Cadmium in PDB 8gzl: Crystal Structure of CD2+-Bound Dna Aptamer
Protein crystallography data
The structure of Crystal Structure of CD2+-Bound Dna Aptamer, PDB code: 8gzl
was solved by
J.H.Gan,
H.H.Liu,
Y.Q.Gao,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
29.37 /
3.00
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
26.8,
45.69,
147.02,
90,
92.87,
90
|
R / Rfree (%)
|
23.3 /
28.4
|
Other elements in 8gzl:
The structure of Crystal Structure of CD2+-Bound Dna Aptamer also contains other interesting chemical elements:
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Crystal Structure of CD2+-Bound Dna Aptamer
(pdb code 8gzl). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 5 binding sites of Cadmium where determined in the
Crystal Structure of CD2+-Bound Dna Aptamer, PDB code: 8gzl:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
Cadmium binding site 1 out
of 5 in 8gzl
Go back to
Cadmium Binding Sites List in 8gzl
Cadmium binding site 1 out
of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd101
b:67.5
occ:1.00
|
O
|
A:HOH201
|
2.3
|
30.0
|
1.0
|
N3
|
A:DC12
|
2.6
|
63.1
|
1.0
|
N7
|
A:DG9
|
2.7
|
72.2
|
1.0
|
N7
|
A:DG16
|
2.7
|
66.0
|
1.0
|
O6
|
A:DG9
|
2.8
|
67.0
|
1.0
|
O2
|
A:DC12
|
2.9
|
91.7
|
1.0
|
C2
|
A:DC12
|
3.1
|
77.1
|
1.0
|
C5
|
A:DG9
|
3.3
|
71.5
|
1.0
|
C6
|
A:DG9
|
3.3
|
67.2
|
1.0
|
C8
|
A:DG16
|
3.5
|
66.6
|
1.0
|
C5
|
A:DG16
|
3.5
|
67.0
|
1.0
|
C4
|
A:DC12
|
3.7
|
66.1
|
1.0
|
O6
|
A:DG16
|
3.8
|
78.1
|
1.0
|
C8
|
A:DG9
|
3.8
|
74.8
|
1.0
|
C6
|
A:DG16
|
4.0
|
70.7
|
1.0
|
N4
|
A:DC12
|
4.0
|
72.2
|
1.0
|
N2
|
A:DG15
|
4.3
|
68.2
|
1.0
|
N3
|
A:DG15
|
4.5
|
73.1
|
1.0
|
N1
|
A:DC12
|
4.5
|
82.0
|
1.0
|
N9
|
A:DG16
|
4.5
|
67.4
|
1.0
|
C4
|
A:DG16
|
4.6
|
67.2
|
1.0
|
C4
|
A:DG9
|
4.6
|
69.0
|
1.0
|
C2
|
A:DG15
|
4.6
|
69.5
|
1.0
|
N1
|
A:DG9
|
4.7
|
66.5
|
1.0
|
N9
|
A:DG9
|
4.9
|
72.2
|
1.0
|
C5
|
A:DC12
|
5.0
|
75.1
|
1.0
|
|
Cadmium binding site 2 out
of 5 in 8gzl
Go back to
Cadmium Binding Sites List in 8gzl
Cadmium binding site 2 out
of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd102
b:71.9
occ:1.00
|
OP2
|
A:DC11
|
2.5
|
75.6
|
1.0
|
N6
|
A:DA13
|
2.9
|
72.0
|
1.0
|
N7
|
A:DA13
|
3.6
|
67.0
|
1.0
|
P
|
A:DC11
|
3.7
|
87.4
|
1.0
|
C6
|
A:DA13
|
3.8
|
73.1
|
1.0
|
OP1
|
A:DC11
|
4.0
|
75.6
|
1.0
|
C5
|
A:DA13
|
4.0
|
69.2
|
1.0
|
O5'
|
A:DC11
|
4.4
|
75.6
|
1.0
|
C5
|
A:DC11
|
4.5
|
75.8
|
1.0
|
C6
|
A:DC11
|
4.6
|
83.4
|
1.0
|
C8
|
A:DA13
|
4.8
|
75.3
|
1.0
|
C4'
|
A:DT10
|
4.9
|
64.1
|
1.0
|
O3'
|
A:DT10
|
5.0
|
65.1
|
1.0
|
|
Cadmium binding site 3 out
of 5 in 8gzl
Go back to
Cadmium Binding Sites List in 8gzl
Cadmium binding site 3 out
of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd101
b:79.1
occ:1.00
|
N3
|
B:DC12
|
2.6
|
72.9
|
1.0
|
N7
|
B:DG9
|
2.7
|
80.4
|
1.0
|
N7
|
B:DG16
|
2.7
|
85.0
|
1.0
|
O6
|
B:DG9
|
2.8
|
84.9
|
1.0
|
O2
|
B:DC12
|
2.9
|
81.6
|
1.0
|
C2
|
B:DC12
|
3.1
|
81.1
|
1.0
|
C5
|
B:DG9
|
3.3
|
83.0
|
1.0
|
C6
|
B:DG9
|
3.4
|
83.7
|
1.0
|
C8
|
B:DG16
|
3.5
|
88.0
|
1.0
|
C5
|
B:DG16
|
3.5
|
82.1
|
1.0
|
C4
|
B:DC12
|
3.7
|
72.2
|
1.0
|
O6
|
B:DG16
|
3.7
|
79.7
|
1.0
|
C8
|
B:DG9
|
3.8
|
82.5
|
1.0
|
C6
|
B:DG16
|
3.9
|
79.2
|
1.0
|
N4
|
B:DC12
|
4.0
|
73.7
|
1.0
|
N2
|
B:DG15
|
4.3
|
81.5
|
1.0
|
N1
|
B:DC12
|
4.4
|
80.5
|
1.0
|
N3
|
B:DG15
|
4.5
|
79.0
|
1.0
|
N9
|
B:DG16
|
4.5
|
87.7
|
1.0
|
C4
|
B:DG16
|
4.5
|
82.2
|
1.0
|
C4
|
B:DG9
|
4.6
|
82.5
|
1.0
|
C2
|
B:DG15
|
4.6
|
80.0
|
1.0
|
N1
|
B:DG9
|
4.7
|
83.9
|
1.0
|
N9
|
B:DG9
|
4.8
|
77.6
|
1.0
|
C5
|
B:DC12
|
4.9
|
70.3
|
1.0
|
|
Cadmium binding site 4 out
of 5 in 8gzl
Go back to
Cadmium Binding Sites List in 8gzl
Cadmium binding site 4 out
of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cd101
b:66.5
occ:1.00
|
O
|
C:HOH202
|
2.3
|
30.0
|
1.0
|
N7
|
C:DG9
|
2.5
|
66.4
|
1.0
|
N3
|
C:DC12
|
2.5
|
63.3
|
1.0
|
N7
|
C:DG16
|
2.7
|
68.6
|
1.0
|
O6
|
C:DG9
|
2.8
|
66.8
|
1.0
|
O2
|
C:DC12
|
3.1
|
85.1
|
1.0
|
C5
|
C:DG9
|
3.1
|
66.7
|
1.0
|
C2
|
C:DC12
|
3.2
|
77.0
|
1.0
|
C6
|
C:DG9
|
3.3
|
66.0
|
1.0
|
O6
|
C:DG16
|
3.3
|
73.8
|
1.0
|
C5
|
C:DG16
|
3.4
|
67.8
|
1.0
|
C4
|
C:DC12
|
3.5
|
69.0
|
1.0
|
C8
|
C:DG9
|
3.6
|
71.7
|
1.0
|
C6
|
C:DG16
|
3.6
|
73.1
|
1.0
|
C8
|
C:DG16
|
3.7
|
71.0
|
1.0
|
N4
|
C:DC12
|
3.7
|
71.4
|
1.0
|
N2
|
C:DG15
|
4.2
|
70.8
|
1.0
|
C4
|
C:DG9
|
4.4
|
67.5
|
1.0
|
C4
|
C:DG16
|
4.5
|
66.7
|
1.0
|
N1
|
C:DC12
|
4.5
|
84.1
|
1.0
|
N3
|
C:DG15
|
4.5
|
64.4
|
1.0
|
C2
|
C:DG15
|
4.6
|
64.2
|
1.0
|
N9
|
C:DG16
|
4.6
|
68.0
|
1.0
|
N9
|
C:DG9
|
4.6
|
69.5
|
1.0
|
N1
|
C:DG9
|
4.7
|
65.1
|
1.0
|
C5
|
C:DC12
|
4.8
|
77.2
|
1.0
|
N1
|
C:DG16
|
4.9
|
75.1
|
1.0
|
|
Cadmium binding site 5 out
of 5 in 8gzl
Go back to
Cadmium Binding Sites List in 8gzl
Cadmium binding site 5 out
of 5 in the Crystal Structure of CD2+-Bound Dna Aptamer
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Crystal Structure of CD2+-Bound Dna Aptamer within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cd101
b:96.2
occ:1.00
|
N3
|
D:DC12
|
2.7
|
99.4
|
1.0
|
N7
|
D:DG16
|
2.7
|
106.0
|
1.0
|
O6
|
D:DG9
|
2.7
|
92.7
|
1.0
|
N7
|
D:DG9
|
2.8
|
99.4
|
1.0
|
O2
|
D:DC12
|
2.9
|
101.1
|
1.0
|
C2
|
D:DC12
|
3.2
|
103.1
|
1.0
|
C6
|
D:DG9
|
3.3
|
95.0
|
1.0
|
C5
|
D:DG9
|
3.4
|
96.0
|
1.0
|
C8
|
D:DG16
|
3.5
|
105.7
|
1.0
|
C5
|
D:DG16
|
3.6
|
104.0
|
1.0
|
C4
|
D:DC12
|
3.8
|
106.6
|
1.0
|
O6
|
D:DG16
|
3.9
|
108.9
|
1.0
|
C8
|
D:DG9
|
4.0
|
106.3
|
1.0
|
C6
|
D:DG16
|
4.1
|
104.1
|
1.0
|
N4
|
D:DC12
|
4.1
|
110.3
|
1.0
|
N9
|
D:DG16
|
4.5
|
103.2
|
1.0
|
N1
|
D:DC12
|
4.5
|
108.7
|
1.0
|
N2
|
D:DG15
|
4.5
|
94.9
|
1.0
|
C4
|
D:DG16
|
4.6
|
102.9
|
1.0
|
N3
|
D:DG15
|
4.6
|
85.4
|
1.0
|
C4
|
D:DG9
|
4.7
|
93.8
|
1.0
|
N1
|
D:DG9
|
4.7
|
94.0
|
1.0
|
C2
|
D:DG15
|
4.8
|
91.3
|
1.0
|
N9
|
D:DG9
|
5.0
|
103.6
|
1.0
|
|
Reference:
H.Liu,
Y.Gao,
J.Mathivanan,
Z.Armour-Garb,
Z.Shao,
Y.Zhang,
X.Zhao,
Q.Shao,
W.Zhang,
J.Yang,
C.Cao,
H.Li,
J.Sheng,
J.Gan.
Crystal Structures and Identification of Novel CD2+-Specific Dna Aptamer. Nucleic Acids Res. V. 51 4625 2023.
ISSN: ESSN 1362-4962
PubMed: 37013991
DOI: 10.1093/NAR/GKAD239
Page generated: Fri Jul 19 20:26:52 2024
|