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

Other elements in 8cah:

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

Iron Binding Sites:

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 8cah

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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 8cah

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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 8cah

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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 8cah

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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 8cah

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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 8cah

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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 8cah

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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 8cah

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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

Reference:

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
Page generated: Fri Aug 9 21:14:45 2024

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