Iron in PDB 8cas: Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)

Enzymatic activity of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)

All present enzymatic activity of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial):
3.6.5.3;

Other elements in 8cas:

The structure of Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial) also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms
Zinc (Zn) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial) (pdb code 8cas). 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 48S Initiation Complex (Partial), PDB code: 8cas:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 8cas

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Iron binding site 1 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Fe705

b:72.7
occ:1.00
 FE1 k:SF4705 0.0 72.7 1.0
S3 k:SF4705 2.3 72.7 1.0
S4 k:SF4705 2.3 72.7 1.0
S2 k:SF4705 2.3 72.7 1.0
FE4 k:SF4705 2.7 72.7 1.0
FE2 k:SF4705 2.7 72.7 1.0
FE3 k:SF4705 2.7 72.7 1.0
CB k:CYS29 3.5 34.9 1.0
S1 k:SF4705 3.9 72.7 1.0
CA k:CYS29 3.9 34.9 1.0
CB k:CYS61 4.1 60.5 1.0
C k:CYS29 4.7 34.9 1.0
N k:PRO30 4.8 39.6 1.0
N k:CYS61 4.8 60.5 1.0

Iron binding site 2 out of 8 in 8cas

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Iron binding site 2 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Fe705

b:72.7
occ:1.00
 FE2 k:SF4705 0.0 72.7 1.0
S1 k:SF4705 2.3 72.7 1.0
S3 k:SF4705 2.3 72.7 1.0
S4 k:SF4705 2.3 72.7 1.0
FE4 k:SF4705 2.7 72.7 1.0
FE3 k:SF4705 2.7 72.7 1.0
FE1 k:SF4705 2.7 72.7 1.0
CB k:CYS55 3.2 42.8 1.0
CA k:CYS55 3.5 42.8 1.0
CB k:ALA9 3.8 68.1 1.0
S2 k:SF4705 3.9 72.7 1.0
N k:ILE56 4.3 72.4 1.0
C k:CYS55 4.4 42.8 1.0
N k:CYS55 4.5 42.8 1.0
N k:ALA9 4.9 68.1 1.0
CA k:ALA9 5.0 68.1 1.0
CB k:CYS38 5.0 79.6 1.0

Iron binding site 3 out of 8 in 8cas

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Iron binding site 3 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Fe705

b:72.7
occ:1.00
 FE3 k:SF4705 0.0 72.7 1.0
S1 k:SF4705 2.3 72.7 1.0
S4 k:SF4705 2.3 72.7 1.0
S2 k:SF4705 2.3 72.7 1.0
FE4 k:SF4705 2.7 72.7 1.0
FE2 k:SF4705 2.7 72.7 1.0
FE1 k:SF4705 2.7 72.7 1.0
CB k:CYS61 3.5 60.5 1.0
CB k:ALA9 3.8 68.1 1.0
S3 k:SF4705 3.9 72.7 1.0
N k:CYS61 4.0 60.5 1.0
CA k:GLY59 4.1 69.9 1.0
N k:GLY59 4.2 69.9 1.0
CA k:CYS61 4.4 60.5 1.0
N k:ILE60 4.4 57.3 1.0
C k:GLY59 4.5 69.9 1.0

Iron binding site 4 out of 8 in 8cas

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Iron binding site 4 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Fe705

b:72.7
occ:1.00
 FE4 k:SF4705 0.0 72.7 1.0
S1 k:SF4705 2.3 72.7 1.0
S3 k:SF4705 2.3 72.7 1.0
S2 k:SF4705 2.3 72.7 1.0
FE1 k:SF4705 2.7 72.7 1.0
FE2 k:SF4705 2.7 72.7 1.0
FE3 k:SF4705 2.7 72.7 1.0
N k:GLY59 3.6 69.9 1.0
N k:CYS58 3.8 77.2 1.0
S4 k:SF4705 3.9 72.7 1.0
CB k:CYS58 3.9 77.2 1.0
N k:ILE56 4.1 72.4 1.0
CA k:CYS58 4.2 77.2 1.0
N k:GLY57 4.3 83.9 1.0
C k:CYS58 4.4 77.2 1.0
CA k:GLY59 4.5 69.9 1.0
N k:ILE60 4.6 57.3 1.0
C k:GLY57 4.7 83.9 1.0
CA k:CYS55 4.8 42.8 1.0
C k:ILE56 4.8 72.4 1.0
CA k:ILE56 4.8 72.4 1.0
CA k:GLY57 4.9 83.9 1.0
C k:CYS55 4.9 42.8 1.0
CB k:CYS55 5.0 42.8 1.0

Iron binding site 5 out of 8 in 8cas

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Iron binding site 5 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Fe706

b:72.7
occ:1.00
 FE1 k:SF4706 0.0 72.7 1.0
S2 k:SF4706 2.3 72.7 1.0
S4 k:SF4706 2.3 72.7 1.0
S3 k:SF4706 2.3 72.7 1.0
FE3 k:SF4706 2.7 72.7 1.0
FE4 k:SF4706 2.7 72.7 1.0
FE2 k:SF4706 2.7 72.7 1.0
CB k:ALA48 3.3 23.7 1.0
S1 k:SF4706 3.9 72.7 1.0
CB k:CYS16 4.2 57.6 1.0
CB k:PRO18 4.2 52.0 1.0
N k:ALA48 4.2 23.7 1.0
CA k:ALA48 4.3 23.7 1.0
O k:CYS16 4.4 57.6 1.0
CA k:CYS16 4.4 57.6 1.0
C k:CYS16 4.4 57.6 1.0
CA k:PRO18 4.7 52.0 1.0
N k:PRO18 4.7 52.0 1.0

Iron binding site 6 out of 8 in 8cas

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Iron binding site 6 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Fe706

b:72.7
occ:1.00
 FE2 k:SF4706 0.0 72.7 1.0
S1 k:SF4706 2.3 72.7 1.0
S4 k:SF4706 2.3 72.7 1.0
S3 k:SF4706 2.3 72.7 1.0
FE3 k:SF4706 2.7 72.7 1.0
FE4 k:SF4706 2.7 72.7 1.0
FE1 k:SF4706 2.7 72.7 1.0
CA k:GLN23 3.8 39.5 1.0
CB k:CYS21 3.8 35.6 1.0
S2 k:SF4706 3.9 72.7 1.0
CA k:PRO18 3.9 52.0 1.0
N k:GLN23 4.0 39.5 1.0
CB k:PRO18 4.0 52.0 1.0
O k:LYS17 4.4 52.0 1.0
N k:PRO18 4.6 52.0 1.0
N k:GLU24 4.6 34.9 1.0
CB k:GLN23 4.6 39.5 1.0
C k:GLN23 4.7 39.5 1.0
C k:CYS21 4.8 35.6 1.0
O k:CYS21 4.8 35.6 1.0
CA k:CYS21 4.8 35.6 1.0
C k:LYS17 4.8 52.0 1.0

Iron binding site 7 out of 8 in 8cas

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Iron binding site 7 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Fe706

b:72.7
occ:1.00
 FE3 k:SF4706 0.0 72.7 1.0
S4 k:SF4706 2.3 72.7 1.0
S2 k:SF4706 2.3 72.7 1.0
S1 k:SF4706 2.3 72.7 1.0
FE4 k:SF4706 2.7 72.7 1.0
FE2 k:SF4706 2.7 72.7 1.0
FE1 k:SF4706 2.7 72.7 1.0
CB k:CYS25 3.3 29.5 1.0
N k:CYS25 3.8 29.5 1.0
S3 k:SF4706 3.9 72.7 1.0
CA k:CYS25 4.2 29.5 1.0
N k:GLU24 4.4 34.9 1.0
CA k:GLN23 4.4 39.5 1.0
CB k:ALA48 4.5 23.7 1.0
C k:GLN23 4.6 39.5 1.0
C k:GLU24 4.9 34.9 1.0

Iron binding site 8 out of 8 in 8cas

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Iron binding site 8 out of 8 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
k:Fe706

b:72.7
occ:1.00
 FE4 k:SF4706 0.0 72.7 1.0
S1 k:SF4706 2.3 72.7 1.0
S2 k:SF4706 2.3 72.7 1.0
S3 k:SF4706 2.3 72.7 1.0
FE3 k:SF4706 2.7 72.7 1.0
FE1 k:SF4706 2.7 72.7 1.0
FE2 k:SF4706 2.7 72.7 1.0
S4 k:SF4706 3.9 72.7 1.0
O k:PHE67 4.2 53.0 1.0
CB k:CYS65 4.7 65.0 1.0
CB k:CYS21 4.7 35.6 1.0
CB k:PHE67 4.9 53.0 1.0
CA k:CYS16 4.9 57.6 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: Thu Jul 27 16:05:17 2023

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