Zinc in PDB 7zag: Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna,Mrna, AIF1A and the C-Terminal Domain of AIF5B.

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

Magnesium

(Mg)

62 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 the C-Terminal Domain of AIF5B. (pdb code 7zag). 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 the C-Terminal Domain of AIF5B., PDB code: 7zag:
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 the C-Terminal Domain of 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 the C-Terminal Domain of AIF5B. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:124.0 occ:1.00 SG C:CYS58 2.3 100.2 1.0 SG C:CYS35 2.3 99.2 1.0 SG C:CYS55 2.3 97.1 1.0 SG C:CYS32 2.4 93.0 1.0 CB C:CYS35 3.1 99.2 1.0 CB C:CYS32 3.3 93.0 1.0 CB C:CYS58 3.3 100.2 1.0 CB C:CYS55 3.3 97.1 1.0 N C:CYS58 3.6 100.2 1.0 N C:CYS35 3.8 99.2 1.0 CA C:CYS35 4.0 99.2 1.0 CA C:CYS58 4.0 100.2 1.0 CB C:LYS57 4.4 99.7 1.0 N C:GLY36 4.6 97.0 1.0 C C:LYS57 4.6 99.7 1.0 CA C:CYS32 4.7 93.0 1.0 CA C:CYS55 4.7 97.1 1.0 C C:CYS35 4.8 99.2 1.0 CB C:ASN34 4.8 95.8 1.0 N C:LYS57 4.8 99.7 1.0 C C:ASN34 4.8 95.8 1.0 CA C:LYS57 4.9 99.7 1.0 C C:CYS58 4.9 100.2 1.0 N C:GLY59 4.9 96.2 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 the C-Terminal Domain of 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 the C-Terminal Domain of AIF5B. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:108.6 occ:1.00 SG C:CYS17 2.3 84.7 1.0 SG C:CYS46 2.3 80.1 1.0 SG C:CYS14 2.3 82.5 1.0 SG C:CYS43 2.3 80.8 1.0 CB C:CYS14 3.3 82.5 1.0 CB C:CYS17 3.3 84.7 1.0 CB C:CYS46 3.5 80.1 1.0 CB C:CYS43 3.5 80.8 1.0 N C:CYS17 3.6 84.7 1.0 CA C:CYS17 4.0 84.7 1.0 N C:CYS43 4.1 80.8 1.0 CB C:SER16 4.4 83.0 1.0 CA C:CYS43 4.4 80.8 1.0 N C:CYS46 4.4 80.1 1.0 CA C:CYS46 4.5 80.1 1.0 C C:SER16 4.7 83.0 1.0 CA C:CYS14 4.7 82.5 1.0 N C:SER16 4.8 83.0 1.0 CA C:SER16 4.9 83.0 1.0 C C:CYS17 4.9 84.7 1.0 N C:GLY18 4.9 82.5 1.0 C C:CYS43 5.0 80.8 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 the C-Terminal Domain of 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 the C-Terminal Domain of AIF5B. within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:98.0 occ:1.00 NE2 F:HIS139 2.1 72.1 1.0 SG F:CYS128 2.2 73.8 1.0 SG F:CYS135 2.3 76.6 1.0 SG F:CYS133 2.3 77.6 1.0 CE1 F:HIS139 2.9 72.1 1.0 CD2 F:HIS139 3.2 72.1 1.0 CB F:CYS128 3.5 73.8 1.0 CB F:CYS135 3.5 76.6 1.0 CB F:CYS133 3.8 77.6 1.0 O F:CYS133 3.9 77.6 1.0 N F:CYS135 3.9 76.6 1.0 C F:CYS133 4.1 77.6 1.0 ND1 F:HIS139 4.1 72.1 1.0 CB F:ARG161 4.3 73.4 1.0 NH1 F:ARG161 4.3 73.4 1.0 CG F:HIS139 4.3 72.1 1.0 CA F:CYS135 4.3 76.6 1.0 N F:ARG161 4.4 73.4 1.0 CA F:CYS133 4.5 77.6 1.0 N F:ARG134 4.6 73.9 1.0 CA F:CYS128 4.7 73.8 1.0 CA F:ARG161 4.8 73.4 1.0 O F:GLY159 4.9 70.5 1.0 C F:ARG134 4.9 73.9 1.0 CA F:ARG134 5.0 73.9 1.0 C F:CYS135 5.0 76.6 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 the C-Terminal Domain of 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 the C-Terminal Domain of AIF5B. within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn101 b:108.0 occ:1.00 SG P:CYS24 2.3 86.7 1.0 SG P:CYS42 2.3 82.1 1.0 SG P:CYS21 2.4 85.8 1.0 CB P:CYS39 2.8 83.8 1.0 SG P:CYS39 3.1 83.8 1.0 CB P:CYS42 3.2 82.1 1.0 CB P:CYS21 3.3 85.8 1.0 N P:CYS39 3.5 83.8 1.0 CB P:CYS24 3.6 86.7 1.0 CA P:CYS39 3.7 83.8 1.0 N P:CYS24 4.1 86.7 1.0 N P:CYS42 4.1 82.1 1.0 CA P:CYS42 4.3 82.1 1.0 CA P:CYS24 4.4 86.7 1.0 C P:CYS39 4.6 83.8 1.0 CA P:CYS21 4.7 85.8 1.0 OE1 P:GLN26 4.7 84.2 1.0 C P:LEU38 4.7 81.9 1.0 CB P:ARG23 4.8 86.2 1.0 O P:CYS39 4.8 83.8 1.0 C P:ARG23 5.0 86.2 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 the C-Terminal Domain of 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 the C-Terminal Domain of AIF5B. within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:117.1 occ:1.00 ND1 R:HIS24 2.0 93.0 1.0 SG R:CYS16 2.2 97.7 1.0 SG R:CYS77 2.3 91.9 1.0 SG R:CYS21 2.3 91.6 1.0 CE1 R:HIS24 2.5 93.0 1.0 CB R:CYS77 3.0 91.9 1.0 CG R:HIS24 3.3 93.0 1.0 CB R:CYS21 3.4 91.6 1.0 CB R:CYS16 3.5 97.7 1.0 NE2 R:HIS24 3.7 93.0 1.0 CB R:HIS24 4.1 93.0 1.0 CD2 R:HIS24 4.2 93.0 1.0 N R:CYS16 4.2 97.7 1.0 CA R:CYS77 4.3 91.9 1.0 N R:CYS77 4.4 91.9 1.0 CA R:CYS16 4.5 97.7 1.0 N R:HIS24 4.5 93.0 1.0 CB R:TRP23 4.5 89.7 1.0 CB R:PRO75 4.6 83.2 1.0 CA R:CYS21 4.8 91.6 1.0 C R:LYS15 4.9 100.9 1.0 CA R:HIS24 4.9 93.0 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 the C-Terminal Domain of 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 the C-Terminal Domain of AIF5B. within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:129.9 occ:1.00 SG W:CYS42 2.3 106.1 1.0 SG W:CYS20 2.4 106.6 1.0 CB W:CYS23 2.4 111.6 1.0 SG W:CYS39 2.4 102.9 1.0 CB W:CYS20 3.0 106.6 1.0 CB W:CYS39 3.2 102.9 1.0 CB W:CYS42 3.4 106.1 1.0 N W:CYS23 3.5 111.6 1.0 CA W:CYS23 3.5 111.6 1.0 SG W:CYS23 3.6 111.6 1.0 N W:CYS42 3.9 106.1 1.0 CA W:CYS42 4.2 106.1 1.0 C W:CYS23 4.4 111.6 1.0 CB W:ASN25 4.5 105.2 1.0 N W:GLY24 4.5 107.4 1.0 CA W:CYS20 4.5 106.6 1.0 N W:ASN25 4.6 105.2 1.0 CA W:CYS39 4.7 102.9 1.0 C W:ASP22 4.8 110.8 1.0 CB W:VAL41 4.9 104.1 1.0 C W:CYS42 5.0 106.1 1.0 N W:GLY43 5.0 103.2 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