Zinc in PDB 6swd: IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi

The structure of IC2 Body 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)

25 atoms

The binding sites of Zinc atom in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi (pdb code 6swd). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the IC2 Body Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi, PDB code: 6swd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the IC2 Body 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 IC2 Body 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:81.1 occ:1.00 SG C:CYS32 2.3 26.5 1.0 SG C:CYS55 2.3 37.2 1.0 SG C:CYS58 2.3 42.2 1.0 SG C:CYS35 2.3 35.2 1.0 CB C:CYS55 2.4 37.2 1.0 CB C:CYS35 3.3 35.2 1.0 CB C:CYS32 3.7 26.5 1.0 CB C:CYS58 3.8 42.2 1.0 N C:CYS58 3.9 42.2 1.0 CA C:CYS55 3.9 37.2 1.0 CA C:CYS58 4.2 42.2 1.0 O C:PRO33 4.3 27.3 1.0 C C:CYS58 4.5 42.2 1.0 C C:CYS55 4.6 37.2 1.0 CA C:CYS35 4.6 35.2 1.0 N C:CYS55 4.7 37.2 1.0 N C:CYS35 4.7 35.2 1.0 O C:CYS58 4.7 42.2 1.0 CB C:TRP60 4.8 34.4 1.0 O C:CYS55 4.9 37.2 1.0 CB C:LYS57 4.9 42.2 1.0 N C:LYS57 4.9 42.2 1.0 C C:LYS57 5.0 42.2 1.0 N C:TRP60 5.0 34.4 1.0

Zinc binding site 2 out of 5 in the IC2 Body 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 IC2 Body 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:66.8 occ:1.00 SG C:CYS17 2.3 23.7 1.0 SG C:CYS14 2.3 22.4 1.0 SG C:CYS43 2.3 20.6 1.0 SG C:CYS46 2.3 20.7 1.0 CB C:CYS14 2.7 22.4 1.0 CB C:CYS43 3.4 20.6 1.0 CB C:CYS46 3.8 20.7 1.0 CB C:CYS17 3.8 23.7 1.0 N C:CYS43 4.0 20.6 1.0 N C:CYS17 4.1 23.7 1.0 CA C:CYS14 4.2 22.4 1.0 CA C:CYS43 4.3 20.6 1.0 CA C:CYS17 4.6 23.7 1.0 C C:CYS14 4.7 22.4 1.0 CB C:SER16 4.8 22.7 1.0 N C:CYS46 5.0 20.7 1.0 N C:SER16 5.0 22.7 1.0 N C:GLY18 5.0 23.5 1.0 CA C:CYS46 5.0 20.7 1.0 N C:CYS14 5.0 22.4 1.0

Zinc binding site 3 out of 5 in the IC2 Body 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 IC2 Body 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:42.4 occ:1.00 NE2 F:HIS139 2.1 9.7 1.0 SG F:CYS128 2.3 8.6 1.0 SG F:CYS135 2.3 13.0 1.0 SG F:CYS133 2.3 11.7 1.0 CD2 F:HIS139 3.0 9.7 1.0 CB F:CYS128 3.1 8.6 1.0 CE1 F:HIS139 3.1 9.7 1.0 CB F:CYS133 3.8 11.7 1.0 CB F:CYS135 3.9 13.0 1.0 N F:CYS135 4.2 13.0 1.0 CG F:HIS139 4.2 9.7 1.0 ND1 F:HIS139 4.2 9.7 1.0 O F:CYS133 4.3 11.7 1.0 CA F:CYS128 4.4 8.6 1.0 CA F:CYS135 4.4 13.0 1.0 O F:CYS135 4.5 13.0 1.0 C F:CYS133 4.5 11.7 1.0 C F:CYS135 4.5 13.0 1.0 CB F:ARG161 4.6 11.9 1.0 NH1 F:ARG161 4.8 11.9 1.0 O F:ARG137 4.8 11.7 1.0 CA F:CYS133 4.8 11.7 1.0 N F:ARG161 4.8 11.9 1.0

Zinc binding site 4 out of 5 in the IC2 Body 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 IC2 Body 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:61.5 occ:1.00 SG R:CYS16 1.8 39.4 1.0 ND1 R:HIS24 1.9 33.7 1.0 SG R:CYS21 2.4 26.4 1.0 SG R:CYS77 2.4 32.5 1.0 CE1 R:HIS24 2.5 33.7 1.0 CG R:HIS24 2.9 33.7 1.0 CB R:CYS16 3.2 39.4 1.0 CB R:HIS24 3.6 33.7 1.0 NE2 R:HIS24 3.6 33.7 1.0 CB R:CYS77 3.8 32.5 1.0 CD2 R:HIS24 3.8 33.7 1.0 CB R:CYS21 3.8 26.4 1.0 CB R:TRP23 3.9 27.2 1.0 N R:HIS24 3.9 33.7 1.0 N R:CYS16 4.3 39.4 1.0 CA R:CYS16 4.4 39.4 1.0 CA R:HIS24 4.4 33.7 1.0 C R:TRP23 4.6 27.2 1.0 CA R:TRP23 4.6 27.2 1.0 CD1 R:TRP23 4.7 27.2 1.0 CG R:TRP23 4.7 27.2 1.0 N R:TRP23 4.7 27.2 1.0 CG R:PRO12 4.7 31.2 1.0

Zinc binding site 5 out of 5 in the IC2 Body 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 IC2 Body 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:86.6 occ:1.00 SG W:CYS23 2.3 48.3 1.0 SG W:CYS42 2.4 45.8 1.0 SG W:CYS20 2.4 38.4 1.0 SG W:CYS39 2.4 41.9 1.0 CB W:CYS23 2.7 48.3 1.0 CB W:CYS39 2.9 41.9 1.0 CB W:CYS20 3.2 38.4 1.0 CB W:CYS42 4.0 45.8 1.0 CA W:CYS23 4.1 48.3 1.0 OD1 W:ASP22 4.1 46.8 1.0 N W:CYS23 4.3 48.3 1.0 CA W:CYS39 4.3 41.9 1.0 CA W:CYS20 4.6 38.4 1.0 N W:CYS42 4.7 45.8 1.0 CG2 W:VAL41 4.8 41.3 1.0 CB W:ASN25 4.8 41.3 1.0 C W:CYS23 4.9 48.3 1.0 CA W:CYS42 4.9 45.8 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