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 Sites List in 2yho
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
Go back to
Zinc Binding Sites List in 2yho
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 Sites List in 2yho
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 Sites List in 2yho
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 Sites List in 2yho
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 Sites List in 2yho
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
Go back to
Zinc Binding Sites List in 2yho
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
|