Zinc in PDB 8jav: Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
(pdb code 8jav). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer), PDB code: 8jav:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 8jav
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Zinc Binding Sites List in 8jav
Zinc binding site 1 out
of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn601
b:54.2
occ:1.00
|
NE2
|
B:HIS89
|
2.0
|
29.2
|
1.0
|
NE2
|
A:HIS89
|
2.0
|
14.5
|
1.0
|
SG
|
A:CYS54
|
2.3
|
13.3
|
1.0
|
SG
|
B:CYS54
|
2.3
|
38.6
|
1.0
|
CE1
|
A:HIS89
|
2.8
|
14.5
|
1.0
|
CE1
|
B:HIS89
|
3.0
|
29.2
|
1.0
|
CD2
|
B:HIS89
|
3.0
|
29.2
|
1.0
|
CD2
|
A:HIS89
|
3.0
|
14.5
|
1.0
|
CB
|
A:CYS54
|
3.5
|
13.3
|
1.0
|
O
|
B:LEU53
|
3.5
|
34.0
|
1.0
|
CB
|
B:CYS54
|
3.7
|
38.6
|
1.0
|
CA
|
A:CYS54
|
3.8
|
13.3
|
1.0
|
ND1
|
A:HIS89
|
3.9
|
14.5
|
1.0
|
CG
|
A:HIS89
|
4.0
|
14.5
|
1.0
|
CA
|
B:CYS54
|
4.1
|
38.6
|
1.0
|
ND1
|
B:HIS89
|
4.1
|
29.2
|
1.0
|
CG
|
B:HIS89
|
4.1
|
29.2
|
1.0
|
N
|
A:CYS54
|
4.2
|
13.3
|
1.0
|
CG2
|
A:VAL91
|
4.3
|
20.9
|
1.0
|
C
|
B:LEU53
|
4.4
|
34.0
|
1.0
|
N
|
B:CYS54
|
4.7
|
38.6
|
1.0
|
C
|
A:LEU53
|
4.8
|
13.7
|
1.0
|
O
|
A:LEU53
|
4.9
|
13.7
|
1.0
|
|
Zinc binding site 2 out
of 8 in 8jav
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Zinc Binding Sites List in 8jav
Zinc binding site 2 out
of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Zn200
b:46.3
occ:1.00
|
ND1
|
R:HIS82
|
2.0
|
34.9
|
1.0
|
SG
|
R:CYS53
|
2.3
|
35.9
|
1.0
|
SG
|
R:CYS68
|
2.3
|
40.3
|
1.0
|
SG
|
R:CYS56
|
2.3
|
43.5
|
1.0
|
CE1
|
R:HIS82
|
2.7
|
34.9
|
1.0
|
CG
|
R:HIS82
|
3.2
|
34.9
|
1.0
|
CB
|
R:CYS68
|
3.3
|
40.3
|
1.0
|
CB
|
R:CYS56
|
3.3
|
43.5
|
1.0
|
CB
|
R:CYS53
|
3.3
|
35.9
|
1.0
|
N
|
R:CYS53
|
3.7
|
35.9
|
1.0
|
NE2
|
R:HIS82
|
3.8
|
34.9
|
1.0
|
CB
|
R:HIS82
|
3.8
|
34.9
|
1.0
|
CA
|
R:CYS68
|
3.9
|
40.3
|
1.0
|
N
|
R:CYS56
|
4.0
|
43.5
|
1.0
|
CA
|
R:CYS53
|
4.1
|
35.9
|
1.0
|
CD2
|
R:HIS82
|
4.1
|
34.9
|
1.0
|
CA
|
R:CYS56
|
4.2
|
43.5
|
1.0
|
C
|
R:CYS53
|
4.7
|
35.9
|
1.0
|
O
|
R:CYS53
|
4.7
|
35.9
|
1.0
|
N
|
R:CYS68
|
4.8
|
40.3
|
1.0
|
C
|
R:LEU52
|
4.8
|
35.6
|
1.0
|
C
|
R:CYS68
|
5.0
|
40.3
|
1.0
|
|
Zinc binding site 3 out
of 8 in 8jav
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Zinc Binding Sites List in 8jav
Zinc binding site 3 out
of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Zn201
b:36.2
occ:1.00
|
ND1
|
R:HIS80
|
2.1
|
28.1
|
1.0
|
SG
|
R:CYS45
|
2.3
|
26.8
|
1.0
|
SG
|
R:CYS83
|
2.3
|
30.5
|
1.0
|
SG
|
R:CYS42
|
2.3
|
27.2
|
1.0
|
CG
|
R:HIS80
|
2.9
|
28.1
|
1.0
|
CB
|
R:CYS42
|
3.0
|
27.2
|
1.0
|
CB
|
R:HIS80
|
3.0
|
28.1
|
1.0
|
CB
|
R:CYS45
|
3.2
|
26.8
|
1.0
|
CE1
|
R:HIS80
|
3.2
|
28.1
|
1.0
|
CB
|
R:CYS83
|
3.2
|
30.5
|
1.0
|
CB
|
R:CYS53
|
3.8
|
35.9
|
1.0
|
N
|
R:CYS45
|
4.1
|
26.8
|
1.0
|
CD2
|
R:HIS80
|
4.1
|
28.1
|
1.0
|
CA
|
R:CYS53
|
4.2
|
35.9
|
1.0
|
NE2
|
R:HIS80
|
4.2
|
28.1
|
1.0
|
CA
|
R:CYS45
|
4.2
|
26.8
|
1.0
|
N
|
R:HIS80
|
4.2
|
28.1
|
1.0
|
CA
|
R:HIS80
|
4.2
|
28.1
|
1.0
|
CA
|
R:CYS42
|
4.5
|
27.2
|
1.0
|
CA
|
R:CYS83
|
4.6
|
30.5
|
1.0
|
O
|
R:CYS42
|
4.6
|
27.2
|
1.0
|
N
|
R:ILE54
|
4.7
|
37.2
|
1.0
|
C
|
R:CYS42
|
4.8
|
27.2
|
1.0
|
C
|
R:CYS45
|
4.9
|
26.8
|
1.0
|
N
|
R:CYS83
|
4.9
|
30.5
|
1.0
|
|
Zinc binding site 4 out
of 8 in 8jav
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Zinc Binding Sites List in 8jav
Zinc binding site 4 out
of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
R:Zn202
b:45.1
occ:1.00
|
SG
|
R:CYS75
|
2.3
|
34.6
|
1.0
|
SG
|
R:CYS94
|
2.3
|
29.3
|
1.0
|
ND1
|
R:HIS77
|
2.3
|
31.1
|
1.0
|
CE1
|
R:HIS77
|
3.1
|
31.1
|
1.0
|
CG
|
R:HIS77
|
3.2
|
31.1
|
1.0
|
CB
|
R:ASP97
|
3.3
|
34.5
|
1.0
|
CB
|
R:CYS94
|
3.3
|
29.3
|
1.0
|
CB
|
R:CYS75
|
3.3
|
34.6
|
1.0
|
N
|
R:ASP97
|
3.5
|
34.5
|
1.0
|
CB
|
R:HIS77
|
3.5
|
31.1
|
1.0
|
O
|
R:ASP97
|
3.7
|
34.5
|
1.0
|
CA
|
R:ASP97
|
3.8
|
34.5
|
1.0
|
NE2
|
R:HIS77
|
4.1
|
31.1
|
1.0
|
CD2
|
R:HIS77
|
4.1
|
31.1
|
1.0
|
C
|
R:ASP97
|
4.2
|
34.5
|
1.0
|
CB
|
R:LEU96
|
4.4
|
31.3
|
1.0
|
C
|
R:LEU96
|
4.6
|
31.3
|
1.0
|
CG
|
R:ASP97
|
4.6
|
34.5
|
1.0
|
CA
|
R:CYS75
|
4.7
|
34.6
|
1.0
|
CA
|
R:CYS94
|
4.7
|
29.3
|
1.0
|
O
|
R:CYS75
|
4.7
|
34.6
|
1.0
|
N
|
R:LEU96
|
4.8
|
31.3
|
1.0
|
CZ3
|
R:TRP101
|
4.8
|
30.5
|
1.0
|
C
|
R:CYS75
|
4.8
|
34.6
|
1.0
|
CA
|
R:LEU96
|
4.8
|
31.3
|
1.0
|
CA
|
R:HIS77
|
4.9
|
31.1
|
1.0
|
C
|
R:CYS94
|
4.9
|
29.3
|
1.0
|
OD2
|
R:ASP97
|
5.0
|
34.5
|
1.0
|
|
Zinc binding site 5 out
of 8 in 8jav
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Zinc Binding Sites List in 8jav
Zinc binding site 5 out
of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_05.jpg) Mono view
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_05_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
J:Zn601
b:48.2
occ:1.00
|
NE2
|
K:HIS89
|
2.0
|
25.6
|
1.0
|
NE2
|
J:HIS89
|
2.0
|
18.7
|
1.0
|
SG
|
J:CYS54
|
2.3
|
9.9
|
1.0
|
SG
|
K:CYS54
|
2.3
|
27.9
|
1.0
|
CE1
|
K:HIS89
|
2.6
|
25.6
|
1.0
|
CE1
|
J:HIS89
|
2.8
|
18.7
|
1.0
|
CD2
|
J:HIS89
|
3.1
|
18.7
|
1.0
|
CD2
|
K:HIS89
|
3.3
|
25.6
|
1.0
|
CB
|
K:CYS54
|
3.6
|
27.9
|
1.0
|
CB
|
J:CYS54
|
3.6
|
9.9
|
1.0
|
ND1
|
K:HIS89
|
3.8
|
25.6
|
1.0
|
CA
|
J:CYS54
|
3.8
|
9.9
|
1.0
|
CA
|
K:CYS54
|
3.8
|
27.9
|
1.0
|
ND1
|
J:HIS89
|
3.9
|
18.7
|
1.0
|
CG
|
J:HIS89
|
4.1
|
18.7
|
1.0
|
CG
|
K:HIS89
|
4.2
|
25.6
|
1.0
|
N
|
J:CYS54
|
4.3
|
9.9
|
1.0
|
N
|
K:CYS54
|
4.3
|
27.9
|
1.0
|
C
|
J:LEU53
|
4.9
|
15.4
|
1.0
|
C
|
K:LEU53
|
5.0
|
25.6
|
1.0
|
|
Zinc binding site 6 out
of 8 in 8jav
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Zinc Binding Sites List in 8jav
Zinc binding site 6 out
of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_06.jpg) Mono view
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_06_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Zn200
b:79.5
occ:1.00
|
ND1
|
V:HIS82
|
2.1
|
70.7
|
1.0
|
SG
|
V:CYS53
|
2.3
|
72.2
|
1.0
|
SG
|
V:CYS68
|
2.3
|
75.9
|
1.0
|
SG
|
V:CYS56
|
2.3
|
78.9
|
1.0
|
CG
|
V:HIS82
|
2.8
|
70.7
|
1.0
|
CB
|
V:HIS82
|
2.8
|
70.7
|
1.0
|
CB
|
V:CYS56
|
3.1
|
78.9
|
1.0
|
CB
|
V:CYS53
|
3.2
|
72.2
|
1.0
|
CE1
|
V:HIS82
|
3.2
|
70.7
|
1.0
|
CB
|
V:CYS68
|
3.3
|
75.9
|
1.0
|
N
|
V:CYS56
|
3.9
|
78.9
|
1.0
|
N
|
V:CYS53
|
3.9
|
72.2
|
1.0
|
CD2
|
V:HIS82
|
4.0
|
70.7
|
1.0
|
CA
|
V:CYS56
|
4.0
|
78.9
|
1.0
|
CA
|
V:CYS53
|
4.1
|
72.2
|
1.0
|
CA
|
V:CYS68
|
4.2
|
75.9
|
1.0
|
NE2
|
V:HIS82
|
4.2
|
70.7
|
1.0
|
CA
|
V:HIS82
|
4.2
|
70.7
|
1.0
|
N
|
V:HIS82
|
4.6
|
70.7
|
1.0
|
C
|
V:CYS53
|
4.7
|
72.2
|
1.0
|
O
|
V:CYS53
|
4.8
|
72.2
|
1.0
|
C
|
V:GLU55
|
4.9
|
74.9
|
1.0
|
C
|
V:HIS82
|
4.9
|
70.7
|
1.0
|
|
Zinc binding site 7 out
of 8 in 8jav
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Zinc Binding Sites List in 8jav
Zinc binding site 7 out
of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_07.jpg) Mono view
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_07_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Zn201
b:67.2
occ:1.00
|
ND1
|
V:HIS80
|
2.1
|
62.4
|
1.0
|
SG
|
V:CYS45
|
2.3
|
55.6
|
1.0
|
SG
|
V:CYS83
|
2.3
|
64.5
|
1.0
|
SG
|
V:CYS42
|
2.3
|
57.3
|
1.0
|
CG
|
V:HIS80
|
2.9
|
62.4
|
1.0
|
CB
|
V:CYS45
|
3.1
|
55.6
|
1.0
|
CB
|
V:HIS80
|
3.1
|
62.4
|
1.0
|
CE1
|
V:HIS80
|
3.2
|
62.4
|
1.0
|
CB
|
V:CYS42
|
3.2
|
57.3
|
1.0
|
CB
|
V:CYS83
|
3.3
|
64.5
|
1.0
|
CB
|
V:CYS53
|
4.0
|
72.2
|
1.0
|
N
|
V:CYS45
|
4.0
|
55.6
|
1.0
|
CD2
|
V:HIS80
|
4.1
|
62.4
|
1.0
|
N
|
V:HIS80
|
4.1
|
62.4
|
1.0
|
CA
|
V:CYS45
|
4.1
|
55.6
|
1.0
|
NE2
|
V:HIS80
|
4.2
|
62.4
|
1.0
|
CA
|
V:HIS80
|
4.2
|
62.4
|
1.0
|
CA
|
V:CYS53
|
4.3
|
72.2
|
1.0
|
CA
|
V:CYS42
|
4.6
|
57.3
|
1.0
|
O
|
V:CYS42
|
4.6
|
57.3
|
1.0
|
CA
|
V:CYS83
|
4.7
|
64.5
|
1.0
|
C
|
V:CYS42
|
4.8
|
57.3
|
1.0
|
C
|
V:CYS45
|
4.9
|
55.6
|
1.0
|
N
|
V:ILE54
|
4.9
|
71.9
|
1.0
|
|
Zinc binding site 8 out
of 8 in 8jav
Go back to
Zinc Binding Sites List in 8jav
Zinc binding site 8 out
of 8 in the Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer)
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_08.jpg) Mono view
![](/pictures/ZN/pdb/ja/8jav-ZN-sphere_08_stereo.jpg) Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of CRL2APPBP2 Bound with the C-Degron of MRPL28 (Tetramer) within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
V:Zn202
b:79.2
occ:1.00
|
OD1
|
V:ASP97
|
2.1
|
71.2
|
1.0
|
SG
|
V:CYS75
|
2.3
|
74.3
|
1.0
|
SG
|
V:CYS94
|
2.3
|
63.8
|
1.0
|
ND1
|
V:HIS77
|
2.3
|
69.6
|
1.0
|
CG
|
V:HIS77
|
2.9
|
69.6
|
1.0
|
CB
|
V:HIS77
|
2.9
|
69.6
|
1.0
|
CG
|
V:ASP97
|
3.0
|
71.2
|
1.0
|
CB
|
V:CYS75
|
3.2
|
74.3
|
1.0
|
OD2
|
V:ASP97
|
3.3
|
71.2
|
1.0
|
CE1
|
V:HIS77
|
3.4
|
69.6
|
1.0
|
CB
|
V:CYS94
|
3.4
|
63.8
|
1.0
|
CD2
|
V:HIS77
|
4.1
|
69.6
|
1.0
|
N
|
V:ASP97
|
4.1
|
71.2
|
1.0
|
CA
|
V:HIS77
|
4.2
|
69.6
|
1.0
|
NE2
|
V:HIS77
|
4.3
|
69.6
|
1.0
|
O
|
V:CYS75
|
4.3
|
74.3
|
1.0
|
N
|
V:HIS77
|
4.4
|
69.6
|
1.0
|
CB
|
V:LEU96
|
4.4
|
66.0
|
1.0
|
CB
|
V:ASP97
|
4.4
|
71.2
|
1.0
|
O
|
V:ASP97
|
4.4
|
71.2
|
1.0
|
CA
|
V:CYS75
|
4.4
|
74.3
|
1.0
|
C
|
V:CYS75
|
4.5
|
74.3
|
1.0
|
CA
|
V:ASP97
|
4.8
|
71.2
|
1.0
|
CA
|
V:CYS94
|
4.8
|
63.8
|
1.0
|
O
|
V:HIS77
|
4.9
|
69.6
|
1.0
|
CZ3
|
V:TRP101
|
5.0
|
65.5
|
1.0
|
CZ
|
V:PHE79
|
5.0
|
59.5
|
1.0
|
N
|
V:LEU96
|
5.0
|
66.0
|
1.0
|
|
Reference:
S.Zhao,
K.Zhang,
C.Xu.
Molecular Basis For CRL2APPBP2-Mediated C-Degron Recognition To Be Published.
Page generated: Thu Dec 28 13:21:36 2023
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