Zinc 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
Iron (Fe) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc where determined in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial), PDB code: 8cas:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 8cas

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Zinc binding site 1 out of 4 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn101

b:15.0
occ:1.00
CB N:CYS24 2.4 19.6 1.0
CB N:CYS42 2.8 18.3 1.0
CB N:CYS39 2.9 15.4 1.0
CB N:CYS21 3.4 17.4 1.0
CA N:CYS24 3.6 19.6 1.0
N N:CYS24 3.7 19.6 1.0
N N:CYS39 3.9 15.4 1.0
CA N:CYS39 4.0 15.4 1.0
CA N:CYS42 4.0 18.3 1.0
N N:CYS42 4.1 18.3 1.0
C N:VAL23 4.4 17.6 1.0
C N:CYS24 4.7 19.6 1.0
CB N:VAL23 4.7 17.6 1.0
O2' 2:G1433 4.7 65.3 1.0
C N:CYS39 4.8 15.4 1.0
CA N:CYS21 4.8 17.4 1.0
CA N:VAL23 4.9 17.6 1.0
O N:VAL23 5.0 17.6 1.0
N N:VAL23 5.0 17.6 1.0

Zinc binding site 2 out of 4 in 8cas

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Zinc binding site 2 out of 4 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn201

b:212.7
occ:1.00
N O:CYS126 2.2 233.1 1.0
CB O:CYS126 2.6 233.1 1.0
CB O:ASN123 2.6 208.5 1.0
CA O:CYS126 2.8 233.1 1.0
C O:THR125 3.1 213.1 1.0
O O:ASN123 3.3 208.5 1.0
C O:ASN123 3.5 208.5 1.0
CA O:ASN123 3.5 208.5 1.0
N O:THR125 3.5 213.1 1.0
CB O:LYS143 3.6 119.8 1.0
CA O:THR125 3.6 213.1 1.0
CB O:THR125 3.7 213.1 1.0
O O:THR125 4.0 213.1 1.0
N O:ASN123 4.1 208.5 1.0
C O:CYS126 4.2 233.1 1.0
N O:CYS144 4.2 103.6 1.0
N O:PRO124 4.3 222.4 1.0
C O:PRO124 4.4 222.4 1.0
C O:LYS143 4.4 119.8 1.0
CA O:LYS143 4.6 119.8 1.0
O O:CYS126 4.6 233.1 1.0
CB O:CYS121 4.7 155.4 1.0
CB O:CYS144 4.9 103.6 1.0
CA O:PRO124 4.9 222.4 1.0
O O:LYS143 5.0 119.8 1.0

Zinc binding site 3 out of 4 in 8cas

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Zinc binding site 3 out of 4 in the Cryo-Em Structure of Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial)


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 Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
m:Zn501

b:275.7
occ:1.00
N m:GLY100 2.3 235.0 1.0
N m:SER101 2.3 220.5 1.0
CA m:GLY100 2.8 235.0 1.0
C m:GLY100 2.9 235.0 1.0
C m:CYS99 3.1 228.3 1.0
CB m:CYS99 3.3 228.3 1.0
CA m:SER101 3.4 220.5 1.0
CB m:SER101 3.4 220.5 1.0
CB m:THR128 3.5 191.9 1.0
CA m:CYS99 3.6 228.3 1.0
O m:CYS99 4.0 228.3 1.0
O m:GLY100 4.1 235.0 1.0
CA m:THR128 4.4 191.9 1.0
C m:SER101 4.5 220.5 1.0
N m:CYS102 4.7 224.7 1.0

Zinc binding site 4 out of 4 in 8cas

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


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 Native OTU2-Bound Ubiquitinated 48S Initiation Complex (Partial) within 5.0Å range:
probe atom residue distance (Å) B Occ
s:Zn301

b:147.4
occ:1.00
O s:SER264 2.3 192.0 1.0
N s:ARG266 2.4 125.5 1.0
CE s:MET257 2.6 130.3 1.0
C s:SER264 2.9 192.0 1.0
CA s:THR265 2.9 155.4 1.0
C s:THR265 3.0 155.4 1.0
O s:MET257 3.0 130.3 1.0
N s:THR265 3.2 155.4 1.0
CA s:ARG266 3.4 125.5 1.0
CB s:ARG266 3.4 125.5 1.0
SD s:MET257 3.6 130.3 1.0
CG s:ARG266 3.6 125.5 1.0
C s:MET257 3.9 130.3 1.0
O s:THR265 4.1 155.4 1.0
O s:ARG266 4.1 125.5 1.0
C s:ARG266 4.2 125.5 1.0
CA s:VAL258 4.2 163.1 1.0
CA s:SER264 4.2 192.0 1.0
CB s:SER264 4.3 192.0 1.0
OG s:SER264 4.3 192.0 1.0
CB s:THR265 4.4 155.4 1.0
N s:VAL258 4.4 163.1 1.0
N s:CYS259 4.7 200.8 1.0
CD s:ARG266 4.8 125.5 1.0
NE s:ARG266 4.8 125.5 1.0
C s:VAL258 4.8 163.1 1.0
CG s:MET257 5.0 130.3 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 Jul 28 06:34:37 2023

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