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Zinc in PDB 2yho: The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor

Enzymatic activity of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor

All present enzymatic activity of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor:
6.3.2.19;

Protein crystallography data

The structure of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor, PDB code: 2yho was solved by L.Fairall, B.T.Goult, C.J.Millard, P.Tontonoz, J.W.R.Schwabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.906 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.690, 137.870, 63.750, 90.00, 106.39, 90.00
R / Rfree (%) 18.56 / 23.33

Zinc Binding Sites:

The binding sites of Zinc atom in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor (pdb code 2yho). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor, PDB code: 2yho:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2yho

Go back to Zinc Binding Sites List in 2yho
Zinc binding site 1 out of 8 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:21.1
occ:1.00
 SG A:CYS408 2.3 18.6 1.0
SG A:CYS411 2.3 23.7 1.0
SG A:CYS390 2.4 19.9 1.0
SG A:CYS387 2.4 19.6 1.0
CB A:CYS387 3.1 18.2 1.0
CB A:CYS390 3.2 24.1 1.0
CB A:CYS411 3.3 21.0 1.0
CB A:CYS408 3.6 19.4 1.0
N A:CYS390 3.7 23.8 1.0
N A:CYS408 4.0 16.6 1.0
CA A:CYS390 4.0 22.2 1.0
N A:CYS411 4.2 18.4 1.0
CA A:CYS408 4.3 18.6 1.0
CA A:CYS411 4.4 19.1 1.0
CA A:CYS387 4.6 23.1 1.0
CB A:GLU393 4.7 22.7 1.0
CB A:VAL389 4.7 22.9 1.0
O A:CYS408 4.8 17.8 1.0
C A:VAL389 4.8 24.4 1.0
O A:HOH2030 4.8 41.3 1.0
C A:CYS408 4.8 18.6 1.0
C A:CYS390 4.9 25.2 1.0
N A:CYS391 5.0 22.9 1.0

Zinc binding site 2 out of 8 in 2yho

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Zinc binding site 2 out of 8 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1002

b:21.7
occ:1.00
 ND1 A:HIS404 2.0 18.9 1.0
SG A:CYS402 2.3 20.2 1.0
SG A:CYS418 2.3 21.1 1.0
SG A:CYS421 2.3 26.0 1.0
CE1 A:HIS404 2.9 29.4 1.0
CB A:CYS418 3.1 18.9 1.0
CG A:HIS404 3.1 21.8 1.0
CB A:CYS402 3.3 24.5 1.0
CB A:CYS421 3.4 23.2 1.0
CB A:HIS404 3.5 19.2 1.0
N A:CYS421 3.8 22.1 1.0
NE2 A:HIS404 4.1 26.6 1.0
CA A:CYS421 4.2 23.9 1.0
CD2 A:HIS404 4.2 22.0 1.0
N A:HIS404 4.2 19.3 1.0
CB A:VAL420 4.5 22.6 1.0
CA A:HIS404 4.5 18.6 1.0
CA A:CYS418 4.5 21.4 1.0
CA A:CYS402 4.6 20.7 1.0
C A:CYS402 4.7 21.2 1.0
CB A:SER423 4.7 30.2 1.0
OG A:SER423 4.8 36.1 1.0
C A:CYS421 4.8 27.7 1.0
C A:VAL420 4.8 26.3 1.0
N A:ARG422 4.9 23.4 1.0
O A:HOH2035 4.9 38.2 1.0
O A:CYS402 4.9 24.2 1.0
N A:SER423 5.0 31.5 1.0

Zinc binding site 3 out of 8 in 2yho

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Zinc binding site 3 out of 8 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:26.0
occ:1.00
 SG C:CYS408 2.3 22.2 1.0
SG C:CYS411 2.3 23.3 1.0
SG C:CYS390 2.4 22.7 1.0
SG C:CYS387 2.4 21.8 1.0
CB C:CYS387 3.1 20.0 1.0
CB C:CYS411 3.2 21.2 1.0
CB C:CYS390 3.3 24.9 1.0
CB C:CYS408 3.5 22.9 1.0
N F:GLY-1 3.6 37.4 1.0
N C:CYS390 3.7 22.2 1.0
N C:CYS408 3.9 22.5 1.0
CA C:CYS390 4.1 24.2 1.0
CA F:GLY-1 4.2 31.1 1.0
N C:CYS411 4.2 21.6 1.0
CA C:CYS408 4.2 20.0 1.0
CA C:CYS411 4.3 20.4 1.0
CB C:VAL389 4.5 29.1 1.0
CG C:GLU393 4.6 29.3 1.0
CA C:CYS387 4.6 21.4 1.0
O C:CYS408 4.7 20.8 1.0
C C:CYS408 4.8 20.4 1.0
C C:VAL389 4.8 26.2 1.0
CG1 C:VAL389 5.0 27.6 1.0
CA C:VAL389 5.0 26.1 1.0
C C:CYS390 5.0 27.2 1.0

Zinc binding site 4 out of 8 in 2yho

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Zinc binding site 4 out of 8 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1002

b:19.3
occ:1.00
 ND1 C:HIS404 2.1 16.3 1.0
SG C:CYS421 2.3 20.4 1.0
SG C:CYS418 2.3 20.4 1.0
SG C:CYS402 2.4 17.5 1.0
CE1 C:HIS404 3.0 22.1 1.0
CG C:HIS404 3.1 20.9 1.0
CB C:CYS418 3.2 20.9 1.0
CB C:CYS402 3.2 16.3 1.0
CB C:HIS404 3.5 16.8 1.0
CB C:CYS421 3.5 22.3 1.0
N C:CYS421 3.7 20.6 1.0
NE2 C:HIS404 4.1 23.3 1.0
CA C:CYS421 4.2 22.5 1.0
CD2 C:HIS404 4.2 20.6 1.0
N C:HIS404 4.4 17.7 1.0
CB C:VAL420 4.4 20.5 1.0
CA C:HIS404 4.5 18.9 1.0
CA C:CYS402 4.6 19.4 1.0
CA C:CYS418 4.6 22.5 1.0
C C:VAL420 4.7 22.5 1.0
C C:CYS402 4.8 21.7 1.0
CB C:SER423 4.8 25.1 1.0
C C:CYS421 4.9 24.0 1.0
N C:ARG422 4.9 24.5 1.0
CA C:VAL420 4.9 21.1 1.0
OG C:SER423 5.0 28.9 1.0
O C:HOH2013 5.0 23.7 1.0

Zinc binding site 5 out of 8 in 2yho

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Zinc binding site 5 out of 8 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1001

b:27.8
occ:1.00
 SG E:CYS411 2.3 24.4 1.0
SG E:CYS387 2.3 26.4 1.0
SG E:CYS408 2.4 25.5 1.0
SG E:CYS390 2.4 30.0 1.0
CB E:CYS387 3.1 21.9 1.0
CB E:CYS411 3.2 26.3 1.0
CB E:CYS390 3.3 27.5 1.0
CB E:CYS408 3.6 25.9 1.0
N E:CYS390 3.7 27.1 1.0
N D:GLY-1 3.8 36.8 1.0
N E:CYS408 3.9 24.9 1.0
CA E:CYS390 4.1 28.5 1.0
N E:CYS411 4.2 24.2 1.0
CA D:GLY-1 4.3 36.3 1.0
CA E:CYS408 4.3 22.9 1.0
CA E:CYS411 4.3 25.1 1.0
CB E:VAL389 4.6 28.8 1.0
CG E:GLU393 4.6 31.0 1.0
CA E:CYS387 4.6 23.5 1.0
OG E:SER410 4.6 37.2 1.0
C E:VAL389 4.8 28.1 1.0
O E:CYS408 4.8 23.5 1.0
C E:CYS408 4.9 21.7 1.0
O E:HOH2017 4.9 34.1 1.0
C E:CYS407 5.0 24.2 1.0

Zinc binding site 6 out of 8 in 2yho

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Zinc binding site 6 out of 8 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1002

b:21.4
occ:1.00
 ND1 E:HIS404 2.0 17.9 1.0
SG E:CYS421 2.3 20.6 1.0
SG E:CYS402 2.3 19.6 1.0
SG E:CYS418 2.4 18.8 1.0
CE1 E:HIS404 3.0 22.3 1.0
CB E:CYS418 3.1 21.9 1.0
CG E:HIS404 3.1 23.3 1.0
CB E:CYS402 3.3 22.8 1.0
CB E:CYS421 3.4 22.0 1.0
CB E:HIS404 3.5 17.0 1.0
N E:CYS421 3.8 20.0 1.0
NE2 E:HIS404 4.1 24.9 1.0
CA E:CYS421 4.1 25.3 1.0
CD2 E:HIS404 4.2 20.9 1.0
N E:HIS404 4.3 20.6 1.0
CB E:VAL420 4.5 22.0 1.0
CA E:HIS404 4.5 21.2 1.0
CA E:CYS418 4.6 25.1 1.0
CA E:CYS402 4.6 24.5 1.0
C E:CYS402 4.8 22.3 1.0
C E:VAL420 4.8 22.3 1.0
C E:CYS421 4.8 25.0 1.0
CB E:SER423 4.9 27.7 1.0
OG E:SER423 4.9 27.8 1.0
N E:ARG422 4.9 23.6 1.0

Zinc binding site 7 out of 8 in 2yho

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Zinc binding site 7 out of 8 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1001

b:24.1
occ:1.00
 SG G:CYS390 2.2 25.3 1.0
SG G:CYS408 2.3 18.8 1.0
SG G:CYS411 2.4 24.2 1.0
SG G:CYS387 2.4 21.3 1.0
CB G:CYS390 3.1 23.0 1.0
CB G:CYS387 3.1 23.0 1.0
CB G:CYS411 3.3 24.2 1.0
CB G:CYS408 3.5 21.3 1.0
N G:CYS390 3.6 21.6 1.0
N G:CYS408 4.0 21.3 1.0
CA G:CYS390 4.0 25.0 1.0
N G:CYS411 4.2 21.2 1.0
CA G:CYS408 4.2 20.9 1.0
CA G:CYS411 4.4 23.7 1.0
CA G:CYS387 4.6 25.0 1.0
CB G:VAL389 4.7 23.8 1.0
C G:VAL389 4.8 24.6 1.0
CB G:GLU393 4.8 29.5 1.0
C G:CYS408 4.8 20.9 1.0
O G:CYS408 4.8 18.2 1.0
C G:CYS390 4.9 25.8 1.0
N G:CYS391 4.9 24.8 1.0

Zinc binding site 8 out of 8 in 2yho

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Zinc binding site 8 out of 8 in the The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1002

b:27.0
occ:1.00
 ND1 G:HIS404 2.0 25.2 1.0
SG G:CYS402 2.3 24.5 1.0
SG G:CYS418 2.4 23.6 1.0
SG G:CYS421 2.5 31.9 1.0
CE1 G:HIS404 2.9 32.0 1.0
CG G:HIS404 3.0 27.2 1.0
CB G:CYS418 3.1 29.8 1.0
CB G:CYS402 3.2 27.2 1.0
CB G:HIS404 3.4 23.0 1.0
CB G:CYS421 3.5 31.8 1.0
N G:CYS421 3.8 29.5 1.0
NE2 G:HIS404 4.0 29.0 1.0
CD2 G:HIS404 4.1 26.0 1.0
CA G:CYS421 4.2 33.7 1.0
N G:HIS404 4.3 21.9 1.0
CB G:VAL420 4.3 26.9 1.0
CA G:HIS404 4.5 23.0 1.0
CA G:CYS402 4.6 23.0 1.0
CA G:CYS418 4.6 30.3 1.0
C G:VAL420 4.8 33.0 1.0
C G:CYS402 4.8 23.3 1.0
OG G:SER423 4.9 42.9 1.0
CB G:SER423 4.9 34.8 1.0
CA G:VAL420 4.9 30.8 1.0
C G:CYS421 4.9 35.6 1.0
N G:VAL420 4.9 28.5 1.0
N G:ARG422 5.0 33.3 1.0
CG1 G:VAL420 5.0 27.9 1.0
O G:HOH2013 5.0 32.5 1.0

Reference:

L.Zhang, L.Fairall, B.T.Goult, A.C.Calkin, C.Hong, C.J.Millard, P.Tontonoz, J.W.Schwabe. The Idol-UBE2D Complex Mediates Sterol-Dependent Degradation of the Ldl Receptor. Genes Dev. V. 25 1262 2011.
ISSN: ISSN 0890-9369
PubMed: 21685362
DOI: 10.1101/GAD.2056211
Page generated: Thu Oct 17 05:50:24 2024

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