Zinc in PDB 5jg6: APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C
Protein crystallography data
The structure of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C, PDB code: 5jg6
was solved by
N.G.Brown,
W.Zhang,
S.Yu,
D.J.Miller,
S.S.Sidhu,
B.A.Schulman,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
36.33 /
2.00
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
131.066,
35.193,
72.768,
90.00,
120.42,
90.00
|
R / Rfree (%)
|
18.5 /
22
|
Zinc Binding Sites:
The binding sites of Zinc atom in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C
(pdb code 5jg6). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the
APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C, PDB code: 5jg6:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
Zinc binding site 1 out
of 6 in 5jg6
Go back to
Zinc Binding Sites List in 5jg6
Zinc binding site 1 out
of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn101
b:23.6
occ:1.00
|
ND1
|
A:HIS56
|
2.0
|
20.8
|
1.0
|
SG
|
A:CYS59
|
2.2
|
24.9
|
1.0
|
SG
|
A:CYS23
|
2.3
|
21.2
|
1.0
|
SG
|
A:CYS26
|
2.4
|
25.7
|
1.0
|
CB
|
A:CYS23
|
2.9
|
35.1
|
1.0
|
CE1
|
A:HIS56
|
3.0
|
23.2
|
1.0
|
CG
|
A:HIS56
|
3.1
|
17.2
|
1.0
|
CB
|
A:CYS26
|
3.2
|
23.5
|
1.0
|
CB
|
A:CYS59
|
3.4
|
18.1
|
1.0
|
CB
|
A:HIS56
|
3.4
|
16.5
|
1.0
|
N
|
A:CYS26
|
3.7
|
28.3
|
1.0
|
N
|
A:HIS56
|
4.0
|
17.7
|
1.0
|
CA
|
A:CYS26
|
4.1
|
26.3
|
1.0
|
NE2
|
A:HIS56
|
4.1
|
24.3
|
1.0
|
CD2
|
A:HIS56
|
4.2
|
17.3
|
1.0
|
CB
|
A:CYS34
|
4.3
|
22.3
|
1.0
|
CA
|
A:HIS56
|
4.3
|
17.4
|
1.0
|
CA
|
A:CYS23
|
4.4
|
36.7
|
1.0
|
CB
|
A:ILE25
|
4.7
|
25.1
|
1.0
|
CA
|
A:CYS34
|
4.7
|
25.6
|
1.0
|
CD
|
A:PRO35
|
4.7
|
42.0
|
1.0
|
CA
|
A:CYS59
|
4.7
|
19.8
|
1.0
|
C
|
A:ILE25
|
4.8
|
34.4
|
1.0
|
C
|
A:CYS23
|
4.8
|
35.6
|
1.0
|
C
|
A:CYS26
|
4.9
|
28.0
|
1.0
|
O
|
A:CYS23
|
4.9
|
28.5
|
1.0
|
O
|
A:HIS56
|
5.0
|
17.4
|
1.0
|
|
Zinc binding site 2 out
of 6 in 5jg6
Go back to
Zinc Binding Sites List in 5jg6
Zinc binding site 2 out
of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn102
b:29.4
occ:1.00
|
ND1
|
A:HIS58
|
2.0
|
23.4
|
1.0
|
SG
|
A:CYS44
|
2.3
|
26.3
|
1.0
|
SG
|
A:CYS34
|
2.3
|
27.8
|
1.0
|
SG
|
A:CYS37
|
2.4
|
34.5
|
1.0
|
CE1
|
A:HIS58
|
2.9
|
23.9
|
1.0
|
CG
|
A:HIS58
|
3.1
|
21.8
|
1.0
|
CB
|
A:CYS44
|
3.3
|
24.1
|
1.0
|
CB
|
A:CYS34
|
3.3
|
22.3
|
1.0
|
CB
|
A:CYS37
|
3.4
|
38.7
|
1.0
|
CB
|
A:HIS58
|
3.6
|
20.6
|
1.0
|
N
|
A:CYS34
|
3.7
|
30.0
|
1.0
|
O
|
A:HOH211
|
3.9
|
18.6
|
1.0
|
CA
|
A:CYS44
|
4.0
|
33.2
|
1.0
|
CA
|
A:CYS34
|
4.0
|
25.6
|
1.0
|
NE2
|
A:HIS58
|
4.0
|
19.8
|
1.0
|
N
|
A:CYS37
|
4.1
|
40.9
|
1.0
|
CD2
|
A:HIS58
|
4.2
|
20.6
|
1.0
|
CA
|
A:CYS37
|
4.3
|
43.4
|
1.0
|
C
|
A:CYS34
|
4.6
|
37.0
|
1.0
|
O
|
A:CYS34
|
4.6
|
35.5
|
1.0
|
C
|
A:CYS33
|
4.9
|
32.6
|
1.0
|
O
|
A:ASP43
|
4.9
|
43.1
|
1.0
|
O
|
A:HOH212
|
5.0
|
34.1
|
1.0
|
CA
|
A:HIS58
|
5.0
|
22.0
|
1.0
|
|
Zinc binding site 3 out
of 6 in 5jg6
Go back to
Zinc Binding Sites List in 5jg6
Zinc binding site 3 out
of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn103
b:24.2
occ:1.00
|
ND1
|
A:HIS53
|
2.0
|
30.6
|
1.0
|
SG
|
A:CYS51
|
2.3
|
22.8
|
1.0
|
SG
|
A:CYS76
|
2.3
|
23.3
|
1.0
|
SG
|
A:CYS73
|
2.4
|
20.3
|
1.0
|
CE1
|
A:HIS53
|
2.9
|
37.4
|
1.0
|
CG
|
A:HIS53
|
3.0
|
33.1
|
1.0
|
CB
|
A:CYS73
|
3.0
|
16.4
|
1.0
|
CB
|
A:CYS51
|
3.2
|
26.0
|
1.0
|
CB
|
A:CYS76
|
3.4
|
20.9
|
1.0
|
CB
|
A:HIS53
|
3.4
|
25.6
|
1.0
|
N
|
A:CYS76
|
3.8
|
28.5
|
1.0
|
NE2
|
A:HIS53
|
4.0
|
41.7
|
1.0
|
CD2
|
A:HIS53
|
4.1
|
40.8
|
1.0
|
CA
|
A:CYS76
|
4.2
|
27.8
|
1.0
|
O
|
A:CYS51
|
4.4
|
26.7
|
1.0
|
CB
|
A:MET75
|
4.4
|
31.4
|
1.0
|
N
|
A:HIS53
|
4.4
|
24.7
|
1.0
|
CA
|
A:CYS51
|
4.5
|
26.9
|
1.0
|
CA
|
A:CYS73
|
4.5
|
22.0
|
1.0
|
C
|
A:CYS51
|
4.6
|
27.4
|
1.0
|
CA
|
A:HIS53
|
4.6
|
23.2
|
1.0
|
C
|
A:MET75
|
4.9
|
34.8
|
1.0
|
C
|
A:CYS76
|
4.9
|
29.4
|
1.0
|
CZ3
|
A:TRP80
|
5.0
|
18.8
|
1.0
|
|
Zinc binding site 4 out
of 6 in 5jg6
Go back to
Zinc Binding Sites List in 5jg6
Zinc binding site 4 out
of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn101
b:17.6
occ:1.00
|
ND1
|
D:HIS56
|
2.1
|
14.8
|
1.0
|
SG
|
D:CYS59
|
2.3
|
19.4
|
1.0
|
SG
|
D:CYS26
|
2.3
|
17.9
|
1.0
|
SG
|
D:CYS23
|
2.4
|
19.4
|
1.0
|
CB
|
D:CYS23
|
2.9
|
16.8
|
1.0
|
CE1
|
D:HIS56
|
3.1
|
15.3
|
1.0
|
CG
|
D:HIS56
|
3.2
|
15.5
|
1.0
|
CB
|
D:CYS26
|
3.2
|
19.5
|
1.0
|
CB
|
D:CYS59
|
3.3
|
15.0
|
1.0
|
CB
|
D:HIS56
|
3.5
|
16.9
|
1.0
|
N
|
D:CYS26
|
3.7
|
18.1
|
1.0
|
N
|
D:HIS56
|
4.1
|
15.8
|
1.0
|
CA
|
D:CYS26
|
4.1
|
15.9
|
1.0
|
NE2
|
D:HIS56
|
4.2
|
17.9
|
1.0
|
CD2
|
D:HIS56
|
4.3
|
15.4
|
1.0
|
CB
|
D:CYS34
|
4.3
|
15.4
|
1.0
|
CA
|
D:HIS56
|
4.4
|
13.6
|
1.0
|
CA
|
D:CYS23
|
4.4
|
16.5
|
1.0
|
CA
|
D:CYS59
|
4.7
|
13.5
|
1.0
|
CB
|
D:ILE25
|
4.7
|
24.8
|
1.0
|
CA
|
D:CYS34
|
4.8
|
16.2
|
1.0
|
C
|
D:ILE25
|
4.8
|
22.6
|
1.0
|
C
|
D:CYS26
|
4.9
|
21.6
|
1.0
|
C
|
D:CYS23
|
4.9
|
21.5
|
1.0
|
CD
|
D:PRO35
|
4.9
|
23.6
|
1.0
|
O
|
D:HIS56
|
5.0
|
13.9
|
1.0
|
|
Zinc binding site 5 out
of 6 in 5jg6
Go back to
Zinc Binding Sites List in 5jg6
Zinc binding site 5 out
of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn102
b:23.1
occ:1.00
|
ND1
|
D:HIS53
|
2.0
|
26.8
|
1.0
|
SG
|
D:CYS73
|
2.3
|
20.4
|
1.0
|
SG
|
D:CYS76
|
2.3
|
24.9
|
1.0
|
SG
|
D:CYS51
|
2.3
|
19.5
|
1.0
|
CE1
|
D:HIS53
|
2.9
|
36.4
|
1.0
|
CB
|
D:CYS73
|
2.9
|
17.3
|
1.0
|
CG
|
D:HIS53
|
3.1
|
21.1
|
1.0
|
CB
|
D:CYS51
|
3.2
|
20.9
|
1.0
|
CB
|
D:CYS76
|
3.5
|
30.6
|
1.0
|
CB
|
D:HIS53
|
3.6
|
13.4
|
1.0
|
N
|
D:CYS76
|
3.8
|
30.6
|
1.0
|
NE2
|
D:HIS53
|
4.0
|
40.5
|
1.0
|
CD2
|
D:HIS53
|
4.1
|
32.8
|
1.0
|
CA
|
D:CYS76
|
4.2
|
29.1
|
1.0
|
O
|
D:CYS51
|
4.4
|
33.3
|
1.0
|
CA
|
D:CYS73
|
4.4
|
15.0
|
1.0
|
CA
|
D:CYS51
|
4.5
|
25.6
|
1.0
|
N
|
D:HIS53
|
4.5
|
16.7
|
1.0
|
C
|
D:CYS51
|
4.6
|
27.5
|
1.0
|
CB
|
D:MET75
|
4.6
|
31.6
|
1.0
|
CA
|
D:HIS53
|
4.7
|
18.3
|
1.0
|
C
|
D:CYS76
|
4.8
|
25.6
|
1.0
|
N
|
D:ARG77
|
4.8
|
20.6
|
1.0
|
C
|
D:MET75
|
4.9
|
34.0
|
1.0
|
OE1
|
D:GLN78
|
4.9
|
48.2
|
1.0
|
CZ3
|
D:TRP80
|
5.0
|
19.0
|
1.0
|
N
|
D:MET75
|
5.0
|
23.6
|
1.0
|
C
|
D:CYS73
|
5.0
|
20.8
|
1.0
|
|
Zinc binding site 6 out
of 6 in 5jg6
Go back to
Zinc Binding Sites List in 5jg6
Zinc binding site 6 out
of 6 in the APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of APC11-Ubv Shows Role of Noncovalent Ring-Ubiquitin Interactions in Processive Multiubiquitination and Ubiquitin Chain Elongation By Apc/C within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn103
b:21.4
occ:1.00
|
ND1
|
D:HIS58
|
2.0
|
19.8
|
1.0
|
SG
|
D:CYS34
|
2.3
|
20.1
|
1.0
|
SG
|
D:CYS37
|
2.3
|
23.7
|
1.0
|
SG
|
D:CYS44
|
2.3
|
19.9
|
1.0
|
CE1
|
D:HIS58
|
2.9
|
20.4
|
1.0
|
CG
|
D:HIS58
|
3.2
|
22.1
|
1.0
|
CB
|
D:CYS34
|
3.3
|
15.4
|
1.0
|
CB
|
D:CYS44
|
3.3
|
15.6
|
1.0
|
CB
|
D:CYS37
|
3.3
|
27.1
|
1.0
|
CB
|
D:HIS58
|
3.6
|
13.7
|
1.0
|
N
|
D:CYS34
|
3.9
|
16.5
|
1.0
|
O
|
D:HOH218
|
3.9
|
43.4
|
1.0
|
O
|
D:HOH212
|
3.9
|
20.2
|
1.0
|
NE2
|
D:HIS58
|
4.1
|
22.5
|
1.0
|
N
|
D:CYS37
|
4.1
|
24.7
|
1.0
|
CA
|
D:CYS44
|
4.1
|
20.8
|
1.0
|
CA
|
D:CYS34
|
4.1
|
16.2
|
1.0
|
CD2
|
D:HIS58
|
4.2
|
24.1
|
1.0
|
CA
|
D:CYS37
|
4.3
|
30.9
|
1.0
|
C
|
D:CYS34
|
4.6
|
24.0
|
1.0
|
O
|
D:CYS34
|
4.6
|
20.3
|
1.0
|
O
|
D:ASP43
|
4.9
|
21.9
|
1.0
|
C
|
D:ASP36
|
5.0
|
32.1
|
1.0
|
CA
|
D:HIS58
|
5.0
|
16.8
|
1.0
|
|
Reference:
N.G.Brown,
R.Vanderlinden,
E.R.Watson,
F.Weissmann,
A.Ordureau,
K.P.Wu,
W.Zhang,
S.Yu,
P.Y.Mercredi,
J.S.Harrison,
I.F.Davidson,
R.Qiao,
Y.Lu,
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PubMed: 27259151
DOI: 10.1016/J.CELL.2016.05.037
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