Iron in PDB 8cah: Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex

The structure of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Magnesium	(Mg)	80 atoms

The binding sites of Iron atom in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex (pdb code 8cah). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex, PDB code: 8cah:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ x:Fe701 b:104.1 occ:1.00 FE1 x:SF4701 0.0 104.1 1.0 SG x:CYS21 2.3 67.6 1.0 S3 x:SF4701 2.3 104.1 1.0 S4 x:SF4701 2.3 104.1 1.0 S2 x:SF4701 2.3 104.1 1.0 FE2 x:SF4701 2.7 104.1 1.0 FE4 x:SF4701 2.7 104.1 1.0 FE3 x:SF4701 2.7 104.1 1.0 CB x:CYS21 2.8 67.6 1.0 S1 x:SF4701 3.9 104.1 1.0 N x:GLN23 4.1 60.9 1.0 CA x:CYS21 4.1 67.6 1.0 CA x:GLN23 4.2 60.9 1.0 CA x:PRO18 4.3 69.0 1.0 C x:CYS21 4.4 67.6 1.0 O x:LYS17 4.5 69.2 1.0 SG x:CYS65 4.7 41.7 1.0 O x:CYS21 4.7 67.6 1.0 N x:PRO18 4.8 69.0 1.0 SG x:CYS16 4.8 75.8 1.0 C x:LYS17 4.8 69.2 1.0 N x:GLU24 4.8 54.2 1.0 N x:ARG22 4.9 64.5 1.0 N x:CYS21 4.9 67.6 1.0 CB x:PRO18 4.9 69.0 1.0 C x:GLN23 5.0 60.9 1.0

Iron binding site 2 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ x:Fe701 b:104.1 occ:1.00 FE2 x:SF4701 0.0 104.1 1.0 S3 x:SF4701 2.3 104.1 1.0 S4 x:SF4701 2.3 104.1 1.0 S1 x:SF4701 2.3 104.1 1.0 FE3 x:SF4701 2.7 104.1 1.0 FE1 x:SF4701 2.7 104.1 1.0 FE4 x:SF4701 2.7 104.1 1.0 SG x:CYS25 3.2 60.3 1.0 CB x:ALA48 3.7 62.0 1.0 S2 x:SF4701 3.9 104.1 1.0 CB x:CYS25 4.0 60.3 1.0 SG x:CYS16 4.4 75.8 1.0 SG x:CYS21 4.5 67.6 1.0 SG x:CYS65 4.9 41.7 1.0 N x:CYS25 4.9 60.3 1.0 CG1 x:VAL41 4.9 66.3 1.0 CG2 x:VAL41 4.9 66.3 1.0 CD1 x:ILE70 4.9 54.2 1.0 CA x:GLN23 5.0 60.9 1.0

Iron binding site 3 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ x:Fe701 b:104.1 occ:1.00 FE3 x:SF4701 0.0 104.1 1.0 SG x:CYS16 2.3 75.8 1.0 S4 x:SF4701 2.3 104.1 1.0 S2 x:SF4701 2.3 104.1 1.0 S1 x:SF4701 2.3 104.1 1.0 FE2 x:SF4701 2.7 104.1 1.0 FE4 x:SF4701 2.7 104.1 1.0 FE1 x:SF4701 2.7 104.1 1.0 CB x:CYS16 3.5 75.8 1.0 S3 x:SF4701 3.9 104.1 1.0 CA x:CYS16 3.9 75.8 1.0 C x:CYS16 4.2 75.8 1.0 N x:LYS17 4.2 69.2 1.0 SG x:CYS21 4.2 67.6 1.0 CB x:ALA69 4.6 62.3 1.0 SG x:CYS65 4.7 41.7 1.0 CB x:ALA48 4.7 62.0 1.0 CB x:CYS21 4.7 67.6 1.0 CG x:PRO18 4.8 69.0 1.0 N x:PRO18 4.9 69.0 1.0 C x:LYS17 4.9 69.2 1.0 O x:CYS16 4.9 75.8 1.0 CG2 x:VAL11 5.0 58.6 1.0

Iron binding site 4 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ x:Fe701 b:104.1 occ:1.00 FE4 x:SF4701 0.0 104.1 1.0 SG x:CYS65 2.3 41.7 1.0 S2 x:SF4701 2.3 104.1 1.0 S1 x:SF4701 2.3 104.1 1.0 S3 x:SF4701 2.3 104.1 1.0 FE1 x:SF4701 2.7 104.1 1.0 FE3 x:SF4701 2.7 104.1 1.0 FE2 x:SF4701 2.7 104.1 1.0 SG x:CYS21 3.0 67.6 1.0 CB x:CYS65 3.8 41.7 1.0 S4 x:SF4701 3.9 104.1 1.0 CB x:CYS21 4.4 67.6 1.0 CD1 x:ILE70 4.5 54.2 1.0 CA x:CYS65 4.7 41.7 1.0 CB x:CYS25 4.7 60.3 1.0 SG x:CYS16 4.9 75.8 1.0 SG x:CYS25 4.9 60.3 1.0 CG1 x:ILE70 4.9 54.2 1.0 CB x:ALA69 4.9 62.3 1.0 O x:PHE67 5.0 54.4 1.0

Iron binding site 5 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ x:Fe702 b:104.1 occ:1.00 FE1 x:SF4702 0.0 104.1 1.0 S3 x:SF4702 2.3 104.1 1.0 S4 x:SF4702 2.3 104.1 1.0 S2 x:SF4702 2.3 104.1 1.0 SG x:CYS29 2.3 43.2 1.0 FE4 x:SF4702 2.7 104.1 1.0 FE2 x:SF4702 2.7 104.1 1.0 FE3 x:SF4702 2.7 104.1 1.0 CB x:CYS29 3.1 43.2 1.0 SG x:CYS38 3.8 57.8 1.0 S1 x:SF4702 3.9 104.1 1.0 CA x:CYS29 3.9 43.2 1.0 CD x:PRO30 4.1 40.6 1.0 N x:PRO30 4.6 40.6 1.0 C x:CYS29 4.6 43.2 1.0 CB x:CYS61 4.6 46.7 1.0 SG x:CYS58 4.6 45.0 1.0 SG x:CYS61 4.7 46.7 1.0 CG2 x:VAL31 4.8 43.4 1.0 CG1 x:ILE39 4.8 54.4 1.0 SG x:CYS55 4.8 104.1 1.0 CD1 x:ILE39 4.9 54.4 1.0 CG x:PRO30 5.0 40.6 1.0

Iron binding site 6 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ x:Fe702 b:104.1 occ:1.00 FE2 x:SF4702 0.0 104.1 1.0 SG x:CYS55 2.3 104.1 1.0 S4 x:SF4702 2.3 104.1 1.0 S3 x:SF4702 2.3 104.1 1.0 S1 x:SF4702 2.3 104.1 1.0 FE3 x:SF4702 2.7 104.1 1.0 FE4 x:SF4702 2.7 104.1 1.0 FE1 x:SF4702 2.7 104.1 1.0 CB x:CYS55 3.4 104.1 1.0 S2 x:SF4702 3.9 104.1 1.0 CA x:CYS55 3.9 104.1 1.0 N x:GLY57 3.9 52.6 1.0 N x:ILE56 4.1 51.1 1.0 CB x:ALA9 4.2 45.9 1.0 C x:CYS55 4.3 104.1 1.0 CA x:GLY57 4.4 52.6 1.0 SG x:CYS38 4.4 57.8 1.0 N x:CYS58 4.6 45.0 1.0 SG x:CYS58 4.8 45.0 1.0 SG x:CYS29 4.8 43.2 1.0 SG x:CYS61 4.8 46.7 1.0 CG2 x:ILE50 4.9 53.1 1.0 C x:ILE56 4.9 51.1 1.0 N x:ALA9 5.0 45.9 1.0

Iron binding site 7 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ x:Fe702 b:104.1 occ:1.00 FE3 x:SF4702 0.0 104.1 1.0 SG x:CYS61 2.3 46.7 1.0 S2 x:SF4702 2.3 104.1 1.0 S1 x:SF4702 2.3 104.1 1.0 S4 x:SF4702 2.3 104.1 1.0 FE2 x:SF4702 2.7 104.1 1.0 FE4 x:SF4702 2.7 104.1 1.0 FE1 x:SF4702 2.7 104.1 1.0 CB x:CYS61 3.0 46.7 1.0 S3 x:SF4702 3.9 104.1 1.0 N x:CYS61 3.9 46.7 1.0 CB x:ALA9 4.0 45.9 1.0 CA x:CYS61 4.0 46.7 1.0 SG x:CYS55 4.6 104.1 1.0 N x:GLY59 4.7 51.3 1.0 SG x:CYS58 4.8 45.0 1.0 N x:ILE60 4.8 41.8 1.0 SG x:CYS29 4.8 43.2 1.0 C x:CYS61 4.8 46.7 1.0 N x:VAL62 4.9 40.4 1.0 CA x:GLY59 5.0 51.3 1.0 CB x:CYS29 5.0 43.2 1.0

Iron binding site 8 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 43S Pre- Initiation Complex within 5.0Å range: probe atom residue distance (Å) B Occ x:Fe702 b:104.1 occ:1.00 FE4 x:SF4702 0.0 104.1 1.0 SG x:CYS58 2.2 45.0 1.0 S2 x:SF4702 2.3 104.1 1.0 S1 x:SF4702 2.3 104.1 1.0 S3 x:SF4702 2.3 104.1 1.0 FE2 x:SF4702 2.7 104.1 1.0 FE1 x:SF4702 2.7 104.1 1.0 FE3 x:SF4702 2.7 104.1 1.0 N x:CYS58 3.5 45.0 1.0 N x:GLY59 3.7 51.3 1.0 CB x:CYS58 3.7 45.0 1.0 S4 x:SF4702 3.9 104.1 1.0 CA x:CYS58 4.0 45.0 1.0 N x:ILE60 4.1 41.8 1.0 CD x:PRO30 4.2 40.6 1.0 C x:CYS58 4.3 45.0 1.0 C x:GLY57 4.6 52.6 1.0 CA x:GLY59 4.6 51.3 1.0 N x:GLY57 4.6 52.6 1.0 N x:CYS61 4.6 46.7 1.0 CG x:PRO30 4.6 40.6 1.0 SG x:CYS29 4.6 43.2 1.0 SG x:CYS61 4.7 46.7 1.0 SG x:CYS55 4.7 104.1 1.0 CB x:ILE60 4.8 41.8 1.0 CA x:GLY57 4.8 52.6 1.0 C x:GLY59 4.8 51.3 1.0 CG1 x:ILE56 4.9 51.1 1.0 CA x:ILE60 4.9 41.8 1.0 CB x:CYS61 5.0 46.7 1.0

K.Ikeuchi, N.Ivic, R.Buschauer, J.Cheng, T.Frohlich, Y.Matsuo, O.Berninghausen, T.Inada, T.Becker, R.Beckmann. Molecular Basis For Recognition and Deubiquitination of 40S Ribosomes By OTU2. Nat Commun V. 14 2730 2023.
ISSN: ESSN 2041-1723
PubMed: 37169754
DOI: 10.1038/S41467-023-38161-W