Zinc in PDB 7uu3: Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex
Protein crystallography data
The structure of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex, PDB code: 7uu3
was solved by
H.J.Yang,
S.-X.Li,
X.-J.Chen,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
45.70 /
3.10
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.709,
67.192,
79.624,
98.29,
108.72,
112.66
|
R / Rfree (%)
|
17 /
21
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex
(pdb code 7uu3). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the
Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex, PDB code: 7uu3:
Jump to Zinc binding site number:
1;
2;
3;
4;
Zinc binding site 1 out
of 4 in 7uu3
Go back to
Zinc Binding Sites List in 7uu3
Zinc binding site 1 out
of 4 in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn401
b:82.9
occ:1.00
|
ND1
|
A:HIS65
|
2.1
|
117.1
|
1.0
|
SG
|
A:CYS97
|
2.3
|
101.2
|
1.0
|
SG
|
A:CYS100
|
2.4
|
91.3
|
1.0
|
CE1
|
A:HIS65
|
3.0
|
112.8
|
1.0
|
CB
|
A:CYS97
|
3.1
|
101.2
|
1.0
|
CG
|
A:HIS65
|
3.1
|
112.2
|
1.0
|
CB
|
A:CYS100
|
3.2
|
94.4
|
1.0
|
CB
|
A:HIS65
|
3.5
|
106.7
|
1.0
|
N
|
A:CYS97
|
3.6
|
95.8
|
1.0
|
OE2
|
A:GLU67
|
3.9
|
87.5
|
1.0
|
CA
|
A:CYS97
|
3.9
|
100.3
|
1.0
|
OE1
|
A:GLU67
|
4.1
|
88.5
|
1.0
|
N
|
A:CYS100
|
4.1
|
107.8
|
1.0
|
NE2
|
A:HIS65
|
4.1
|
113.0
|
1.0
|
CD
|
A:GLU67
|
4.2
|
87.8
|
1.0
|
CD2
|
A:HIS65
|
4.2
|
113.6
|
1.0
|
CA
|
A:CYS100
|
4.3
|
99.8
|
1.0
|
C
|
A:CYS97
|
4.6
|
105.3
|
1.0
|
O
|
A:ALA62
|
4.7
|
117.9
|
1.0
|
O
|
A:CYS97
|
4.8
|
106.6
|
1.0
|
C
|
A:PRO96
|
4.8
|
91.0
|
1.0
|
|
Zinc binding site 2 out
of 4 in 7uu3
Go back to
Zinc Binding Sites List in 7uu3
Zinc binding site 2 out
of 4 in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn402
b:91.8
occ:1.00
|
ND1
|
A:HIS257
|
2.2
|
76.8
|
1.0
|
SG
|
A:CYS290
|
2.3
|
77.5
|
1.0
|
SG
|
A:CYS287
|
2.6
|
90.8
|
1.0
|
CE1
|
A:HIS257
|
3.0
|
80.2
|
1.0
|
CB
|
A:CYS290
|
3.1
|
79.8
|
1.0
|
CG
|
A:HIS257
|
3.1
|
75.2
|
1.0
|
CB
|
A:CYS287
|
3.5
|
87.0
|
1.0
|
CB
|
A:HIS257
|
3.5
|
74.7
|
1.0
|
N
|
A:CYS287
|
3.6
|
79.2
|
1.0
|
NE2
|
A:HIS257
|
4.1
|
77.7
|
1.0
|
CA
|
A:CYS287
|
4.1
|
83.4
|
1.0
|
CD2
|
A:HIS257
|
4.1
|
76.5
|
1.0
|
CA
|
A:CYS290
|
4.3
|
81.9
|
1.0
|
N
|
A:CYS290
|
4.4
|
86.4
|
1.0
|
C
|
A:PRO286
|
4.6
|
76.5
|
1.0
|
CA
|
A:PRO286
|
4.7
|
66.8
|
1.0
|
C
|
A:CYS287
|
4.8
|
85.3
|
1.0
|
O
|
A:CYS287
|
5.0
|
91.5
|
1.0
|
|
Zinc binding site 3 out
of 4 in 7uu3
Go back to
Zinc Binding Sites List in 7uu3
Zinc binding site 3 out
of 4 in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn401
b:60.2
occ:1.00
|
ND1
|
B:HIS65
|
2.1
|
85.9
|
1.0
|
SG
|
B:CYS97
|
2.2
|
61.3
|
1.0
|
SG
|
B:CYS100
|
2.3
|
68.6
|
1.0
|
CE1
|
B:HIS65
|
3.0
|
75.7
|
1.0
|
CG
|
B:HIS65
|
3.2
|
73.4
|
1.0
|
CB
|
B:CYS100
|
3.2
|
67.4
|
1.0
|
CB
|
B:CYS97
|
3.3
|
62.7
|
1.0
|
CB
|
B:HIS65
|
3.5
|
69.2
|
1.0
|
N
|
B:CYS97
|
3.8
|
60.7
|
1.0
|
N
|
B:CYS100
|
4.0
|
70.7
|
1.0
|
OE2
|
B:GLU67
|
4.1
|
83.5
|
1.0
|
CA
|
B:CYS97
|
4.1
|
60.7
|
1.0
|
NE2
|
B:HIS65
|
4.2
|
72.3
|
1.0
|
OE1
|
B:GLU67
|
4.2
|
80.8
|
1.0
|
CA
|
B:CYS100
|
4.2
|
67.8
|
1.0
|
CD2
|
B:HIS65
|
4.2
|
72.2
|
1.0
|
CD
|
B:GLU67
|
4.4
|
80.5
|
1.0
|
C
|
B:CYS97
|
4.7
|
63.7
|
1.0
|
O
|
B:CYS97
|
4.9
|
62.7
|
1.0
|
|
Zinc binding site 4 out
of 4 in 7uu3
Go back to
Zinc Binding Sites List in 7uu3
Zinc binding site 4 out
of 4 in the Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Crystal Structure of APOBEC3G Complex with 3'Overhangs Rna-Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn402
b:101.0
occ:1.00
|
SG
|
B:CYS290
|
2.3
|
104.1
|
1.0
|
ND1
|
B:HIS257
|
2.3
|
113.7
|
1.0
|
SG
|
B:CYS287
|
2.8
|
112.8
|
1.0
|
CG
|
B:HIS257
|
3.1
|
111.3
|
1.0
|
CE1
|
B:HIS257
|
3.2
|
116.8
|
1.0
|
CB
|
B:CYS290
|
3.4
|
108.3
|
1.0
|
CB
|
B:CYS287
|
3.4
|
114.7
|
1.0
|
CB
|
B:HIS257
|
3.4
|
105.9
|
1.0
|
N
|
B:CYS287
|
3.7
|
107.5
|
1.0
|
CA
|
B:CYS287
|
4.1
|
110.5
|
1.0
|
CD2
|
B:HIS257
|
4.2
|
113.3
|
1.0
|
NE2
|
B:HIS257
|
4.2
|
114.7
|
1.0
|
CA
|
B:CYS290
|
4.6
|
112.5
|
1.0
|
N
|
B:CYS290
|
4.7
|
116.9
|
1.0
|
C
|
B:PRO286
|
4.8
|
108.2
|
1.0
|
CA
|
B:PRO286
|
4.9
|
99.1
|
1.0
|
CA
|
B:HIS257
|
4.9
|
97.1
|
1.0
|
C
|
B:CYS287
|
5.0
|
111.2
|
1.0
|
|
Reference:
H.Yang,
K.Kim,
S.Li,
J.Pacheco,
X.S.Chen.
Structural Basis of Sequence-Specific Rna Recognition By the Antiviral Factor APOBEC3G. Nat Commun V. 13 7498 2022.
ISSN: ESSN 2041-1723
PubMed: 36470880
DOI: 10.1038/S41467-022-35201-9
Page generated: Sat Apr 8 04:28:59 2023
|