Zinc in PDB 6swc: IC2B Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi

The structure of IC2B 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 IC2B Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi (pdb code 6swc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the IC2B Model of Cryo-Em Structure of A Full Archaeal Ribosomal Translation Initiation Complex Devoid of AIF1 in P. Abyssi, PDB code: 6swc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the IC2B 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 IC2B 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:0.1 occ:1.00 CB C:CYS55 2.0 58.3 1.0 SG C:CYS55 2.3 58.3 1.0 SG C:CYS35 2.3 52.7 1.0 SG C:CYS58 2.3 63.4 1.0 SG C:CYS32 2.4 42.9 1.0 CB C:CYS58 2.8 63.4 1.0 CA C:CYS55 3.5 58.3 1.0 CB C:CYS35 3.6 52.7 1.0 N C:CYS58 3.7 63.4 1.0 CB C:CYS32 3.8 42.9 1.0 CA C:CYS58 3.8 63.4 1.0 N C:CYS55 4.1 58.3 1.0 O C:PRO33 4.3 43.0 1.0 C C:CYS55 4.5 58.3 1.0 CB C:TRP60 4.5 53.5 1.0 C C:CYS58 4.6 63.4 1.0 O C:TRP60 4.6 53.5 1.0 N C:TRP60 4.8 53.5 1.0 CA C:CYS35 4.9 52.7 1.0 CE3 C:TRP60 4.9 53.5 1.0 O C:CYS55 5.0 58.3 1.0 N C:CYS35 5.0 52.7 1.0 C C:LYS57 5.0 59.2 1.0

Zinc binding site 2 out of 6 in the IC2B 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 IC2B 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:96.3 occ:1.00 SG C:CYS46 2.3 33.7 1.0 SG C:CYS17 2.3 44.2 1.0 SG C:CYS14 2.3 41.4 1.0 SG C:CYS43 2.4 32.6 1.0 CB C:CYS14 2.9 41.4 1.0 CB C:CYS43 3.2 32.6 1.0 CB C:CYS46 3.5 33.7 1.0 N C:CYS43 3.7 32.6 1.0 CB C:CYS17 3.9 44.2 1.0 N C:CYS17 3.9 44.2 1.0 CA C:CYS43 4.1 32.6 1.0 CA C:CYS14 4.4 41.4 1.0 CB C:SER16 4.5 43.0 1.0 CA C:CYS17 4.5 44.2 1.0 N C:GLY18 4.7 40.2 1.0 N C:SER16 4.8 43.0 1.0 C C:ARG42 4.8 30.3 1.0 CA C:CYS46 4.8 33.7 1.0 OG C:SER16 4.9 43.0 1.0 N C:CYS46 4.9 33.7 1.0 C C:SER16 4.9 43.0 1.0 C C:CYS14 5.0 41.4 1.0 CA C:SER16 5.0 43.0 1.0

Zinc binding site 3 out of 6 in the IC2B 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 IC2B 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:68.3 occ:1.00 NE2 F:HIS139 2.1 21.9 1.0 SG F:CYS133 2.3 24.3 1.0 SG F:CYS135 2.3 27.7 1.0 SG F:CYS128 2.3 23.2 1.0 CE1 F:HIS139 3.0 21.9 1.0 CD2 F:HIS139 3.2 21.9 1.0 CB F:CYS128 3.2 23.2 1.0 CB F:CYS133 3.7 24.3 1.0 CB F:CYS135 4.0 27.7 1.0 ND1 F:HIS139 4.2 21.9 1.0 CG F:HIS139 4.3 21.9 1.0 NH1 F:ARG161 4.3 22.2 1.0 N F:CYS135 4.3 27.7 1.0 CA F:CYS128 4.5 23.2 1.0 CB F:ARG161 4.5 22.2 1.0 CA F:CYS135 4.6 27.7 1.0 C F:CYS135 4.7 27.7 1.0 O F:CYS135 4.7 27.7 1.0 O F:ARG137 4.7 25.9 1.0 C F:CYS133 4.8 24.3 1.0 N F:ARG161 4.8 22.2 1.0 CA F:CYS133 4.8 24.3 1.0 O F:CYS133 5.0 24.3 1.0

Zinc binding site 4 out of 6 in the IC2B 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 IC2B 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:60.0 occ:1.00 SG P:CYS39 2.3 20.6 1.0 SG P:CYS24 2.3 30.4 1.0 SG P:CYS21 2.3 25.8 1.0 SG P:CYS42 2.4 22.8 1.0 CB P:CYS24 2.9 30.4 1.0 CB P:CYS39 3.2 20.6 1.0 CB P:CYS42 3.2 22.8 1.0 CB P:CYS21 3.4 25.8 1.0 N P:CYS24 3.6 30.4 1.0 N P:CYS39 3.7 20.6 1.0 CA P:CYS24 3.9 30.4 1.0 CA P:CYS39 4.0 20.6 1.0 CA P:CYS42 4.4 22.8 1.0 N P:CYS42 4.4 22.8 1.0 C P:ARG23 4.6 30.2 1.0 CB P:ARG23 4.7 30.2 1.0 C P:LEU38 4.8 20.5 1.0 CA P:CYS21 4.8 25.8 1.0 N P:GLY25 4.8 27.7 1.0 C P:CYS24 4.9 30.4 1.0 N P:ARG23 4.9 30.2 1.0 CA P:ARG23 5.0 30.2 1.0

Zinc binding site 5 out of 6 in the IC2B 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 IC2B 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:0.6 occ:1.00 CE1 R:HIS24 1.0 63.3 1.0 ND1 R:HIS24 1.9 63.3 1.0 SG R:CYS16 1.9 70.5 1.0 NE2 R:HIS24 2.1 63.3 1.0 SG R:CYS77 2.4 52.6 1.0 SG R:CYS21 2.4 52.3 1.0 CG R:HIS24 3.0 63.3 1.0 CD2 R:HIS24 3.1 63.3 1.0 CB R:CYS16 3.3 70.5 1.0 CB R:CYS77 3.4 52.6 1.0 CB R:CYS21 3.9 52.3 1.0 N R:CYS16 4.3 70.5 1.0 CB R:HIS24 4.3 63.3 1.0 CA R:CYS16 4.3 70.5 1.0 CD1 R:TRP23 4.4 52.5 1.0 CG R:PRO12 4.6 61.9 1.0 CB R:PRO75 4.6 39.9 1.0 CB R:TRP23 4.7 52.5 1.0 CA R:CYS77 4.8 52.6 1.0 N R:HIS24 4.8 63.3 1.0 CG R:TRP23 4.9 52.5 1.0 N R:CYS77 4.9 52.6 1.0

Zinc binding site 6 out of 6 in the IC2B 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 IC2B 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:0.3 occ:1.00 SG W:CYS23 2.4 79.2 1.0 SG W:CYS42 2.4 73.3 1.0 SG W:CYS39 2.4 68.6 1.0 SG W:CYS20 2.4 69.2 1.0 CB W:CYS23 2.6 79.2 1.0 CB W:CYS39 3.1 68.6 1.0 CB W:CYS20 3.1 69.2 1.0 CB W:CYS42 3.9 73.3 1.0 CA W:CYS23 4.0 79.2 1.0 CB W:ASN25 4.1 69.6 1.0 N W:CYS23 4.2 79.2 1.0 OD1 W:ASP22 4.3 74.2 1.0 CA W:CYS39 4.3 68.6 1.0 N W:CYS42 4.4 73.3 1.0 CA W:CYS20 4.5 69.2 1.0 CA W:CYS42 4.7 73.3 1.0 C W:CYS23 4.8 79.2 1.0 N W:ASN25 4.8 69.6 1.0 C W:ASP22 5.0 74.2 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