1.0 O F:ARG137 2.9 49.7 1.0 CE1 F:HIS139 3.1 48.2 1.0 CG F:HIS139 3.5 48.2 1.0 N F:ARG137 3.5 49.7 1.0 CB F:CYS135 3.7 48.8 1.0 O F:CYS135 3.7 48.8 1.0 ND1 F:HIS139 3.8 48.2 1.0 CA F:CYS128 3.8 42.9 1.0 C F:CYS135 3.8 48.8 1.0 C F:ARG137 3.9 49.7 1.0 CB F:CYS133 4.1 45.7 1.0 CA F:ARG137 4.2 49.7 1.0 CA F:CYS135 4.2 48.8 1.0 N F:ARG136 4.3 46.9 1.0 O F:CYS133 4.4 45.7 1.0 CB F:ARG137 4.4 49.7 1.0 C F:ARG136 4.5 46.9 1.0 CA F:ARG136 4.5 46.9 1.0 N F:CYS135 4.6 48.8 1.0 N F:CYS128 4.6 42.9 1.0 O F:GLY127 4.6 43.4 1.0 C F:CYS128 4.7 42.9 1.0 N F:HIS139 4.7 48.2 1.0 O F:CYS128 4.8 42.9 1.0 CB F:HIS139 4.8 48.2 1.0 C F:CYS133 4.9 45.7 1.0 C F:GLY127 5.0 43.4 1.0

Zinc binding site 4 out of 6 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn101 b:0.7 occ:1.00 SG P:CYS39 2.3 74.8 1.0 SG P:CYS24 2.3 79.2 1.0 SG P:CYS21 2.3 77.7 1.0 SG P:CYS42 2.4 76.8 1.0 CB P:CYS24 2.8 79.2 1.0 CB P:CYS39 2.8 74.8 1.0 N P:CYS39 3.0 74.8 1.0 CB P:CYS42 3.1 76.8 1.0 N P:CYS24 3.3 79.2 1.0 CA P:CYS39 3.5 74.8 1.0 CB P:CYS21 3.5 77.7 1.0 CA P:CYS24 3.7 79.2 1.0 C P:LEU38 4.0 69.9 1.0 CA P:LEU38 4.3 69.9 1.0 CA P:CYS42 4.4 76.8 1.0 N P:ARG23 4.4 76.8 1.0 C P:ARG23 4.4 76.8 1.0 CB P:LEU38 4.5 69.9 1.0 N P:CYS42 4.6 76.8 1.0 N P:ILE22 4.7 74.5 1.0 C P:CYS39 4.7 74.8 1.0 CA P:CYS21 4.7 77.7 1.0 CG P:LEU38 4.7 69.9 1.0 C P:CYS24 4.8 79.2 1.0 CA P:ARG23 4.8 76.8 1.0 N P:GLY25 4.9 79.1 1.0 CB P:ARG23 4.9 76.8 1.0

Zinc binding site 5 out of 6 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:0.7 occ:1.00 CB R:CYS16 1.0 87.6 1.0 SG R:CYS16 1.8 87.6 1.0 CA R:CYS16 1.8 87.6 1.0 ND1 R:HIS24 1.9 84.4 1.0 N R:CYS16 2.2 87.6 1.0 CE1 R:HIS24 2.2 84.4 1.0 CG R:HIS24 2.3 84.4 1.0 SG R:CYS21 2.4 79.1 1.0 SG R:CYS77 2.5 67.4 1.0 NE2 R:HIS24 2.8 84.4 1.0 C R:CYS16 2.8 87.6 1.0 CD2 R:HIS24 2.8 84.4 1.0 CB R:CYS21 3.2 79.1 1.0 CB R:HIS24 3.2 84.4 1.0 O R:CYS16 3.4 87.6 1.0 C R:LYS15 3.5 89.7 1.0 N R:ASP17 3.5 82.9 1.0 CB R:CYS77 3.7 67.4 1.0 O R:LYS15 4.3 89.7 1.0 CA R:LYS15 4.4 89.7 1.0 CA R:HIS24 4.6 84.4 1.0 CA R:CYS21 4.7 79.1 1.0 CA R:ASP17 4.8 82.9 1.0 NZ R:LYS15 4.8 89.7 1.0 N R:CYS77 4.8 67.4 1.0 N R:HIS24 4.8 84.4 1.0 CA R:CYS77 4.9 67.4 1.0

Zinc binding site 6 out of 6 in the IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of IC2A Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:0.6 occ:1.00 SG W:CYS42 2.4 1.0 1.0 SG W:CYS20 2.4 0.3 1.0 SG W:CYS23 2.4 0.1 1.0 SG W:CYS39 2.4 0.8 1.0 CB W:CYS39 2.5 0.8 1.0 CB W:CYS23 3.0 0.1 1.0 OD1 W:ASP22 3.1 0.9 1.0 N W:CYS23 3.6 0.1 1.0 CB W:CYS20 3.9 0.3 1.0 CA W:CYS23 3.9 0.1 1.0 CA W:CYS39 4.1 0.8 1.0 CB W:CYS42 4.1 1.0 1.0 CG W:ASP22 4.2 0.9 1.0 N W:CYS42 4.5 1.0 1.0 CD2 W:LEU46 4.6 99.3 1.0 N W:GLY43 4.6 0.7 1.0 C W:ASP22 4.7 0.9 1.0 OD2 W:ASP22 4.7 0.9 1.0 N W:ASP22 4.8 0.9 1.0 N W:CYS39 4.8 0.8 1.0 C W:CYS39 4.8 0.8 1.0 CA W:CYS42 4.8 1.0 1.0 CA W:CYS20 4.9 0.3 1.0 C W:CYS23 4.9 0.1 1.0 O W:CYS39 5.0 0.8 1.0

P.D.Coureux, C.Lazennec-Schurdevin, S.Bourcier, Y.Mechulam, E.Schmitt. Cryo-Em Study of An Archaeal 30S Initiation Complex Gives Insights Into Evolution of Translation Initiation. Commun Biol V. 3 58 2020.
ISSN: ESSN 2399-3642
PubMed: 32029867
DOI: 10.1038/S42003-020-0780-0