Zinc in PDB 7t92: Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex (pdb code 7t92). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex, PDB code: 7t92:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7t92

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Zinc binding site 1 out of 5 in the Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:65.3
occ:0.80
HB2 B:CYS432 2.2 43.1 1.0
SG B:CYS415 2.3 48.8 1.0
SG B:CYS412 2.3 45.4 1.0
SG B:CYS432 2.3 43.1 1.0
SG B:CYS435 2.3 45.2 1.0
HB3 B:CYS412 2.7 45.4 1.0
CB B:CYS432 2.7 43.1 1.0
CB B:CYS412 2.9 45.4 1.0
HB2 B:CYS412 3.0 45.4 1.0
HB3 B:CYS415 3.1 48.8 1.0
H B:CYS432 3.2 43.1 1.0
HB2 B:CYS435 3.2 45.2 1.0
H B:CYS415 3.2 48.8 1.0
HB3 B:CYS432 3.3 43.1 1.0
CB B:CYS435 3.3 45.2 1.0
CB B:CYS415 3.4 48.8 1.0
HB3 B:CYS435 3.6 45.2 1.0
N B:CYS432 3.9 43.1 1.0
CA B:CYS432 3.9 43.1 1.0
HB B:ILE414 4.0 46.2 1.0
N B:CYS415 4.0 48.8 1.0
HB2 B:CYS415 4.1 48.8 1.0
CA B:CYS415 4.3 48.8 1.0
CA B:CYS412 4.4 45.4 1.0
H B:CYS435 4.5 45.2 1.0
HA B:CYS432 4.5 43.1 1.0
H B:GLY417 4.6 48.6 1.0
HB3 B:TYR431 4.7 40.1 1.0
HA B:ILE419 4.7 42.6 1.0
CA B:CYS435 4.7 45.2 1.0
HG22 B:ILE414 4.8 46.2 1.0
HA B:CYS412 4.8 45.4 1.0
H B:CYS412 4.8 45.4 1.0
C B:CYS432 4.9 43.1 1.0
C B:CYS412 4.9 45.4 1.0
CB B:ILE414 4.9 46.2 1.0
O B:CYS412 4.9 45.4 1.0
H B:ILE414 4.9 46.2 1.0
O B:CYS432 5.0 43.1 1.0
H B:GLU416 5.0 50.7 1.0

Zinc binding site 2 out of 5 in 7t92

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Zinc binding site 2 out of 5 in the Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:60.8
occ:1.00
SG A:CYS337 2.3 52.8 1.0
HB3 A:CYS311 2.3 45.5 1.0
SG A:CYS334 2.3 43.4 1.0
SG A:CYS313 2.3 42.4 1.0
SG A:CYS311 2.3 45.5 1.0
CB A:CYS311 2.8 45.5 1.0
HB2 A:CYS334 3.0 43.4 1.0
CB A:CYS334 3.1 43.4 1.0
HB3 A:CYS334 3.1 43.4 1.0
H A:CYS337 3.1 52.8 1.0
HB2 A:CYS311 3.3 45.5 1.0
HB2 A:CYS313 3.5 42.4 1.0
CB A:CYS313 3.6 42.4 1.0
HH A:TYR315 3.7 36.3 1.0
HB2 A:ARG336 3.7 46.3 1.0
CB A:CYS337 3.8 52.8 1.0
N A:CYS337 3.8 52.8 1.0
H A:CYS313 3.9 42.4 1.0
HD11 A:ILE341 3.9 42.1 1.0
HB3 A:CYS337 3.9 52.8 1.0
HB3 A:GLU339 4.0 48.9 1.0
HA A:CYS311 4.1 45.5 1.0
CA A:CYS311 4.1 45.5 1.0
H A:GLU339 4.1 48.9 1.0
H A:ARG336 4.1 46.3 1.0
HB3 A:CYS313 4.2 42.4 1.0
CA A:CYS337 4.3 52.8 1.0
OH A:TYR315 4.3 36.3 1.0
H A:GLY338 4.4 50.4 1.0
HB2 A:CYS337 4.5 52.8 1.0
CA A:CYS334 4.6 43.4 1.0
N A:CYS313 4.6 42.4 1.0
CB A:ARG336 4.6 46.3 1.0
HD12 A:ILE341 4.7 42.1 1.0
CD1 A:ILE341 4.7 42.1 1.0
N A:GLY338 4.7 50.4 1.0
C A:CYS337 4.7 52.8 1.0
C A:ARG336 4.7 46.3 1.0
CA A:CYS313 4.8 42.4 1.0
HB3 A:ALA308 4.8 39.8 1.0
HB2 A:GLU339 4.8 48.9 1.0
C A:CYS311 4.8 45.5 1.0
N A:GLU339 4.8 48.9 1.0
CB A:GLU339 4.8 48.9 1.0
N A:ARG336 4.8 46.3 1.0
HA A:CYS334 4.9 43.4 1.0
HB3 A:ARG336 4.9 46.3 1.0
CA A:ARG336 5.0 46.3 1.0
HG12 A:ILE341 5.0 42.1 1.0

Zinc binding site 3 out of 5 in 7t92

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Zinc binding site 3 out of 5 in the Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:50.0
occ:1.00
SG A:CYS273 2.3 40.1 1.0
SG A:CYS316 2.3 31.5 1.0
SG A:CYS270 2.3 37.2 1.0
SG A:CYS319 2.3 32.8 1.0
HB3 A:CYS270 2.9 37.2 1.0
HB2 A:CYS316 2.9 31.5 1.0
CB A:CYS270 3.1 37.2 1.0
H A:CYS316 3.1 31.5 1.0
HB2 A:CYS270 3.2 37.2 1.0
CB A:CYS316 3.2 31.5 1.0
H A:CYS273 3.3 40.1 1.0
HB2 A:CYS319 3.4 32.8 1.0
CB A:CYS319 3.5 32.8 1.0
CB A:CYS273 3.7 40.1 1.0
HB A:ILE272 3.7 37.6 1.0
HB2 A:CYS273 3.8 40.1 1.0
HB3 A:CYS319 3.8 32.8 1.0
N A:CYS316 3.9 31.5 1.0
HG3 C:GLN446 3.9 29.4 1.0
N A:CYS273 3.9 40.1 1.0
HB3 A:CYS316 4.0 31.5 1.0
HB2 C:GLN446 4.0 29.4 1.0
CA A:CYS316 4.2 31.5 1.0
HB3 A:TYR315 4.3 36.3 1.0
CA A:CYS273 4.3 40.1 1.0
H A:CYS319 4.4 32.8 1.0
HE1 C:HIS447 4.4 29.5 1.0
HB3 A:CYS273 4.5 40.1 1.0
HA A:CYS273 4.5 40.1 1.0
CA A:CYS270 4.5 37.2 1.0
HG22 A:ILE272 4.6 37.6 1.0
HA A:ILE302 4.6 34.7 1.0
CG C:GLN446 4.6 29.4 1.0
CB A:ILE272 4.7 37.6 1.0
CB C:GLN446 4.7 29.4 1.0
H A:ILE272 4.8 37.6 1.0
HB3 C:GLN446 4.8 29.4 1.0
CA A:CYS319 4.8 32.8 1.0
HA A:CYS316 4.8 31.5 1.0
HD12 A:ILE272 4.9 37.6 1.0
C A:ILE272 4.9 37.6 1.0
HA A:CYS270 4.9 37.2 1.0
HG12 A:ILE302 4.9 34.7 1.0
O A:ASP301 5.0 38.4 1.0
N A:CYS319 5.0 32.8 1.0

Zinc binding site 4 out of 5 in 7t92

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Zinc binding site 4 out of 5 in the Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:43.9
occ:1.00
ND1 C:HIS419 2.1 26.8 1.0
SG C:CYS436 2.3 28.1 1.0
SG C:CYS417 2.3 28.8 1.0
SG C:CYS439 2.3 27.6 1.0
HE1 C:HIS419 2.7 26.8 1.0
CE1 C:HIS419 2.7 26.8 1.0
HB3 C:CYS436 3.0 28.1 1.0
CB C:CYS436 3.1 28.1 1.0
HB2 C:CYS436 3.1 28.1 1.0
H C:CYS439 3.1 27.6 1.0
HB2 C:CYS417 3.2 28.8 1.0
CG C:HIS419 3.3 26.8 1.0
HB2 C:HIS419 3.3 26.8 1.0
CB C:CYS417 3.4 28.8 1.0
CB C:CYS439 3.7 27.6 1.0
HB3 C:CYS439 3.7 27.6 1.0
HB3 C:CYS417 3.7 28.8 1.0
HB2 C:LEU438 3.8 26.6 1.0
CB C:HIS419 3.8 26.8 1.0
N C:CYS439 3.9 27.6 1.0
HB2 C:ARG441 4.0 30.3 1.0
NE2 C:HIS419 4.0 26.8 1.0
H C:HIS419 4.0 26.8 1.0
CD2 C:HIS419 4.2 26.8 1.0
H C:LEU438 4.3 26.6 1.0
HB C:THR415 4.3 26.2 1.0
H C:ARG441 4.3 30.3 1.0
CA C:CYS439 4.3 27.6 1.0
HB2 C:CYS439 4.4 27.6 1.0
HB3 C:HIS419 4.4 26.8 1.0
CA C:CYS436 4.5 28.1 1.0
HZ C:PHE421 4.5 25.3 1.0
CA C:CYS417 4.6 28.8 1.0
HE2 C:HIS419 4.7 26.8 1.0
N C:HIS419 4.7 26.8 1.0
CB C:LEU438 4.7 26.6 1.0
H C:CYS417 4.7 28.8 1.0
H C:ARG440 4.8 28.6 1.0
HE1 C:PHE421 4.9 25.3 1.0
HA C:CYS436 4.9 28.1 1.0
C C:CYS417 4.9 28.8 1.0
HG21 C:THR415 4.9 26.2 1.0
CA C:HIS419 4.9 26.8 1.0
CB C:ARG441 4.9 30.3 1.0
C C:CYS439 5.0 27.6 1.0
HG1 C:THR415 5.0 26.2 1.0
C C:LEU438 5.0 26.6 1.0

Zinc binding site 5 out of 5 in 7t92

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Zinc binding site 5 out of 5 in the Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the Peroxisomal Retro-Translocon Formed By A Heterotrimeric Ubiquitin Ligase Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:45.9
occ:1.00
SG C:CYS402 2.3 29.4 1.0
SG C:CYS405 2.3 31.0 1.0
SG C:CYS425 2.3 27.9 1.0
SG C:CYS422 2.3 26.8 1.0
HB3 C:CYS405 2.9 31.0 1.0
HB2 C:CYS422 2.9 26.8 1.0
H C:CYS405 3.2 31.0 1.0
CB C:CYS405 3.2 31.0 1.0
CB C:CYS422 3.2 26.8 1.0
HB2 C:CYS425 3.5 27.9 1.0
HB3 C:CYS402 3.6 29.4 1.0
CB C:CYS425 3.6 27.9 1.0
H C:CYS422 3.6 26.8 1.0
CB C:CYS402 3.6 29.4 1.0
HB3 C:CYS422 3.8 26.8 1.0
N C:CYS405 3.9 31.0 1.0
HB3 C:CYS425 3.9 27.9 1.0
HB2 C:CYS405 3.9 31.0 1.0
HB2 C:CYS402 4.0 29.4 1.0
CA C:CYS405 4.1 31.0 1.0
HB2 C:LEU404 4.1 28.6 1.0
N C:CYS422 4.3 26.8 1.0
CA C:CYS422 4.4 26.8 1.0
HZ2 C:LYS410 4.5 33.0 1.0
H C:GLU407 4.5 35.0 1.0
H C:CYS425 4.5 27.9 1.0
H C:CYS402 4.6 29.4 1.0
H C:LEU406 4.7 31.5 1.0
HD12 C:LEU409 4.7 30.7 1.0
C C:CYS405 4.8 31.0 1.0
HA C:LEU409 4.8 30.7 1.0
HB2 C:GLU407 4.8 35.0 1.0
HZ3 C:LYS410 4.8 33.0 1.0
H C:LYS410 4.8 33.0 1.0
HG2 C:LYS410 4.8 33.0 1.0
CA C:CYS402 4.9 29.4 1.0
H C:LEU404 4.9 28.6 1.0
CA C:CYS425 4.9 27.9 1.0
HA C:CYS405 4.9 31.0 1.0
N C:LEU406 5.0 31.5 1.0
HA C:CYS422 5.0 26.8 1.0

Reference:

P.Feng, X.Wu, S.K.Erramilli, J.A.Paulo, P.Knejski, S.P.Gygi, A.A.Kossiakoff, T.A.Rapoport. A Peroxisomal Ubiquitin Ligase Complex Forms A Retrotranslocation Channel. Nature V. 607 374 2022.
ISSN: ESSN 1476-4687
PubMed: 35768507
DOI: 10.1038/S41586-022-04903-X
Page generated: Sat Apr 8 03:26:30 2023

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