Zinc in PDB 8bvl: Crystal Structure of the Ibr-RING2 Domain of Hoil-1

Enzymatic activity of Crystal Structure of the Ibr-RING2 Domain of Hoil-1

All present enzymatic activity of Crystal Structure of the Ibr-RING2 Domain of Hoil-1:
2.3.2.31;

Protein crystallography data

The structure of Crystal Structure of the Ibr-RING2 Domain of Hoil-1, PDB code: 8bvl was solved by B.Stieglitz, M.G.Koliopoulos, K.Rittinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.16 / 2.24
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.908, 59.263, 57.206, 90, 90.31, 90
R / Rfree (%) 23.4 / 29.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1 (pdb code 8bvl). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1, PDB code: 8bvl:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 8bvl

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Zinc binding site 1 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


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 the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:27.8
occ:1.00
 SG A:CYS376 2.3 29.2 1.0
SG A:CYS394 2.3 31.5 1.0
SG A:CYS371 2.4 30.0 1.0
SG A:CYS391 2.4 22.2 1.0
CB A:CYS391 3.0 27.9 1.0
CB A:CYS371 3.3 27.1 1.0
CB A:CYS376 3.4 26.7 1.0
CB A:CYS394 3.4 29.3 1.0
N A:CYS394 3.8 29.3 1.0
OG1 A:THR373 4.0 34.7 1.0
CB A:THR373 4.0 28.6 1.0
CA A:CYS394 4.2 30.4 1.0
CB A:VAL393 4.4 28.0 1.0
CA A:CYS391 4.5 24.4 1.0
CA A:GLY378 4.5 29.5 1.0
N A:GLY378 4.6 34.9 1.0
CA A:CYS371 4.7 31.3 1.0
CA A:CYS376 4.8 33.8 1.0
CG2 A:THR373 4.8 25.3 1.0
C A:CYS394 4.9 26.8 1.0
C A:VAL393 4.9 31.5 1.0
N A:THR373 5.0 24.7 1.0
N A:PHE395 5.0 33.4 1.0
N A:VAL393 5.0 30.0 1.0
CA A:VAL393 5.0 30.1 1.0

Zinc binding site 2 out of 10 in 8bvl

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Zinc binding site 2 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


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 the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:29.8
occ:1.00
 SG A:CYS465 2.3 26.8 1.0
SG A:CYS450 2.3 27.5 1.0
SG A:CYS447 2.4 29.3 1.0
SG A:CYS468 2.4 28.9 1.0
CB A:CYS465 3.1 28.7 1.0
CB A:CYS447 3.2 27.7 1.0
CB A:CYS450 3.2 27.2 1.0
CB A:CYS468 3.5 22.1 1.0
N A:CYS450 3.7 30.4 1.0
N A:CYS468 3.7 23.3 1.0
CA A:CYS450 4.0 29.4 1.0
CA A:CYS468 4.2 30.8 1.0
CB A:VAL467 4.5 33.2 1.0
CG1 A:ILE452 4.5 31.6 1.0
CA A:CYS465 4.6 32.9 1.0
CB A:GLN449 4.6 26.3 1.0
CA A:CYS447 4.7 29.6 1.0
C A:CYS450 4.7 26.8 1.0
C A:VAL467 4.8 28.3 1.0
N A:GLN451 4.8 26.1 1.0
C A:GLN449 4.8 28.5 1.0
N A:VAL467 4.9 31.6 1.0
C A:CYS468 4.9 27.4 1.0
CG A:GLN449 4.9 27.5 1.0
CG1 A:VAL467 4.9 23.1 1.0
CB A:THR470 5.0 28.3 1.0
CA A:VAL467 5.0 28.7 1.0
N A:HIS469 5.0 27.8 1.0

Zinc binding site 3 out of 10 in 8bvl

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Zinc binding site 3 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


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 the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:33.4
occ:1.00
 NE2 A:HIS406 2.2 35.1 1.0
SG A:CYS402 2.3 31.2 1.0
SG A:CYS411 2.4 32.3 1.0
SG A:CYS399 2.4 25.4 1.0
CB A:CYS411 3.1 23.7 1.0
CB A:CYS402 3.2 31.8 1.0
CE1 A:HIS406 3.2 34.8 1.0
CD2 A:HIS406 3.2 34.1 1.0
CB A:CYS399 3.3 32.7 1.0
CA A:CYS411 3.6 26.9 1.0
N A:CYS402 3.9 30.6 1.0
CA A:CYS402 4.2 29.9 1.0
ND1 A:HIS406 4.3 37.7 1.0
N A:CYS411 4.3 30.6 1.0
CG A:HIS406 4.4 40.1 1.0
CA A:CYS399 4.8 28.7 1.0
OG1 A:THR466 4.9 31.3 1.0
C A:CYS411 4.9 35.6 1.0
C A:LEU401 4.9 28.8 1.0

Zinc binding site 4 out of 10 in 8bvl

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Zinc binding site 4 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


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 the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:24.7
occ:1.00
 SG A:CYS473 2.3 25.5 1.0
SG A:CYS509 2.4 22.7 1.0
SG A:CYS502 2.4 24.2 1.0
SG A:CYS493 2.4 25.6 1.0
ZN A:ZN605 2.9 28.3 1.0
CB A:CYS502 3.2 27.5 1.0
CB A:CYS473 3.3 29.0 1.0
CB A:CYS509 3.3 26.4 1.0
CB A:CYS493 3.5 23.2 1.0
CB A:CYS495 3.9 18.8 1.0
CG2 A:THR476 4.4 18.5 1.0
CD A:ARG480 4.4 21.4 1.0
OG1 A:THR476 4.5 27.8 1.0
CA A:CYS473 4.5 25.5 1.0
SG A:CYS495 4.6 28.4 1.0
CA A:CYS502 4.7 23.3 1.0
SG A:CYS506 4.7 22.1 1.0
NE A:ARG480 4.7 23.7 1.0
CA A:CYS509 4.8 23.1 1.0
CA A:CYS493 4.9 24.1 1.0
CB A:VAL475 4.9 24.0 1.0
CA A:CYS495 5.0 25.9 1.0

Zinc binding site 5 out of 10 in 8bvl

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Zinc binding site 5 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


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 the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:28.3
occ:1.00
 SG A:CYS506 2.3 22.1 1.0
SG A:CYS502 2.3 24.2 1.0
SG A:CYS495 2.4 28.4 1.0
SG A:CYS509 2.4 22.7 1.0
ZN A:ZN604 2.9 24.7 1.0
CB A:CYS495 3.0 18.8 1.0
CB A:CYS506 3.3 24.2 1.0
CB A:CYS509 3.5 26.4 1.0
CB A:CYS502 3.6 27.5 1.0
O A:HOH729 3.6 24.1 1.0
N A:CYS502 3.8 22.4 1.0
N A:CYS509 4.1 25.9 1.0
CA A:CYS502 4.3 23.3 1.0
CA A:CYS495 4.3 25.9 1.0
CA A:CYS509 4.4 23.1 1.0
SG A:CYS493 4.5 25.6 1.0
CA A:CYS506 4.7 27.0 1.0
SG A:CYS473 4.9 25.5 1.0
C A:PRO501 4.9 26.2 1.0
N A:HIS503 4.9 27.9 1.0

Zinc binding site 6 out of 10 in 8bvl

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Zinc binding site 6 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:29.6
occ:1.00
 SG B:CYS394 2.3 31.6 1.0
SG B:CYS391 2.4 22.5 1.0
SG B:CYS376 2.4 29.1 1.0
SG B:CYS371 2.4 29.9 1.0
CB B:CYS391 3.1 24.7 1.0
CB B:CYS371 3.3 27.8 1.0
CB B:CYS394 3.3 27.5 1.0
CB B:CYS376 3.4 24.6 1.0
N B:CYS394 3.7 26.3 1.0
OG1 B:THR373 4.0 25.1 1.0
CB B:THR373 4.1 26.1 1.0
CA B:CYS394 4.1 26.9 1.0
CB B:VAL393 4.4 32.6 1.0
CA B:GLY378 4.5 28.1 1.0
N B:GLY378 4.5 32.0 1.0
CA B:CYS391 4.5 26.0 1.0
CA B:CYS371 4.7 32.6 1.0
C B:CYS394 4.8 23.8 1.0
CA B:CYS376 4.8 29.9 1.0
C B:VAL393 4.8 30.1 1.0
N B:PHE395 4.9 29.2 1.0
CG2 B:THR373 4.9 25.1 1.0
N B:VAL393 5.0 29.7 1.0
CA B:VAL393 5.0 30.6 1.0

Zinc binding site 7 out of 10 in 8bvl

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Zinc binding site 7 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:29.4
occ:1.00
 SG B:CYS465 2.3 24.7 1.0
SG B:CYS450 2.3 23.9 1.0
SG B:CYS447 2.4 28.1 1.0
SG B:CYS468 2.4 27.4 1.0
CB B:CYS447 3.2 28.5 1.0
CB B:CYS465 3.2 25.9 1.0
CB B:CYS450 3.3 26.7 1.0
CB B:CYS468 3.5 23.0 1.0
N B:CYS450 3.7 31.2 1.0
N B:CYS468 3.8 27.5 1.0
CA B:CYS450 4.0 26.3 1.0
CA B:CYS468 4.2 30.3 1.0
CG1 B:ILE452 4.4 31.2 1.0
CB B:VAL467 4.4 30.2 1.0
CB B:GLN449 4.6 24.9 1.0
CA B:CYS447 4.6 30.3 1.0
CD1 B:ILE452 4.7 33.9 1.0
CA B:CYS465 4.7 30.0 1.0
C B:CYS450 4.7 27.4 1.0
C B:GLN449 4.8 29.1 1.0
C B:VAL467 4.8 32.3 1.0
N B:GLN451 4.8 27.6 1.0
CG B:GLN449 4.9 28.9 1.0
N B:VAL467 4.9 31.7 1.0
C B:CYS468 4.9 31.9 1.0
CA B:VAL467 4.9 26.9 1.0
CG1 B:VAL467 5.0 23.7 1.0
CB B:THR470 5.0 31.0 1.0

Zinc binding site 8 out of 10 in 8bvl

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Zinc binding site 8 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:33.7
occ:1.00
 NE2 B:HIS406 2.3 35.7 1.0
SG B:CYS402 2.3 30.2 1.0
SG B:CYS399 2.3 30.1 1.0
SG B:CYS411 2.4 24.4 1.0
CB B:CYS411 3.1 23.1 1.0
CB B:CYS402 3.1 36.3 1.0
CE1 B:HIS406 3.2 36.5 1.0
CB B:CYS399 3.3 26.8 1.0
CD2 B:HIS406 3.3 32.5 1.0
CA B:CYS411 3.6 26.9 1.0
CD1 B:LEU401 3.8 30.2 1.0
N B:CYS402 3.9 28.7 1.0
CA B:CYS402 4.1 31.6 1.0
N B:CYS411 4.3 35.0 1.0
ND1 B:HIS406 4.3 41.0 1.0
CG B:HIS406 4.4 38.1 1.0
CG B:LEU401 4.6 37.7 1.0
CA B:CYS399 4.7 25.5 1.0
C B:CYS411 4.9 30.2 1.0
OG1 B:THR466 4.9 37.3 1.0

Zinc binding site 9 out of 10 in 8bvl

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Zinc binding site 9 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:27.4
occ:1.00
 SG B:CYS493 2.3 24.9 1.0
SG B:CYS509 2.3 24.2 1.0
SG B:CYS502 2.3 19.8 1.0
SG B:CYS473 2.3 27.8 1.0
ZN B:ZN605 3.0 28.4 1.0
CB B:CYS502 3.2 25.3 1.0
CB B:CYS509 3.3 23.3 1.0
CB B:CYS493 3.3 23.9 1.0
CB B:CYS473 3.3 26.8 1.0
CB B:CYS495 3.9 21.7 1.0
CD B:ARG480 4.3 18.1 1.0
CG2 B:THR476 4.4 26.6 1.0
CA B:CYS473 4.5 27.9 1.0
NE B:ARG480 4.6 20.3 1.0
SG B:CYS495 4.6 26.1 1.0
SG B:CYS506 4.7 21.5 1.0
CA B:CYS502 4.7 24.9 1.0
OG1 B:THR476 4.7 29.1 1.0
CA B:CYS509 4.7 20.2 1.0
CA B:CYS493 4.8 21.7 1.0
CB B:VAL475 4.9 22.1 1.0
O B:CYS509 5.0 23.1 1.0

Zinc binding site 10 out of 10 in 8bvl

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Zinc binding site 10 out of 10 in the Crystal Structure of the Ibr-RING2 Domain of Hoil-1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Ibr-RING2 Domain of Hoil-1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn605

b:28.4
occ:1.00
 SG B:CYS506 2.3 21.5 1.0
SG B:CYS502 2.4 19.8 1.0
SG B:CYS509 2.4 24.2 1.0
SG B:CYS495 2.4 26.1 1.0
ZN B:ZN604 3.0 27.4 1.0
CB B:CYS495 3.0 21.7 1.0
CB B:CYS506 3.3 24.4 1.0
CB B:CYS502 3.5 25.3 1.0
CB B:CYS509 3.5 23.3 1.0
O B:HOH728 3.6 29.1 1.0
N B:CYS502 3.8 22.5 1.0
N B:CYS509 4.1 23.0 1.0
CA B:CYS502 4.2 24.9 1.0
CA B:CYS495 4.4 26.8 1.0
CA B:CYS509 4.4 20.2 1.0
SG B:CYS493 4.5 24.9 1.0
CA B:CYS506 4.7 29.7 1.0
N B:HIS503 4.8 27.0 1.0
C B:PRO501 4.9 24.7 1.0
SG B:CYS473 4.9 27.8 1.0

Reference:

Q.Wu, M.G.Koliopoulos, K.Rittinger, B.Stieglitz. Structural Basis For Ubiquitylation By Hoil-1 Front Mol Biosci 2023.
ISSN: ESSN 2296-889X
DOI: 10.3389/FMOLB.2022.1098144
Page generated: Wed Oct 30 18:27:11 2024

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