Zinc in PDB 8i3x: Rice APIP6-Ring Homodimer
Protein crystallography data
The structure of Rice APIP6-Ring Homodimer, PDB code: 8i3x
was solved by
Y.Zheng,
X.Zhang,
Y.Liu,
J.Liu,
D.Wang,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.64 /
1.78
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
34.239,
46.577,
83.182,
90,
90,
90
|
R / Rfree (%)
|
18.6 /
23.2
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Rice APIP6-Ring Homodimer
(pdb code 8i3x). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Rice APIP6-Ring Homodimer, PDB code: 8i3x:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 8i3x
Go back to
Zinc Binding Sites List in 8i3x
Zinc binding site 1 out
of 4 in the Rice APIP6-Ring Homodimer
![](/pictures/ZN/pdb/i3/8i3x-ZN-sphere_01.jpg) Mono view
![](/pictures/ZN/pdb/i3/8i3x-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 Rice APIP6-Ring Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn101
b:30.0
occ:1.00
|
CD2
|
A:HIS61
|
2.2
|
36.9
|
1.0
|
SG
|
A:CYS64
|
2.4
|
31.2
|
1.0
|
SG
|
A:CYS38
|
2.4
|
36.8
|
1.0
|
SG
|
A:CYS35
|
2.4
|
34.4
|
1.0
|
CB
|
A:CYS35
|
3.1
|
34.1
|
1.0
|
CG
|
A:HIS61
|
3.1
|
31.9
|
1.0
|
CB
|
A:CYS64
|
3.3
|
34.3
|
1.0
|
CB
|
A:CYS38
|
3.3
|
40.9
|
1.0
|
NE2
|
A:HIS61
|
3.3
|
35.1
|
1.0
|
CB
|
A:HIS61
|
3.5
|
26.8
|
1.0
|
N
|
A:CYS38
|
3.8
|
35.8
|
1.0
|
NH2
|
A:ARG49
|
4.0
|
40.6
|
1.0
|
N
|
A:HIS61
|
4.0
|
31.1
|
1.0
|
CA
|
A:CYS38
|
4.1
|
36.3
|
1.0
|
NH1
|
A:ARG49
|
4.2
|
48.0
|
1.0
|
ND1
|
A:HIS61
|
4.3
|
37.6
|
1.0
|
CA
|
A:HIS61
|
4.4
|
26.2
|
1.0
|
CE1
|
A:HIS61
|
4.4
|
32.5
|
1.0
|
CZ
|
A:ARG49
|
4.4
|
41.8
|
1.0
|
CA
|
A:CYS35
|
4.5
|
30.2
|
1.0
|
CB
|
A:ILE37
|
4.6
|
30.0
|
1.0
|
CA
|
A:CYS64
|
4.7
|
30.1
|
1.0
|
C
|
A:ILE37
|
4.8
|
36.2
|
1.0
|
C
|
A:CYS38
|
4.8
|
38.4
|
1.0
|
O
|
A:CYS35
|
4.8
|
30.3
|
1.0
|
N
|
A:LEU39
|
4.9
|
38.2
|
1.0
|
C
|
A:CYS35
|
4.9
|
29.7
|
1.0
|
O
|
A:HOH259
|
4.9
|
43.7
|
1.0
|
|
Zinc binding site 2 out
of 4 in 8i3x
Go back to
Zinc Binding Sites List in 8i3x
Zinc binding site 2 out
of 4 in the Rice APIP6-Ring Homodimer
![](/pictures/ZN/pdb/i3/8i3x-ZN-sphere_02.jpg) Mono view
![](/pictures/ZN/pdb/i3/8i3x-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 Rice APIP6-Ring Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn102
b:30.0
occ:1.00
|
CD2
|
A:HIS58
|
2.1
|
34.3
|
1.0
|
SG
|
A:CYS80
|
2.3
|
37.9
|
1.0
|
SG
|
A:CYS56
|
2.3
|
34.7
|
1.0
|
SG
|
A:CYS77
|
2.4
|
31.1
|
1.0
|
CB
|
A:CYS77
|
3.1
|
30.8
|
1.0
|
CG
|
A:HIS58
|
3.1
|
35.9
|
1.0
|
NE2
|
A:HIS58
|
3.1
|
46.6
|
1.0
|
CB
|
A:CYS56
|
3.3
|
40.9
|
1.0
|
CB
|
A:CYS80
|
3.4
|
39.6
|
1.0
|
CB
|
A:HIS58
|
3.6
|
35.9
|
1.0
|
N
|
A:CYS80
|
3.7
|
35.0
|
1.0
|
CA
|
A:CYS80
|
4.2
|
37.8
|
1.0
|
ND1
|
A:HIS58
|
4.3
|
40.9
|
1.0
|
CE1
|
A:HIS58
|
4.3
|
36.0
|
1.0
|
O
|
A:HOH248
|
4.4
|
48.9
|
1.0
|
CB
|
A:ASN79
|
4.4
|
36.5
|
1.0
|
N
|
A:HIS58
|
4.5
|
35.0
|
1.0
|
CA
|
A:CYS77
|
4.5
|
26.8
|
1.0
|
CA
|
A:CYS56
|
4.6
|
41.8
|
1.0
|
C
|
A:ASN79
|
4.7
|
37.3
|
1.0
|
O
|
A:HOH249
|
4.7
|
38.9
|
1.0
|
CA
|
A:HIS58
|
4.7
|
28.6
|
1.0
|
C
|
A:CYS56
|
4.8
|
40.1
|
1.0
|
C
|
A:CYS80
|
4.9
|
38.1
|
1.0
|
CA
|
A:ASN79
|
4.9
|
33.5
|
1.0
|
N
|
A:ASN79
|
4.9
|
29.1
|
1.0
|
O
|
A:CYS56
|
5.0
|
44.5
|
1.0
|
|
Zinc binding site 3 out
of 4 in 8i3x
Go back to
Zinc Binding Sites List in 8i3x
Zinc binding site 3 out
of 4 in the Rice APIP6-Ring Homodimer
![](/pictures/ZN/pdb/i3/8i3x-ZN-sphere_03.jpg) Mono view
![](/pictures/ZN/pdb/i3/8i3x-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 Rice APIP6-Ring Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn101
b:30.0
occ:1.00
|
ND1
|
B:HIS61
|
2.3
|
38.0
|
1.0
|
SG
|
B:CYS38
|
2.3
|
44.4
|
1.0
|
SG
|
B:CYS35
|
2.4
|
43.1
|
1.0
|
SG
|
B:CYS64
|
2.4
|
39.2
|
1.0
|
CB
|
B:CYS35
|
3.1
|
46.0
|
1.0
|
CE1
|
B:HIS61
|
3.2
|
42.9
|
1.0
|
CG
|
B:HIS61
|
3.3
|
35.5
|
1.0
|
CB
|
B:CYS64
|
3.3
|
31.5
|
1.0
|
CB
|
B:CYS38
|
3.3
|
46.8
|
1.0
|
CB
|
B:HIS61
|
3.5
|
37.1
|
1.0
|
N
|
B:CYS38
|
3.7
|
50.8
|
1.0
|
NH2
|
B:ARG49
|
3.9
|
43.9
|
1.0
|
N
|
B:HIS61
|
4.0
|
34.3
|
1.0
|
CA
|
B:CYS38
|
4.1
|
50.8
|
1.0
|
NH1
|
B:ARG49
|
4.3
|
48.4
|
1.0
|
NE2
|
B:HIS61
|
4.3
|
42.5
|
1.0
|
CD2
|
B:HIS61
|
4.4
|
34.8
|
1.0
|
CA
|
B:HIS61
|
4.4
|
34.9
|
1.0
|
CZ
|
B:ARG49
|
4.4
|
46.0
|
1.0
|
CA
|
B:CYS35
|
4.5
|
44.8
|
1.0
|
CB
|
B:ILE37
|
4.5
|
44.2
|
1.0
|
CA
|
B:CYS64
|
4.7
|
31.2
|
1.0
|
C
|
B:ILE37
|
4.7
|
52.7
|
1.0
|
O
|
B:CYS35
|
4.8
|
49.0
|
1.0
|
C
|
B:CYS38
|
4.9
|
48.7
|
1.0
|
C
|
B:CYS35
|
4.9
|
49.3
|
1.0
|
N
|
B:ILE37
|
5.0
|
45.2
|
1.0
|
CG2
|
B:ILE37
|
5.0
|
44.3
|
1.0
|
CA
|
B:ILE37
|
5.0
|
48.4
|
1.0
|
|
Zinc binding site 4 out
of 4 in 8i3x
Go back to
Zinc Binding Sites List in 8i3x
Zinc binding site 4 out
of 4 in the Rice APIP6-Ring Homodimer
![](/pictures/ZN/pdb/i3/8i3x-ZN-sphere_04.jpg) Mono view
![](/pictures/ZN/pdb/i3/8i3x-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 Rice APIP6-Ring Homodimer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn102
b:30.0
occ:1.00
|
ND1
|
B:HIS58
|
2.2
|
79.0
|
1.0
|
SG
|
B:CYS80
|
2.4
|
61.0
|
1.0
|
SG
|
B:CYS77
|
2.4
|
57.6
|
1.0
|
SG
|
B:CYS56
|
2.5
|
57.3
|
1.0
|
CE1
|
B:HIS58
|
2.6
|
68.9
|
1.0
|
CG
|
B:HIS58
|
2.6
|
56.8
|
1.0
|
NE2
|
B:HIS58
|
3.2
|
64.1
|
1.0
|
CD2
|
B:HIS58
|
3.2
|
65.5
|
1.0
|
CB
|
B:CYS77
|
3.3
|
48.2
|
1.0
|
CB
|
B:CYS80
|
3.4
|
64.3
|
1.0
|
CB
|
B:HIS58
|
3.4
|
48.8
|
1.0
|
N
|
B:CYS80
|
3.6
|
62.6
|
1.0
|
CB
|
B:CYS56
|
3.7
|
60.8
|
1.0
|
CB
|
B:ASN79
|
4.0
|
61.4
|
1.0
|
CA
|
B:CYS80
|
4.1
|
64.2
|
1.0
|
N
|
B:HIS58
|
4.4
|
44.8
|
1.0
|
CA
|
B:HIS58
|
4.5
|
44.3
|
1.0
|
C
|
B:ASN79
|
4.6
|
67.2
|
1.0
|
CA
|
B:ASN79
|
4.7
|
60.9
|
1.0
|
N
|
B:ASN79
|
4.7
|
56.3
|
1.0
|
CA
|
B:CYS77
|
4.8
|
40.8
|
1.0
|
CA
|
B:CYS56
|
4.9
|
54.1
|
1.0
|
C
|
B:CYS80
|
4.9
|
59.2
|
1.0
|
C
|
B:CYS56
|
4.9
|
46.5
|
1.0
|
CG
|
B:ASN79
|
5.0
|
59.0
|
1.0
|
O
|
B:CYS56
|
5.0
|
54.8
|
1.0
|
|
Reference:
Y.Zheng,
X.Zhang,
Y.Liu,
T.Zhu,
X.Wu,
Y.Ning,
J.Liu,
D.Wang.
Crystal Structure of Rice APIP6 Reveals A New Dimerization Mode of Ring-Type E3 Ligases That Facilities the Construction of Its Working Model Phytopathol Res V. 5 2023.
DOI: 10.1186/S42483-023-00186-W
Page generated: Thu Dec 28 13:15:50 2023
|