Zinc in PDB 5ypc: P62/SQSTM1 Zz Domain with Phe-Peptide
Protein crystallography data
The structure of P62/SQSTM1 Zz Domain with Phe-Peptide, PDB code: 5ypc
was solved by
D.H.Kwon,
L.Kim,
H.K.Song,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.37 /
1.96
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
94.815,
46.290,
54.877,
90.00,
103.56,
90.00
|
R / Rfree (%)
|
20.2 /
23
|
Zinc Binding Sites:
The binding sites of Zinc atom in the P62/SQSTM1 Zz Domain with Phe-Peptide
(pdb code 5ypc). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
P62/SQSTM1 Zz Domain with Phe-Peptide, PDB code: 5ypc:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5ypc
Go back to
Zinc Binding Sites List in 5ypc
Zinc binding site 1 out
of 8 in the P62/SQSTM1 Zz Domain with Phe-Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of P62/SQSTM1 Zz Domain with Phe-Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn101
b:43.9
occ:1.00
|
SG
|
A:CYS4
|
2.3
|
38.4
|
1.0
|
SG
|
A:CYS30
|
2.3
|
43.0
|
1.0
|
SG
|
A:CYS27
|
2.4
|
41.5
|
1.0
|
SG
|
A:CYS7
|
2.5
|
49.9
|
1.0
|
HB2
|
A:CYS30
|
2.9
|
49.8
|
1.0
|
HB3
|
A:CYS7
|
3.1
|
57.4
|
1.0
|
HB3
|
A:CYS4
|
3.1
|
57.0
|
1.0
|
H
|
A:CYS27
|
3.2
|
44.9
|
1.0
|
H
|
A:CYS7
|
3.2
|
54.8
|
1.0
|
CB
|
A:CYS4
|
3.2
|
47.5
|
1.0
|
CB
|
A:CYS30
|
3.2
|
41.5
|
1.0
|
HB2
|
A:CYS4
|
3.4
|
57.0
|
1.0
|
CB
|
A:CYS7
|
3.4
|
47.9
|
1.0
|
H
|
A:CYS30
|
3.4
|
44.7
|
1.0
|
HB3
|
A:CYS27
|
3.5
|
52.2
|
1.0
|
CB
|
A:CYS27
|
3.6
|
43.5
|
1.0
|
N
|
A:CYS7
|
3.7
|
45.6
|
1.0
|
HB3
|
A:CYS30
|
3.9
|
49.8
|
1.0
|
N
|
A:CYS27
|
4.0
|
37.4
|
1.0
|
N
|
A:CYS30
|
4.1
|
37.2
|
1.0
|
HA3
|
A:GLY6
|
4.1
|
53.3
|
1.0
|
CA
|
A:CYS7
|
4.2
|
49.8
|
1.0
|
HB2
|
A:CYS7
|
4.2
|
57.4
|
1.0
|
H
|
A:GLY6
|
4.2
|
52.8
|
1.0
|
CA
|
A:CYS30
|
4.3
|
37.3
|
1.0
|
CA
|
A:CYS27
|
4.3
|
39.9
|
1.0
|
HB2
|
A:CYS27
|
4.3
|
52.2
|
1.0
|
HB
|
A:VAL29
|
4.4
|
57.1
|
1.0
|
H
|
A:GLY9
|
4.5
|
62.5
|
1.0
|
C
|
A:GLY6
|
4.6
|
45.8
|
1.0
|
HA
|
A:LEU26
|
4.6
|
43.2
|
1.0
|
HA
|
A:CYS30
|
4.7
|
44.8
|
1.0
|
CA
|
A:CYS4
|
4.7
|
39.2
|
1.0
|
CA
|
A:GLY6
|
4.7
|
44.4
|
1.0
|
O
|
A:CYS27
|
4.8
|
35.4
|
1.0
|
N
|
A:GLY6
|
4.8
|
44.0
|
1.0
|
HD22
|
A:LEU26
|
4.8
|
41.2
|
1.0
|
C
|
A:CYS27
|
4.8
|
35.8
|
1.0
|
H
|
A:ASN8
|
4.9
|
56.4
|
1.0
|
HA
|
A:CYS7
|
4.9
|
59.8
|
1.0
|
C
|
A:CYS7
|
4.9
|
52.1
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5ypc
Go back to
Zinc Binding Sites List in 5ypc
Zinc binding site 2 out
of 8 in the P62/SQSTM1 Zz Domain with Phe-Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of P62/SQSTM1 Zz Domain with Phe-Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn102
b:32.1
occ:1.00
|
ND1
|
A:HIS39
|
2.0
|
30.6
|
1.0
|
NE2
|
A:HIS36
|
2.0
|
33.0
|
1.0
|
SG
|
A:CYS18
|
2.2
|
30.0
|
1.0
|
SG
|
A:CYS21
|
2.3
|
32.9
|
1.0
|
CE1
|
A:HIS36
|
2.8
|
37.9
|
1.0
|
CE1
|
A:HIS39
|
2.9
|
34.3
|
1.0
|
HE1
|
A:HIS36
|
2.9
|
45.5
|
1.0
|
H
|
A:CYS21
|
2.9
|
38.7
|
1.0
|
HE1
|
A:HIS39
|
3.0
|
41.2
|
1.0
|
CG
|
A:HIS39
|
3.0
|
29.8
|
1.0
|
HB2
|
A:HIS39
|
3.1
|
36.7
|
1.0
|
HB2
|
A:CYS21
|
3.1
|
54.2
|
1.0
|
CD2
|
A:HIS36
|
3.2
|
34.9
|
1.0
|
CB
|
A:CYS21
|
3.3
|
45.2
|
1.0
|
HB2
|
A:CYS18
|
3.3
|
34.5
|
1.0
|
CB
|
A:CYS18
|
3.4
|
28.7
|
1.0
|
HB
|
A:VAL20
|
3.4
|
43.2
|
1.0
|
CB
|
A:HIS39
|
3.4
|
30.6
|
1.0
|
HD2
|
A:HIS36
|
3.4
|
41.9
|
1.0
|
HB3
|
A:HIS39
|
3.5
|
36.7
|
1.0
|
HB3
|
A:CYS18
|
3.6
|
34.5
|
1.0
|
N
|
A:CYS21
|
3.6
|
32.3
|
1.0
|
ND1
|
A:HIS36
|
4.0
|
31.7
|
1.0
|
NE2
|
A:HIS39
|
4.0
|
32.3
|
1.0
|
CA
|
A:CYS21
|
4.0
|
43.4
|
1.0
|
HB3
|
A:CYS21
|
4.1
|
54.2
|
1.0
|
CD2
|
A:HIS39
|
4.1
|
32.4
|
1.0
|
H
|
A:VAL20
|
4.2
|
38.0
|
1.0
|
CG
|
A:HIS36
|
4.2
|
36.1
|
1.0
|
HB3
|
A:TYR24
|
4.3
|
36.0
|
1.0
|
CB
|
A:VAL20
|
4.3
|
36.0
|
1.0
|
HA
|
A:CYS21
|
4.5
|
52.0
|
1.0
|
C
|
A:VAL20
|
4.6
|
37.6
|
1.0
|
HG12
|
A:VAL20
|
4.7
|
46.3
|
1.0
|
CA
|
A:CYS18
|
4.7
|
31.3
|
1.0
|
HD1
|
A:HIS36
|
4.8
|
38.0
|
1.0
|
HE2
|
A:HIS39
|
4.8
|
38.7
|
1.0
|
CA
|
A:VAL20
|
4.9
|
32.5
|
1.0
|
N
|
A:VAL20
|
4.9
|
31.7
|
1.0
|
HA
|
A:CYS18
|
4.9
|
37.6
|
1.0
|
HB2
|
A:TYR24
|
4.9
|
36.0
|
1.0
|
CB
|
A:TYR24
|
4.9
|
30.0
|
1.0
|
CA
|
A:HIS39
|
4.9
|
32.9
|
1.0
|
CG1
|
A:VAL20
|
5.0
|
38.5
|
1.0
|
CG
|
A:TYR24
|
5.0
|
34.3
|
1.0
|
HD1
|
A:TYR24
|
5.0
|
46.0
|
1.0
|
HD2
|
A:HIS39
|
5.0
|
38.9
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5ypc
Go back to
Zinc Binding Sites List in 5ypc
Zinc binding site 3 out
of 8 in the P62/SQSTM1 Zz Domain with Phe-Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of P62/SQSTM1 Zz Domain with Phe-Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn101
b:51.4
occ:1.00
|
SG
|
B:CYS30
|
2.1
|
49.6
|
1.0
|
SG
|
B:CYS4
|
2.4
|
42.8
|
1.0
|
SG
|
B:CYS27
|
2.4
|
45.7
|
1.0
|
SG
|
B:CYS7
|
2.4
|
55.3
|
1.0
|
HB3
|
B:CYS7
|
2.8
|
55.5
|
1.0
|
HB2
|
B:CYS30
|
3.0
|
61.0
|
1.0
|
H
|
B:CYS7
|
3.1
|
61.8
|
1.0
|
HB3
|
B:CYS4
|
3.2
|
50.2
|
1.0
|
CB
|
B:CYS7
|
3.2
|
46.2
|
1.0
|
CB
|
B:CYS30
|
3.2
|
50.8
|
1.0
|
H
|
B:CYS27
|
3.2
|
47.9
|
1.0
|
CB
|
B:CYS4
|
3.3
|
41.9
|
1.0
|
HB2
|
B:CYS4
|
3.4
|
50.2
|
1.0
|
H
|
B:CYS30
|
3.5
|
52.4
|
1.0
|
HB3
|
B:CYS27
|
3.5
|
47.8
|
1.0
|
O
|
B:HOH218
|
3.5
|
66.3
|
1.0
|
N
|
B:CYS7
|
3.6
|
51.5
|
1.0
|
CB
|
B:CYS27
|
3.6
|
39.8
|
1.0
|
HB3
|
B:CYS30
|
3.9
|
61.0
|
1.0
|
HB2
|
B:CYS7
|
4.0
|
55.5
|
1.0
|
CA
|
B:CYS7
|
4.0
|
50.8
|
1.0
|
N
|
B:CYS27
|
4.0
|
40.0
|
1.0
|
N
|
B:CYS30
|
4.1
|
43.7
|
1.0
|
H
|
B:GLY6
|
4.2
|
56.5
|
1.0
|
CA
|
B:CYS30
|
4.3
|
42.2
|
1.0
|
HA3
|
B:GLY6
|
4.3
|
59.4
|
1.0
|
CA
|
B:CYS27
|
4.4
|
36.8
|
1.0
|
HB2
|
B:CYS27
|
4.4
|
47.8
|
1.0
|
HB
|
B:VAL29
|
4.4
|
51.8
|
1.0
|
H
|
B:GLY9
|
4.5
|
67.9
|
1.0
|
C
|
B:GLY6
|
4.5
|
48.5
|
1.0
|
HA
|
B:LEU26
|
4.6
|
43.0
|
1.0
|
HA
|
B:CYS30
|
4.7
|
50.7
|
1.0
|
CA
|
B:CYS4
|
4.7
|
40.5
|
1.0
|
CA
|
B:GLY6
|
4.7
|
49.5
|
1.0
|
HA
|
B:CYS7
|
4.8
|
61.0
|
1.0
|
C
|
B:CYS7
|
4.8
|
56.7
|
1.0
|
N
|
B:GLY6
|
4.8
|
47.0
|
1.0
|
HD22
|
B:LEU26
|
4.9
|
47.5
|
1.0
|
C
|
B:CYS27
|
4.9
|
36.8
|
1.0
|
O
|
B:CYS27
|
4.9
|
37.5
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5ypc
Go back to
Zinc Binding Sites List in 5ypc
Zinc binding site 4 out
of 8 in the P62/SQSTM1 Zz Domain with Phe-Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of P62/SQSTM1 Zz Domain with Phe-Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn102
b:31.8
occ:1.00
|
ND1
|
B:HIS39
|
2.0
|
29.9
|
1.0
|
NE2
|
B:HIS36
|
2.0
|
33.2
|
1.0
|
SG
|
B:CYS18
|
2.2
|
28.0
|
1.0
|
SG
|
B:CYS21
|
2.4
|
35.4
|
1.0
|
H
|
B:CYS21
|
2.9
|
44.3
|
1.0
|
CE1
|
B:HIS36
|
3.0
|
36.2
|
1.0
|
CE1
|
B:HIS39
|
3.0
|
35.4
|
1.0
|
HB2
|
B:CYS21
|
3.0
|
47.5
|
1.0
|
CG
|
B:HIS39
|
3.0
|
34.7
|
1.0
|
HE1
|
B:HIS36
|
3.1
|
43.5
|
1.0
|
CD2
|
B:HIS36
|
3.1
|
32.0
|
1.0
|
HB2
|
B:HIS39
|
3.1
|
34.5
|
1.0
|
HE1
|
B:HIS39
|
3.1
|
42.5
|
1.0
|
CB
|
B:CYS21
|
3.2
|
39.5
|
1.0
|
HD2
|
B:HIS36
|
3.3
|
38.4
|
1.0
|
HB2
|
B:CYS18
|
3.4
|
34.4
|
1.0
|
CB
|
B:CYS18
|
3.4
|
28.7
|
1.0
|
HB3
|
B:HIS39
|
3.4
|
34.5
|
1.0
|
CB
|
B:HIS39
|
3.4
|
28.8
|
1.0
|
HB
|
B:VAL20
|
3.5
|
48.2
|
1.0
|
HB3
|
B:CYS18
|
3.6
|
34.4
|
1.0
|
N
|
B:CYS21
|
3.6
|
36.9
|
1.0
|
CA
|
B:CYS21
|
4.0
|
39.5
|
1.0
|
HB3
|
B:CYS21
|
4.0
|
47.5
|
1.0
|
NE2
|
B:HIS39
|
4.1
|
33.0
|
1.0
|
ND1
|
B:HIS36
|
4.1
|
33.2
|
1.0
|
CD2
|
B:HIS39
|
4.1
|
30.3
|
1.0
|
HB3
|
B:TYR24
|
4.2
|
46.2
|
1.0
|
CG
|
B:HIS36
|
4.2
|
34.1
|
1.0
|
H
|
B:VAL20
|
4.2
|
42.5
|
1.0
|
HA
|
B:CYS21
|
4.4
|
47.3
|
1.0
|
CB
|
B:VAL20
|
4.5
|
40.2
|
1.0
|
C
|
B:VAL20
|
4.7
|
39.1
|
1.0
|
CA
|
B:CYS18
|
4.7
|
33.5
|
1.0
|
HB2
|
B:TYR24
|
4.8
|
46.2
|
1.0
|
HA
|
B:CYS18
|
4.8
|
40.2
|
1.0
|
CB
|
B:TYR24
|
4.8
|
38.5
|
1.0
|
HD1
|
B:HIS36
|
4.9
|
39.9
|
1.0
|
HE2
|
B:HIS39
|
4.9
|
39.6
|
1.0
|
CA
|
B:HIS39
|
4.9
|
33.3
|
1.0
|
N
|
B:VAL20
|
4.9
|
35.4
|
1.0
|
HD1
|
B:TYR24
|
4.9
|
42.2
|
1.0
|
CG
|
B:TYR24
|
4.9
|
34.1
|
1.0
|
CA
|
B:VAL20
|
4.9
|
38.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5ypc
Go back to
Zinc Binding Sites List in 5ypc
Zinc binding site 5 out
of 8 in the P62/SQSTM1 Zz Domain with Phe-Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of P62/SQSTM1 Zz Domain with Phe-Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn101
b:33.5
occ:1.00
|
SG
|
C:CYS4
|
2.3
|
32.0
|
1.0
|
SG
|
C:CYS7
|
2.3
|
35.4
|
1.0
|
SG
|
C:CYS30
|
2.4
|
34.4
|
1.0
|
SG
|
C:CYS27
|
2.4
|
33.0
|
1.0
|
HB2
|
C:CYS30
|
2.9
|
34.8
|
1.0
|
HB3
|
C:CYS7
|
3.0
|
43.6
|
1.0
|
H
|
C:CYS7
|
3.0
|
46.6
|
1.0
|
HB3
|
C:CYS4
|
3.1
|
39.3
|
1.0
|
H
|
C:CYS27
|
3.2
|
35.2
|
1.0
|
CB
|
C:CYS7
|
3.2
|
36.3
|
1.0
|
CB
|
C:CYS4
|
3.2
|
32.7
|
1.0
|
CB
|
C:CYS30
|
3.3
|
29.0
|
1.0
|
HB2
|
C:CYS4
|
3.4
|
39.3
|
1.0
|
H
|
C:CYS30
|
3.5
|
35.8
|
1.0
|
N
|
C:CYS7
|
3.5
|
38.9
|
1.0
|
HB3
|
C:CYS27
|
3.5
|
41.5
|
1.0
|
CB
|
C:CYS27
|
3.6
|
34.6
|
1.0
|
HB3
|
C:CYS30
|
3.9
|
34.8
|
1.0
|
HA3
|
C:GLY6
|
3.9
|
33.5
|
1.0
|
CA
|
C:CYS7
|
4.0
|
34.1
|
1.0
|
N
|
C:CYS27
|
4.0
|
29.3
|
1.0
|
HB2
|
C:CYS7
|
4.0
|
43.6
|
1.0
|
H
|
C:GLY6
|
4.1
|
30.9
|
1.0
|
N
|
C:CYS30
|
4.1
|
29.8
|
1.0
|
CA
|
C:CYS30
|
4.3
|
33.5
|
1.0
|
CA
|
C:CYS27
|
4.3
|
31.1
|
1.0
|
C
|
C:GLY6
|
4.4
|
37.7
|
1.0
|
HB
|
C:VAL29
|
4.4
|
40.3
|
1.0
|
HB2
|
C:CYS27
|
4.4
|
41.5
|
1.0
|
CA
|
C:GLY6
|
4.5
|
28.0
|
1.0
|
H
|
C:GLY9
|
4.5
|
41.6
|
1.0
|
HA
|
C:LEU26
|
4.6
|
31.7
|
1.0
|
HD22
|
C:LEU26
|
4.6
|
36.8
|
1.0
|
N
|
C:GLY6
|
4.6
|
25.8
|
1.0
|
CA
|
C:CYS4
|
4.6
|
33.4
|
1.0
|
HA
|
C:CYS30
|
4.7
|
40.2
|
1.0
|
H
|
C:ASN8
|
4.7
|
41.2
|
1.0
|
HA
|
C:CYS7
|
4.7
|
40.9
|
1.0
|
C
|
C:CYS7
|
4.8
|
37.8
|
1.0
|
O
|
C:CYS27
|
4.8
|
26.7
|
1.0
|
C
|
C:CYS27
|
4.9
|
27.7
|
1.0
|
C
|
C:CYS4
|
5.0
|
37.3
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5ypc
Go back to
Zinc Binding Sites List in 5ypc
Zinc binding site 6 out
of 8 in the P62/SQSTM1 Zz Domain with Phe-Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of P62/SQSTM1 Zz Domain with Phe-Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn102
b:32.8
occ:1.00
|
NE2
|
C:HIS36
|
2.0
|
31.4
|
1.0
|
ND1
|
C:HIS39
|
2.1
|
29.1
|
1.0
|
SG
|
C:CYS18
|
2.2
|
30.6
|
1.0
|
SG
|
C:CYS21
|
2.3
|
36.4
|
1.0
|
CE1
|
C:HIS36
|
2.9
|
31.6
|
1.0
|
H
|
C:CYS21
|
3.0
|
42.8
|
1.0
|
CE1
|
C:HIS39
|
3.0
|
36.0
|
1.0
|
HE1
|
C:HIS36
|
3.0
|
38.0
|
1.0
|
CD2
|
C:HIS36
|
3.1
|
29.8
|
1.0
|
HB2
|
C:CYS21
|
3.1
|
45.3
|
1.0
|
HE1
|
C:HIS39
|
3.1
|
43.3
|
1.0
|
CG
|
C:HIS39
|
3.2
|
37.2
|
1.0
|
HB2
|
C:HIS39
|
3.3
|
36.9
|
1.0
|
CB
|
C:CYS21
|
3.3
|
37.8
|
1.0
|
HB
|
C:VAL20
|
3.3
|
42.0
|
1.0
|
HD2
|
C:HIS36
|
3.3
|
35.8
|
1.0
|
CB
|
C:CYS18
|
3.4
|
34.5
|
1.0
|
HB2
|
C:CYS18
|
3.4
|
41.4
|
1.0
|
HB3
|
C:CYS18
|
3.6
|
41.4
|
1.0
|
CB
|
C:HIS39
|
3.6
|
30.7
|
1.0
|
HB3
|
C:HIS39
|
3.6
|
36.9
|
1.0
|
N
|
C:CYS21
|
3.6
|
35.6
|
1.0
|
ND1
|
C:HIS36
|
4.0
|
30.4
|
1.0
|
CA
|
C:CYS21
|
4.1
|
39.2
|
1.0
|
HB3
|
C:CYS21
|
4.1
|
45.3
|
1.0
|
H
|
C:VAL20
|
4.1
|
38.2
|
1.0
|
CG
|
C:HIS36
|
4.1
|
33.3
|
1.0
|
NE2
|
C:HIS39
|
4.2
|
36.0
|
1.0
|
CB
|
C:VAL20
|
4.3
|
35.0
|
1.0
|
CD2
|
C:HIS39
|
4.3
|
38.0
|
1.0
|
HB3
|
C:TYR24
|
4.5
|
40.2
|
1.0
|
HA
|
C:CYS21
|
4.5
|
47.0
|
1.0
|
HG12
|
C:VAL20
|
4.6
|
48.4
|
1.0
|
C
|
C:VAL20
|
4.7
|
37.1
|
1.0
|
CA
|
C:CYS18
|
4.7
|
30.4
|
1.0
|
HD1
|
C:HIS36
|
4.8
|
36.5
|
1.0
|
CA
|
C:VAL20
|
4.8
|
34.7
|
1.0
|
N
|
C:VAL20
|
4.8
|
31.9
|
1.0
|
HA
|
C:CYS18
|
4.8
|
36.5
|
1.0
|
CG1
|
C:VAL20
|
4.9
|
40.3
|
1.0
|
HG11
|
C:VAL20
|
4.9
|
48.4
|
1.0
|
HE2
|
C:HIS39
|
4.9
|
43.2
|
1.0
|
HD1
|
C:TYR24
|
5.0
|
34.0
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5ypc
Go back to
Zinc Binding Sites List in 5ypc
Zinc binding site 7 out
of 8 in the P62/SQSTM1 Zz Domain with Phe-Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of P62/SQSTM1 Zz Domain with Phe-Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn101
b:36.9
occ:1.00
|
SG
|
D:CYS30
|
2.2
|
34.6
|
1.0
|
SG
|
D:CYS4
|
2.3
|
33.8
|
1.0
|
SG
|
D:CYS7
|
2.4
|
38.1
|
1.0
|
SG
|
D:CYS27
|
2.5
|
39.4
|
1.0
|
HB3
|
D:CYS7
|
2.8
|
41.8
|
1.0
|
HB2
|
D:CYS30
|
3.1
|
42.2
|
1.0
|
HB3
|
D:CYS4
|
3.2
|
47.8
|
1.0
|
CB
|
D:CYS7
|
3.2
|
34.8
|
1.0
|
H
|
D:CYS27
|
3.2
|
43.5
|
1.0
|
CB
|
D:CYS4
|
3.3
|
39.8
|
1.0
|
H
|
D:CYS7
|
3.3
|
44.3
|
1.0
|
CB
|
D:CYS30
|
3.3
|
35.1
|
1.0
|
HB2
|
D:CYS4
|
3.4
|
47.8
|
1.0
|
H
|
D:CYS30
|
3.5
|
48.3
|
1.0
|
HB3
|
D:CYS27
|
3.5
|
47.0
|
1.0
|
CB
|
D:CYS27
|
3.6
|
39.2
|
1.0
|
N
|
D:CYS7
|
3.6
|
36.9
|
1.0
|
HB3
|
D:CYS30
|
3.9
|
42.2
|
1.0
|
HB2
|
D:CYS7
|
4.0
|
41.8
|
1.0
|
CA
|
D:CYS7
|
4.0
|
43.4
|
1.0
|
N
|
D:CYS27
|
4.0
|
36.3
|
1.0
|
N
|
D:CYS30
|
4.2
|
40.2
|
1.0
|
H
|
D:GLY6
|
4.2
|
41.8
|
1.0
|
HA3
|
D:GLY6
|
4.2
|
45.2
|
1.0
|
CA
|
D:CYS27
|
4.3
|
32.0
|
1.0
|
CA
|
D:CYS30
|
4.3
|
33.0
|
1.0
|
C
|
D:GLY6
|
4.4
|
31.6
|
1.0
|
HB2
|
D:CYS27
|
4.4
|
47.0
|
1.0
|
H
|
D:GLY9
|
4.4
|
49.6
|
1.0
|
HB
|
D:VAL29
|
4.4
|
49.6
|
1.0
|
HA
|
D:LEU26
|
4.6
|
43.5
|
1.0
|
CA
|
D:GLY6
|
4.6
|
37.7
|
1.0
|
CA
|
D:CYS4
|
4.7
|
36.9
|
1.0
|
HD22
|
D:LEU26
|
4.7
|
44.1
|
1.0
|
HA
|
D:CYS30
|
4.7
|
39.5
|
1.0
|
HA
|
D:CYS7
|
4.8
|
52.1
|
1.0
|
N
|
D:GLY6
|
4.8
|
34.8
|
1.0
|
O
|
D:CYS27
|
4.8
|
30.6
|
1.0
|
C
|
D:CYS7
|
4.8
|
41.2
|
1.0
|
C
|
D:CYS27
|
4.8
|
33.6
|
1.0
|
H
|
D:ASN8
|
4.8
|
41.6
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5ypc
Go back to
Zinc Binding Sites List in 5ypc
Zinc binding site 8 out
of 8 in the P62/SQSTM1 Zz Domain with Phe-Peptide
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of P62/SQSTM1 Zz Domain with Phe-Peptide within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn102
b:35.5
occ:1.00
|
NE2
|
D:HIS36
|
1.9
|
37.8
|
1.0
|
ND1
|
D:HIS39
|
2.1
|
37.2
|
1.0
|
SG
|
D:CYS21
|
2.2
|
35.9
|
1.0
|
SG
|
D:CYS18
|
2.3
|
33.2
|
1.0
|
CE1
|
D:HIS36
|
2.7
|
35.8
|
1.0
|
HE1
|
D:HIS36
|
2.7
|
43.0
|
1.0
|
H
|
D:CYS21
|
3.0
|
39.9
|
1.0
|
CE1
|
D:HIS39
|
3.0
|
44.1
|
1.0
|
HE1
|
D:HIS39
|
3.1
|
53.0
|
1.0
|
CD2
|
D:HIS36
|
3.1
|
38.8
|
1.0
|
CG
|
D:HIS39
|
3.2
|
40.2
|
1.0
|
HB2
|
D:CYS21
|
3.2
|
48.3
|
1.0
|
HB2
|
D:HIS39
|
3.2
|
46.8
|
1.0
|
CB
|
D:CYS21
|
3.3
|
40.3
|
1.0
|
HB2
|
D:CYS18
|
3.5
|
34.4
|
1.0
|
HD2
|
D:HIS36
|
3.5
|
46.6
|
1.0
|
CB
|
D:CYS18
|
3.5
|
28.7
|
1.0
|
HB
|
D:VAL20
|
3.5
|
62.7
|
1.0
|
CB
|
D:HIS39
|
3.5
|
39.0
|
1.0
|
HB3
|
D:HIS39
|
3.6
|
46.8
|
1.0
|
N
|
D:CYS21
|
3.7
|
33.2
|
1.0
|
HB3
|
D:CYS18
|
3.7
|
34.4
|
1.0
|
ND1
|
D:HIS36
|
3.9
|
37.4
|
1.0
|
HB3
|
D:CYS21
|
4.1
|
48.3
|
1.0
|
CG
|
D:HIS36
|
4.1
|
36.6
|
1.0
|
CA
|
D:CYS21
|
4.1
|
38.1
|
1.0
|
H
|
D:VAL20
|
4.1
|
40.0
|
1.0
|
NE2
|
D:HIS39
|
4.1
|
44.1
|
1.0
|
CD2
|
D:HIS39
|
4.2
|
44.7
|
1.0
|
CB
|
D:VAL20
|
4.4
|
52.3
|
1.0
|
HD1
|
D:HIS36
|
4.6
|
44.9
|
1.0
|
HA
|
D:CYS21
|
4.7
|
45.8
|
1.0
|
C
|
D:VAL20
|
4.7
|
46.3
|
1.0
|
HB3
|
D:TYR24
|
4.7
|
39.2
|
1.0
|
CA
|
D:CYS18
|
4.8
|
30.2
|
1.0
|
N
|
D:VAL20
|
4.9
|
33.3
|
1.0
|
CA
|
D:VAL20
|
4.9
|
35.6
|
1.0
|
HE2
|
D:HIS39
|
4.9
|
52.9
|
1.0
|
HA
|
D:CYS18
|
4.9
|
36.2
|
1.0
|
|
Reference:
D.H.Kwon,
O.H.Park,
L.Kim,
Y.O.Jung,
Y.Park,
H.Jeong,
J.Hyun,
Y.K.Kim,
H.K.Song.
Insights Into Degradation Mechanism of N-End Rule Substrates By P62/SQSTM1 Autophagy Adapter. Nat Commun V. 9 3291 2018.
ISSN: ESSN 2041-1723
PubMed: 30120248
DOI: 10.1038/S41467-018-05825-X
Page generated: Mon Oct 28 16:07:05 2024
|