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Zinc in PDB 7yuj: Crystal Structure of Hoil-1L(365-510)

Enzymatic activity of Crystal Structure of Hoil-1L(365-510)

All present enzymatic activity of Crystal Structure of Hoil-1L(365-510):
2.3.2.31;

Protein crystallography data

The structure of Crystal Structure of Hoil-1L(365-510), PDB code: 7yuj 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) 26.62 / 1.87
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.252, 59.87, 57.818, 90, 90.92, 90
R / Rfree (%) 15.3 / 18.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Hoil-1L(365-510) (pdb code 7yuj). 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 Hoil-1L(365-510), PDB code: 7yuj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 7yuj

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Zinc binding site 1 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn601

b:21.5
occ:1.00
 SG A:CYS473 2.2 22.8 1.0
SG A:CYS493 2.3 20.7 1.0
SG A:CYS502 2.4 22.9 1.0
SG A:CYS509 2.4 21.0 1.0
ZN A:ZN602 3.2 23.7 1.0
CB A:CYS473 3.2 22.2 1.0
CB A:CYS502 3.2 24.1 1.0
CB A:CYS493 3.3 20.8 1.0
CB A:CYS509 3.4 19.0 1.0
CB A:CYS495 4.0 22.3 1.0
CD A:ARG480 4.2 17.8 1.0
OG1 A:THR476 4.4 25.8 1.0
CA A:CYS473 4.4 22.6 1.0
NE A:ARG480 4.5 22.0 1.0
CG2 A:THR476 4.6 25.9 1.0
SG A:CYS495 4.6 26.0 1.0
CA A:CYS493 4.7 23.1 1.0
CA A:CYS502 4.7 23.7 1.0
CA A:CYS509 4.8 23.8 1.0
SG A:CYS506 4.8 23.2 1.0
CB A:VAL475 4.9 28.3 1.0
CA A:CYS495 5.0 19.3 1.0
N A:CYS495 5.0 18.8 1.0

Zinc binding site 2 out of 10 in 7yuj

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Zinc binding site 2 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn602

b:23.7
occ:1.00
 SG A:CYS506 2.3 23.2 1.0
SG A:CYS495 2.3 26.0 1.0
SG A:CYS502 2.4 22.9 1.0
SG A:CYS509 2.4 21.0 1.0
CB A:CYS495 3.1 22.3 1.0
ZN A:ZN601 3.2 21.5 1.0
CB A:CYS506 3.2 23.1 1.0
CB A:CYS509 3.4 19.0 1.0
CB A:CYS502 3.5 24.1 1.0
O A:HOH773 3.6 31.5 1.0
N A:CYS502 3.8 20.4 1.0
N A:CYS509 4.0 23.1 1.0
O A:HOH716 4.2 36.4 1.0
CA A:CYS502 4.3 23.7 1.0
CA A:CYS509 4.3 23.8 1.0
CA A:CYS495 4.4 19.3 1.0
CA A:CYS506 4.6 20.6 1.0
SG A:CYS493 4.7 20.7 1.0
SG A:CYS473 4.9 22.8 1.0
C A:PRO501 4.9 25.5 1.0
N A:HIS503 4.9 25.6 1.0

Zinc binding site 3 out of 10 in 7yuj

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Zinc binding site 3 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn603

b:24.3
occ:1.00
 SG A:CYS450 2.2 21.8 1.0
SG A:CYS465 2.3 25.6 1.0
SG A:CYS447 2.3 22.7 1.0
SG A:CYS468 2.4 30.0 1.0
CB A:CYS465 3.1 22.1 1.0
CB A:CYS447 3.2 23.1 1.0
CB A:CYS450 3.3 24.0 1.0
CB A:CYS468 3.5 25.2 1.0
N A:CYS450 3.6 25.5 1.0
N A:CYS468 3.7 27.8 1.0
CA A:CYS450 4.0 29.4 1.0
CA A:CYS468 4.2 29.3 1.0
CB A:VAL467 4.5 30.7 1.0
CG1 A:ILE452 4.6 29.6 1.0
CB A:GLN449 4.6 26.6 1.0
CA A:CYS465 4.6 28.1 1.0
CA A:CYS447 4.7 24.6 1.0
C A:CYS450 4.7 29.6 1.0
C A:VAL467 4.7 31.0 1.0
N A:GLN451 4.8 22.4 1.0
C A:GLN449 4.8 25.5 1.0
N A:VAL467 4.8 28.8 1.0
C A:CYS468 4.8 27.6 1.0
CA A:VAL467 4.9 32.4 1.0
N A:HIS469 4.9 27.4 1.0
CD1 A:ILE452 4.9 32.5 1.0
N A:GLN449 5.0 23.6 1.0
CB A:THR470 5.0 29.3 1.0

Zinc binding site 4 out of 10 in 7yuj

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Zinc binding site 4 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn604

b:24.4
occ:1.00
 SG A:CYS391 2.2 22.1 1.0
SG A:CYS376 2.3 26.1 1.0
SG A:CYS371 2.4 26.4 1.0
SG A:CYS394 2.4 25.8 1.0
CB A:CYS391 3.1 28.6 1.0
CB A:CYS371 3.2 22.7 1.0
CB A:CYS376 3.3 26.7 1.0
CB A:CYS394 3.4 24.8 1.0
N A:CYS394 3.8 23.6 1.0
OG1 A:THR373 4.0 29.0 1.0
CB A:THR373 4.0 27.3 1.0
CA A:CYS394 4.2 25.2 1.0
CA A:CYS391 4.5 24.6 1.0
N A:GLY378 4.6 25.4 1.0
CA A:GLY378 4.6 22.8 1.0
CB A:VAL393 4.6 24.5 1.0
CA A:CYS371 4.7 24.6 1.0
CA A:CYS376 4.7 30.8 1.0
CG2 A:THR373 4.8 29.1 1.0
C A:VAL393 4.9 30.6 1.0
C A:CYS394 4.9 32.6 1.0
N A:THR373 4.9 28.8 1.0

Zinc binding site 5 out of 10 in 7yuj

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Zinc binding site 5 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn605

b:27.6
occ:1.00
 NE2 A:HIS406 2.2 27.0 1.0
SG A:CYS402 2.3 30.1 1.0
SG A:CYS411 2.3 29.2 1.0
SG A:CYS399 2.3 31.6 1.0
CE1 A:HIS406 3.1 28.8 1.0
CB A:CYS411 3.2 33.1 1.0
CB A:CYS399 3.2 29.3 1.0
CD2 A:HIS406 3.2 32.1 1.0
CB A:CYS402 3.3 27.9 1.0
CA A:CYS411 3.7 29.0 1.0
N A:CYS402 4.0 30.1 1.0
O A:HOH783 4.0 37.5 1.0
CA A:CYS402 4.2 25.7 1.0
ND1 A:HIS406 4.3 32.6 1.0
CG A:HIS406 4.3 27.7 1.0
N A:CYS411 4.4 28.4 1.0
CA A:CYS399 4.6 26.9 1.0
OG1 A:THR466 4.8 34.5 1.0
C A:LEU401 5.0 34.5 1.0
CB A:LEU401 5.0 29.5 1.0
C A:CYS411 5.0 29.3 1.0

Zinc binding site 6 out of 10 in 7yuj

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Zinc binding site 6 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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 Hoil-1L(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn601

b:27.1
occ:1.00
 SG B:CYS391 2.2 24.3 1.0
SG B:CYS371 2.3 29.7 1.0
SG B:CYS376 2.4 29.8 1.0
SG B:CYS394 2.4 28.3 1.0
CB B:CYS391 3.0 26.0 1.0
CB B:CYS371 3.2 23.6 1.0
CB B:CYS376 3.4 36.4 1.0
CB B:CYS394 3.4 25.3 1.0
N B:CYS394 3.8 30.0 1.0
OG1 B:THR373 3.9 31.3 1.0
CB B:THR373 3.9 34.2 1.0
CA B:CYS394 4.2 31.4 1.0
CA B:CYS391 4.5 27.6 1.0
CB B:VAL393 4.6 33.0 1.0
N B:GLY378 4.6 27.4 1.0
CA B:GLY378 4.6 27.8 1.0
CA B:CYS371 4.6 31.4 1.0
CG2 B:THR373 4.8 34.6 1.0
CA B:CYS376 4.8 38.1 1.0
N B:THR373 4.9 31.9 1.0
C B:VAL393 4.9 31.6 1.0
C B:CYS394 4.9 33.1 1.0

Zinc binding site 7 out of 10 in 7yuj

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Zinc binding site 7 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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 Hoil-1L(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn602

b:30.8
occ:1.00
 SG B:CYS402 2.3 34.1 1.0
NE2 B:HIS406 2.3 32.1 1.0
SG B:CYS411 2.3 28.6 1.0
SG B:CYS399 2.3 36.1 1.0
CB B:CYS411 3.1 30.8 1.0
CE1 B:HIS406 3.2 33.3 1.0
CB B:CYS402 3.3 29.8 1.0
CB B:CYS399 3.3 32.5 1.0
CD2 B:HIS406 3.3 32.5 1.0
CA B:CYS411 3.7 28.9 1.0
N B:CYS402 3.9 27.6 1.0
CA B:CYS402 4.2 28.2 1.0
ND1 B:HIS406 4.3 35.2 1.0
CG B:HIS406 4.4 33.3 1.0
N B:CYS411 4.4 32.0 1.0
CA B:CYS399 4.7 29.3 1.0
OG1 B:THR466 4.8 32.2 1.0
CB B:LEU401 4.8 29.0 1.0
C B:LEU401 4.9 32.3 1.0
C B:CYS411 5.0 26.5 1.0

Zinc binding site 8 out of 10 in 7yuj

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Zinc binding site 8 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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 Hoil-1L(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn603

b:25.0
occ:1.00
 SG B:CYS450 2.2 26.5 1.0
SG B:CYS447 2.3 26.2 1.0
SG B:CYS465 2.3 25.8 1.0
SG B:CYS468 2.3 28.5 1.0
CB B:CYS465 3.2 23.7 1.0
CB B:CYS447 3.2 23.5 1.0
CB B:CYS450 3.2 30.5 1.0
CB B:CYS468 3.5 27.0 1.0
N B:CYS450 3.6 26.9 1.0
N B:CYS468 3.8 26.5 1.0
CA B:CYS450 4.0 33.9 1.0
CA B:CYS468 4.2 27.7 1.0
CB B:VAL467 4.5 32.7 1.0
CG1 B:ILE452 4.6 39.4 1.0
CB B:GLN449 4.6 26.0 1.0
C B:CYS450 4.6 27.5 1.0
CA B:CYS447 4.7 25.7 1.0
CA B:CYS465 4.7 25.1 1.0
N B:GLN451 4.7 26.6 1.0
C B:GLN449 4.7 28.0 1.0
C B:VAL467 4.8 27.5 1.0
N B:VAL467 4.8 31.4 1.0
C B:CYS468 4.9 28.6 1.0
CG B:GLN449 4.9 28.0 1.0
CA B:VAL467 4.9 33.3 1.0
CD1 B:ILE452 5.0 37.5 1.0
N B:HIS469 5.0 25.6 1.0

Zinc binding site 9 out of 10 in 7yuj

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Zinc binding site 9 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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 Hoil-1L(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn604

b:22.4
occ:1.00
 SG B:CYS473 2.3 24.2 1.0
SG B:CYS493 2.3 21.7 1.0
SG B:CYS502 2.4 21.7 1.0
SG B:CYS509 2.4 21.5 1.0
CB B:CYS493 3.2 19.9 1.0
ZN B:ZN606 3.2 22.7 1.0
CB B:CYS473 3.2 20.5 1.0
CB B:CYS502 3.3 19.6 1.0
CB B:CYS509 3.3 20.2 1.0
CB B:CYS495 4.0 20.9 1.0
CD B:ARG480 4.3 18.8 1.0
CA B:CYS473 4.4 21.7 1.0
OG1 B:THR476 4.5 25.8 1.0
CG2 B:THR476 4.6 24.6 1.0
SG B:CYS495 4.6 26.1 1.0
NE B:ARG480 4.6 21.8 1.0
CA B:CYS493 4.6 21.1 1.0
CB B:VAL475 4.7 20.9 1.0
CA B:CYS502 4.7 23.4 1.0
SG B:CYS506 4.8 20.4 1.0
CA B:CYS509 4.8 22.3 1.0
CG2 B:VAL475 4.9 23.8 1.0
N B:CYS495 5.0 23.6 1.0
CA B:CYS495 5.0 25.3 1.0

Zinc binding site 10 out of 10 in 7yuj

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Zinc binding site 10 out of 10 in the Crystal Structure of Hoil-1L(365-510)


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 Hoil-1L(365-510) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn606

b:22.7
occ:1.00
 SG B:CYS506 2.2 20.4 1.0
SG B:CYS495 2.3 26.1 1.0
SG B:CYS509 2.4 21.5 1.0
SG B:CYS502 2.5 21.7 1.0
CB B:CYS495 3.2 20.9 1.0
ZN B:ZN604 3.2 22.4 1.0
CB B:CYS506 3.2 19.9 1.0
CB B:CYS509 3.5 20.2 1.0
O B:HOH783 3.5 25.6 1.0
CB B:CYS502 3.6 19.6 1.0
N B:CYS502 3.8 19.5 1.0
N B:CYS509 4.0 20.9 1.0
CA B:CYS509 4.3 22.3 1.0
CA B:CYS502 4.3 23.4 1.0
CA B:CYS495 4.4 25.3 1.0
CA B:CYS506 4.6 19.1 1.0
SG B:CYS493 4.8 21.7 1.0
CG2 B:VAL475 4.8 23.8 1.0
O B:HOH701 4.8 41.1 1.0
SG B:CYS473 4.9 24.2 1.0
C B:PRO501 4.9 24.1 1.0
NH2 B:ARG496 4.9 59.5 0.5
N B:HIS503 4.9 23.9 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: Wed Oct 30 16:05:51 2024

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