Zinc in PDB 7zah: Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B

The structure of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B also contains other interesting chemical elements:

Magnesium

(Mg)

63 atoms

The binding sites of Zinc atom in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B (pdb code 7zah). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B, PDB code: 7zah:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:115.7 occ:1.00 SG C:CYS35 2.3 65.1 1.0 SG C:CYS58 2.3 71.2 1.0 SG C:CYS55 2.3 65.2 1.0 SG C:CYS32 2.7 56.9 1.0 CB C:CYS35 3.3 65.1 1.0 CB C:CYS55 3.3 65.2 1.0 CB C:CYS58 3.3 71.2 1.0 CB C:CYS32 3.5 56.9 1.0 N C:CYS58 3.6 71.2 1.0 N C:CYS35 4.0 65.1 1.0 CA C:CYS58 4.0 71.2 1.0 CA C:CYS35 4.3 65.1 1.0 CB C:LYS57 4.3 71.4 1.0 C C:LYS57 4.6 71.4 1.0 CA C:CYS55 4.7 65.2 1.0 N C:LYS57 4.7 71.4 1.0 CA C:LYS57 4.8 71.4 1.0 ND2 C:ASN34 4.9 61.1 1.0 N C:GLY36 4.9 63.1 1.0 C C:CYS58 4.9 71.2 1.0 N C:GLY59 4.9 64.2 1.0 CA C:CYS32 5.0 56.9 1.0 C C:CYS35 5.0 65.1 1.0

Zinc binding site 2 out of 6 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:71.0 occ:1.00 SG C:CYS14 2.3 41.1 1.0 SG C:CYS46 2.3 39.0 1.0 SG C:CYS43 2.3 39.4 1.0 SG C:CYS17 2.3 43.8 1.0 CB C:CYS14 3.3 41.1 1.0 CB C:CYS17 3.3 43.8 1.0 CB C:CYS46 3.5 39.0 1.0 CB C:CYS43 3.6 39.4 1.0 N C:CYS17 3.7 43.8 1.0 CA C:CYS17 4.1 43.8 1.0 N C:CYS43 4.1 39.4 1.0 N C:CYS46 4.4 39.0 1.0 CA C:CYS43 4.4 39.4 1.0 CA C:CYS46 4.5 39.0 1.0 CB C:SER16 4.6 42.6 1.0 CA C:CYS14 4.7 41.1 1.0 C C:SER16 4.8 42.6 1.0 C C:CYS17 4.9 43.8 1.0 OG C:SER16 4.9 42.6 1.0 N C:SER16 4.9 42.6 1.0 N C:GLY18 5.0 41.4 1.0

Zinc binding site 3 out of 6 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:49.5 occ:1.00 NE2 F:HIS139 2.1 32.3 1.0 SG F:CYS135 2.3 37.3 1.0 SG F:CYS128 2.3 33.3 1.0 SG F:CYS133 2.3 38.3 1.0 CE1 F:HIS139 2.9 32.3 1.0 CD2 F:HIS139 3.3 32.3 1.0 CB F:CYS128 3.3 33.3 1.0 CB F:CYS135 3.6 37.3 1.0 CB F:CYS133 3.7 38.3 1.0 N F:CYS135 4.0 37.3 1.0 O F:CYS133 4.0 38.3 1.0 ND1 F:HIS139 4.1 32.3 1.0 C F:CYS133 4.2 38.3 1.0 CG F:HIS139 4.3 32.3 1.0 CA F:CYS135 4.3 37.3 1.0 CB F:ARG161 4.4 34.7 1.0 N F:ARG161 4.6 34.7 1.0 CA F:CYS133 4.6 38.3 1.0 CA F:CYS128 4.6 33.3 1.0 NH1 F:ARG161 4.6 34.7 1.0 N F:ARG134 4.7 34.6 1.0 O F:ARG137 4.8 35.9 1.0 C F:CYS135 4.9 37.3 1.0 N F:ARG136 4.9 37.4 1.0 C F:ARG134 5.0 34.6 1.0 CD F:ARG161 5.0 34.7 1.0 O F:GLY159 5.0 31.0 1.0 CA F:ARG161 5.0 34.7 1.0

Zinc binding site 4 out of 6 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn101 b:57.9 occ:1.00 SG P:CYS24 2.2 44.0 1.0 SG P:CYS42 2.3 38.7 1.0 SG P:CYS21 2.4 42.6 1.0 SG P:CYS39 2.8 40.7 1.0 CB P:CYS39 3.0 40.7 1.0 CB P:CYS21 3.3 42.6 1.0 CB P:CYS42 3.3 38.7 1.0 CB P:CYS24 3.6 44.0 1.0 N P:CYS39 3.8 40.7 1.0 CA P:CYS39 4.0 40.7 1.0 N P:CYS24 4.1 44.0 1.0 N P:CYS42 4.3 38.7 1.0 CA P:CYS42 4.4 38.7 1.0 CA P:CYS24 4.4 44.0 1.0 OE1 P:GLN26 4.7 41.6 1.0 CA P:CYS21 4.8 42.6 1.0 CB P:ARG23 4.9 43.9 1.0 C P:ARG23 4.9 43.9 1.0 CB P:GLN26 4.9 41.6 1.0 C P:CYS39 5.0 40.7 1.0 O2' 2:G1176 5.0 35.0 1.0

Zinc binding site 5 out of 6 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:86.7 occ:1.00 ND1 R:HIS24 2.1 62.1 1.0 SG R:CYS77 2.2 57.3 1.0 SG R:CYS16 2.2 69.8 1.0 SG R:CYS21 2.3 57.4 1.0 CE1 R:HIS24 2.8 62.1 1.0 CG R:HIS24 3.2 62.1 1.0 CB R:CYS77 3.3 57.3 1.0 CB R:CYS21 3.4 57.4 1.0 CB R:CYS16 3.5 69.8 1.0 CB R:HIS24 3.7 62.1 1.0 NE2 R:HIS24 4.0 62.1 1.0 N R:CYS16 4.2 69.8 1.0 CD2 R:HIS24 4.2 62.1 1.0 N R:HIS24 4.2 62.1 1.0 CB R:TRP23 4.4 56.4 1.0 CA R:CYS16 4.4 69.8 1.0 CA R:CYS77 4.5 57.3 1.0 N R:CYS77 4.6 57.3 1.0 CA R:HIS24 4.6 62.1 1.0 CB R:PRO75 4.7 48.1 1.0 CA R:CYS21 4.8 57.4 1.0 C R:LYS15 4.9 72.9 1.0 C R:TRP23 4.9 56.4 1.0

Zinc binding site 6 out of 6 in the Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna, AIF1A and AIF5B within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:112.6 occ:1.00 SG W:CYS42 2.3 82.1 1.0 SG W:CYS20 2.4 86.7 1.0 SG W:CYS39 2.4 72.5 1.0 CB W:CYS23 2.5 94.4 1.0 CB W:CYS20 3.2 86.7 1.0 CB W:CYS39 3.3 72.5 1.0 N W:CYS23 3.4 94.4 1.0 CA W:CYS23 3.5 94.4 1.0 CB W:CYS42 3.5 82.1 1.0 SG W:CYS23 3.8 94.4 1.0 N W:CYS42 4.0 82.1 1.0 CA W:CYS42 4.4 82.1 1.0 C W:CYS23 4.4 94.4 1.0 CB W:ASN25 4.4 82.3 1.0 N W:GLY24 4.6 90.0 1.0 C W:ASP22 4.6 94.1 1.0 CA W:CYS20 4.7 86.7 1.0 N W:ASN25 4.7 82.3 1.0 CA W:CYS39 4.8 72.5 1.0 CB W:VAL41 4.9 77.5 1.0 CB W:ASP22 4.9 94.1 1.0 N W:GLY43 5.0 76.7 1.0

R.Kazan, G.Bourgeois, C.Lazennec-Schurdevin, E.Larquet, Y.Mechulam, P.D.Coureux, E.Schmitt. Role of AIF5B in Archaeal Translation Initiation. Nucleic Acids Res. V. 50 6532 2022.
ISSN: ESSN 1362-4962
PubMed: 35694843
DOI: 10.1093/NAR/GKAC490