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Zinc in PDB 7yui: Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin

Enzymatic activity of Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin

All present enzymatic activity of Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin:
2.3.2.31;

Protein crystallography data

The structure of Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin, PDB code: 7yui was solved by L.X.Xiao, L.F.Pan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.59 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 58.5, 90.304, 117.439, 90, 90, 90
R / Rfree (%) 20.3 / 25.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin (pdb code 7yui). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin, PDB code: 7yui:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 7yui

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Zinc binding site 1 out of 5 in the Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:48.9
occ:1.00
 SG B:CYS371 2.3 50.5 1.0
SG B:CYS376 2.4 48.5 1.0
SG B:CYS391 2.4 47.3 1.0
SG B:CYS394 2.4 60.6 1.0
CB B:CYS394 2.9 35.0 1.0
CB B:CYS371 3.2 44.6 1.0
CB B:CYS391 3.2 46.0 1.0
N B:CYS394 3.3 46.8 1.0
CB B:CYS376 3.5 45.6 1.0
CA B:CYS394 3.7 40.2 1.0
OG1 B:THR373 4.0 38.4 1.0
CB B:THR373 4.1 39.1 1.0
CB B:VAL393 4.2 51.0 1.0
C B:VAL393 4.5 48.3 1.0
CA B:CYS371 4.7 41.6 1.0
C B:CYS394 4.7 49.7 1.0
CA B:CYS391 4.7 49.8 1.0
CA B:VAL393 4.7 51.0 1.0
N B:PHE395 4.8 52.1 1.0
N B:VAL393 4.8 49.5 1.0
N B:GLY378 4.8 48.1 1.0
CG1 B:VAL393 4.8 47.1 1.0
CA B:GLY378 4.9 44.8 1.0
CA B:CYS376 4.9 38.8 1.0
CG2 B:THR373 4.9 32.0 1.0

Zinc binding site 2 out of 5 in 7yui

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Zinc binding site 2 out of 5 in the Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:41.7
occ:1.00
 SG B:CYS202 2.3 43.5 1.0
SG B:CYS199 2.3 39.7 1.0
SG B:CYS216 2.3 38.5 1.0
SG B:CYS213 2.4 38.3 1.0
CB B:CYS199 3.1 38.3 1.0
CB B:CYS202 3.2 28.1 1.0
CB B:CYS213 3.2 36.5 1.0
CB B:CYS216 3.3 27.7 1.0
N B:CYS216 3.8 34.0 1.0
N B:CYS202 3.8 41.1 1.0
CA B:CYS202 4.0 28.7 1.0
CA B:CYS216 4.1 35.8 1.0
CA B:CYS199 4.5 41.0 1.0
CB B:ARG218 4.6 40.2 1.0
CA B:CYS213 4.7 39.3 1.0
CB B:MET215 4.7 41.8 1.0
C B:CYS216 4.7 40.0 1.0
C B:CYS202 4.7 35.4 1.0
C B:GLY201 4.8 43.8 1.0
CB B:PHE204 4.8 32.0 1.0
C B:MET215 4.9 40.4 1.0
N B:ARG218 4.9 43.9 1.0
N B:THR203 5.0 35.4 1.0
N B:PHE204 5.0 24.1 1.0
ND2 B:ASN206 5.0 32.8 1.0
N B:CYS217 5.0 26.8 1.0

Zinc binding site 3 out of 5 in 7yui

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Zinc binding site 3 out of 5 in the Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:52.0
occ:1.00
 NE2 B:HIS406 2.1 66.3 1.0
SG B:CYS399 2.4 43.8 1.0
SG B:CYS411 2.4 52.7 1.0
SG B:CYS402 2.4 47.3 1.0
CE1 B:HIS406 3.1 64.9 1.0
CD2 B:HIS406 3.1 61.6 1.0
CB B:CYS411 3.1 38.3 1.0
CB B:CYS402 3.1 34.9 1.0
CB B:CYS399 3.4 46.4 1.0
CA B:CYS411 3.4 45.5 1.0
N B:CYS402 3.6 44.2 1.0
CA B:CYS402 4.0 54.3 1.0
ND1 B:HIS406 4.2 59.5 1.0
CG B:HIS406 4.2 64.1 1.0
N B:CYS411 4.2 48.2 1.0
CB B:LEU401 4.4 45.5 1.0
C B:CYS411 4.6 49.2 1.0
C B:LEU401 4.7 41.1 1.0
O B:CYS411 4.8 51.2 1.0
CA B:CYS399 4.8 39.8 1.0
C B:ASN410 5.0 52.4 1.0
CA B:LEU401 5.0 44.3 1.0

Zinc binding site 4 out of 5 in 7yui

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Zinc binding site 4 out of 5 in the Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:61.0
occ:1.00
 SG B:CYS285 2.2 81.6 1.0
SG B:CYS282 2.5 58.9 1.0
CB B:CYS305 2.8 47.4 1.0
CB B:CYS285 2.9 50.2 1.0
SG B:CYS308 2.9 48.7 1.0
CB B:CYS308 3.2 32.6 1.0
SG B:CYS305 3.3 91.7 1.0
CB B:CYS282 3.4 54.0 1.0
N B:CYS285 3.5 76.2 1.0
CA B:CYS285 3.7 65.2 1.0
N B:CYS305 3.7 52.6 1.0
CA B:CYS305 3.9 55.5 1.0
N B:CYS308 4.1 40.9 1.0
CA B:CYS308 4.3 39.9 1.0
C B:VAL284 4.5 48.9 1.0
O B:HOH632 4.6 49.2 1.0
CB B:VAL284 4.7 42.1 1.0
C B:CYS305 4.8 46.0 1.0
CA B:CYS282 4.9 53.2 1.0
C B:PHE304 4.9 48.0 1.0

Zinc binding site 5 out of 5 in 7yui

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Zinc binding site 5 out of 5 in the Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Hoil-1L(195-423) in Complex with the Linear Tetra-Ubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:53.0
occ:1.00
 SG B:CYS300 2.1 100.2 1.0
SG B:CYS323 2.2 63.9 1.0
SG B:CYS332 2.6 51.5 1.0
CB B:CYS323 2.6 49.1 1.0
CB B:CYS300 2.8 29.9 1.0
ND1 B:HIS302 3.1 46.6 1.0
CB B:CYS332 3.2 39.8 1.0
CB B:HIS302 3.8 32.9 1.0
CG B:HIS302 3.9 56.1 1.0
CA B:CYS323 4.1 54.7 1.0
CE1 B:HIS302 4.1 54.3 1.0
CB B:PHE325 4.1 50.7 1.0
CA B:CYS300 4.2 41.8 1.0
CD1 B:LEU297 4.5 27.9 1.0
C B:CYS323 4.5 50.9 1.0
O B:CYS323 4.7 50.1 1.0
CA B:CYS332 4.7 48.6 1.0
CE2 B:PHE304 4.8 45.6 1.0
N B:CYS323 4.8 51.5 1.0
N B:HIS302 4.9 40.6 1.0
C B:CYS300 4.9 46.1 1.0
N B:PHE325 4.9 40.2 1.0
CA B:HIS302 5.0 43.0 1.0
CG B:PHE325 5.0 46.1 1.0

Reference:

L.X.Xiao, L.F.Pan. Mechanistic Insights Into the Enzymatic Activity of E3 Ligase Hoil-1L and Its Regulation By the Linear Ubiquitin Chain-Binding To Be Published.
Page generated: Fri Aug 22 07:16:34 2025

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