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

The structure of Cryo-Em Structure of A Pyrococcus Abyssi 30S Bound to Met-Initiator Trna, Mrna and AIF1A. 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 and AIF1A. (pdb code 7zai). 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 and AIF1A., PDB code: 7zai:
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 and AIF1A.


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 and AIF1A. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:105.1 occ:1.00 SG C:CYS58 2.3 86.5 1.0 SG C:CYS35 2.3 84.0 1.0 SG C:CYS55 2.4 83.3 1.0 SG C:CYS32 2.4 79.5 1.0 CB C:CYS35 3.2 84.0 1.0 CB C:CYS32 3.3 79.5 1.0 CB C:CYS58 3.3 86.5 1.0 CB C:CYS55 3.3 83.3 1.0 N C:CYS35 3.7 84.0 1.0 N C:CYS58 3.7 86.5 1.0 CA C:CYS35 4.0 84.0 1.0 CA C:CYS58 4.1 86.5 1.0 N C:GLY36 4.6 82.6 1.0 CB C:LYS57 4.6 86.0 1.0 CB C:ASN34 4.6 81.8 1.0 CA C:CYS32 4.8 79.5 1.0 C C:ASN34 4.8 81.8 1.0 C C:CYS35 4.8 84.0 1.0 CA C:CYS55 4.8 83.3 1.0 C C:LYS57 4.8 86.0 1.0 C C:CYS58 4.9 86.5 1.0 N C:GLY59 4.9 82.5 1.0 N C:LYS57 5.0 86.0 1.0 N C:ASN34 5.0 81.8 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 and AIF1A.


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 and AIF1A. within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn102 b:91.0 occ:1.00 SG C:CYS17 2.3 71.0 1.0 SG C:CYS14 2.3 69.7 1.0 SG C:CYS46 2.3 66.4 1.0 SG C:CYS43 2.3 68.2 1.0 CB C:CYS14 3.2 69.7 1.0 CB C:CYS46 3.4 66.4 1.0 CB C:CYS17 3.4 71.0 1.0 CB C:CYS43 3.5 68.2 1.0 N C:CYS17 3.7 71.0 1.0 N C:CYS43 4.1 68.2 1.0 CA C:CYS17 4.2 71.0 1.0 CA C:CYS43 4.4 68.2 1.0 N C:CYS46 4.4 66.4 1.0 CB C:SER16 4.5 69.7 1.0 CA C:CYS46 4.5 66.4 1.0 CA C:CYS14 4.7 69.7 1.0 C C:SER16 4.8 69.7 1.0 N C:SER16 4.9 69.7 1.0 C C:CYS43 5.0 68.2 1.0 C C:CYS17 5.0 71.0 1.0 CA C:SER16 5.0 69.7 1.0 N C:GLY18 5.0 69.4 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 and AIF1A.


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 and AIF1A. within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn301 b:82.7 occ:1.00 NE2 F:HIS139 2.0 59.2 1.0 SG F:CYS128 2.3 61.2 1.0 SG F:CYS135 2.3 63.3 1.0 SG F:CYS133 2.3 63.6 1.0 CE1 F:HIS139 2.8 59.2 1.0 CD2 F:HIS139 3.2 59.2 1.0 CB F:CYS128 3.4 61.2 1.0 CB F:CYS133 3.7 63.6 1.0 CB F:CYS135 3.7 63.3 1.0 O F:CYS133 3.9 63.6 1.0 ND1 F:HIS139 4.0 59.2 1.0 N F:CYS135 4.1 63.3 1.0 C F:CYS133 4.1 63.6 1.0 CG F:HIS139 4.2 59.2 1.0 CB F:ARG161 4.3 60.3 1.0 N F:ARG161 4.4 60.3 1.0 CA F:CYS135 4.5 63.3 1.0 CA F:CYS133 4.5 63.6 1.0 N F:ARG134 4.6 61.4 1.0 CA F:CYS128 4.6 61.2 1.0 O F:GLY159 4.7 57.4 1.0 NH1 F:ARG161 4.7 60.3 1.0 CA F:ARG161 4.8 60.3 1.0 O F:ARG137 5.0 61.8 1.0 C F:ARG134 5.0 61.4 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 and AIF1A.


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 and AIF1A. within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn101 b:87.8 occ:1.00 SG P:CYS24 2.3 72.6 1.0 SG P:CYS42 2.3 68.3 1.0 SG P:CYS21 2.4 71.5 1.0 CB P:CYS39 2.9 70.1 1.0 CB P:CYS42 3.2 68.3 1.0 SG P:CYS39 3.2 70.1 1.0 CB P:CYS21 3.3 71.5 1.0 N P:CYS39 3.6 70.1 1.0 CB P:CYS24 3.7 72.6 1.0 CA P:CYS39 3.8 70.1 1.0 N P:CYS42 4.1 68.3 1.0 N P:CYS24 4.1 72.6 1.0 CA P:CYS42 4.3 68.3 1.0 CA P:CYS24 4.5 72.6 1.0 C P:CYS39 4.7 70.1 1.0 CB P:ARG23 4.7 73.1 1.0 CA P:CYS21 4.8 71.5 1.0 C P:LEU38 4.8 69.3 1.0 OE1 P:GLN26 4.8 69.8 1.0 O P:CYS39 4.9 70.1 1.0 C P:ARG23 4.9 73.1 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 and AIF1A.


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 and AIF1A. within 5.0Å range: probe atom residue distance (Å) B Occ R:Zn201 b:98.7 occ:1.00 ND1 R:HIS24 2.0 79.5 1.0 SG R:CYS16 2.3 84.2 1.0 SG R:CYS77 2.3 79.4 1.0 SG R:CYS21 2.3 77.5 1.0 CE1 R:HIS24 2.5 79.5 1.0 CB R:CYS77 3.1 79.4 1.0 CG R:HIS24 3.3 79.5 1.0 CB R:CYS21 3.4 77.5 1.0 CB R:CYS16 3.5 84.2 1.0 NE2 R:HIS24 3.8 79.5 1.0 CB R:HIS24 4.0 79.5 1.0 N R:CYS16 4.1 84.2 1.0 CD2 R:HIS24 4.2 79.5 1.0 CA R:CYS77 4.3 79.4 1.0 CA R:CYS16 4.4 84.2 1.0 N R:CYS77 4.4 79.4 1.0 N R:HIS24 4.4 79.5 1.0 CB R:PRO75 4.6 71.7 1.0 CB R:TRP23 4.6 76.8 1.0 CA R:CYS21 4.8 77.5 1.0 C R:LYS15 4.8 86.0 1.0 CA R:HIS24 4.9 79.5 1.0 C R:CYS16 5.0 84.2 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 and AIF1A.


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 and AIF1A. within 5.0Å range: probe atom residue distance (Å) B Occ W:Zn101 b:114.7 occ:1.00 SG W:CYS42 2.3 93.8 1.0 SG W:CYS20 2.4 95.5 1.0 SG W:CYS39 2.4 89.9 1.0 CB W:CYS23 2.4 99.5 1.0 CB W:CYS20 3.0 95.5 1.0 CB W:CYS39 3.2 89.9 1.0 N W:CYS23 3.5 99.5 1.0 CA W:CYS23 3.5 99.5 1.0 CB W:CYS42 3.5 93.8 1.0 SG W:CYS23 3.6 99.5 1.0 N W:CYS42 4.0 93.8 1.0 CA W:CYS42 4.3 93.8 1.0 C W:CYS23 4.4 99.5 1.0 N W:GLY24 4.5 96.3 1.0 CA W:CYS20 4.5 95.5 1.0 CB W:ASN25 4.5 94.1 1.0 N W:ASN25 4.6 94.1 1.0 CA W:CYS39 4.7 89.9 1.0 C W:ASP22 4.8 99.5 1.0 CB W:VAL41 4.8 91.9 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