Cadmium in PDB 488d: Catalytic Rna Enzyme-Product Complex
Protein crystallography data
The structure of Catalytic Rna Enzyme-Product Complex, PDB code: 488d
was solved by
J.B.Murray,
H.Szoke,
A.Szoke,
W.G.Scott,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.60 /
3.10
|
Space group
|
P 31 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
65.503,
65.503,
136.484,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
25.8 /
30.1
|
Cadmium Binding Sites:
The binding sites of Cadmium atom in the Catalytic Rna Enzyme-Product Complex
(pdb code 488d). This binding sites where shown within
5.0 Angstroms radius around Cadmium atom.
In total 8 binding sites of Cadmium where determined in the
Catalytic Rna Enzyme-Product Complex, PDB code: 488d:
Jump to Cadmium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Cadmium binding site 1 out
of 8 in 488d
Go back to
Cadmium Binding Sites List in 488d
Cadmium binding site 1 out
of 8 in the Catalytic Rna Enzyme-Product Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 1 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd1
b:79.9
occ:1.00
|
N7
|
A:G23
|
2.1
|
35.0
|
1.0
|
C5
|
A:G23
|
3.0
|
29.9
|
1.0
|
O6
|
A:G23
|
3.1
|
36.7
|
1.0
|
C8
|
A:G23
|
3.2
|
31.5
|
1.0
|
C6
|
A:G23
|
3.3
|
30.1
|
1.0
|
C5
|
A:U24
|
3.9
|
25.9
|
1.0
|
C4
|
A:U24
|
4.0
|
25.2
|
1.0
|
N7
|
A:G22
|
4.0
|
27.6
|
1.0
|
C4
|
A:G23
|
4.2
|
26.3
|
1.0
|
O4
|
A:U24
|
4.2
|
33.3
|
1.0
|
N9
|
A:G23
|
4.3
|
30.0
|
1.0
|
C6
|
A:U24
|
4.4
|
25.4
|
1.0
|
N3
|
A:U24
|
4.5
|
24.2
|
1.0
|
C8
|
A:G22
|
4.7
|
31.0
|
1.0
|
OP2
|
A:G23
|
4.7
|
51.7
|
1.0
|
N1
|
A:G23
|
4.7
|
27.3
|
1.0
|
N1
|
A:U24
|
4.9
|
23.6
|
1.0
|
C5
|
A:G22
|
4.9
|
29.7
|
1.0
|
O6
|
A:G22
|
4.9
|
40.9
|
1.0
|
C2
|
A:U24
|
4.9
|
24.1
|
1.0
|
|
Cadmium binding site 2 out
of 8 in 488d
Go back to
Cadmium Binding Sites List in 488d
Cadmium binding site 2 out
of 8 in the Catalytic Rna Enzyme-Product Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 2 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd2
b:24.9
occ:1.00
|
N7
|
A:G50
|
2.0
|
38.9
|
1.0
|
C5
|
A:G50
|
2.9
|
41.7
|
1.0
|
O6
|
A:G50
|
3.0
|
53.3
|
1.0
|
C8
|
A:G50
|
3.1
|
37.6
|
1.0
|
C6
|
A:G50
|
3.3
|
46.9
|
1.0
|
C4
|
A:G50
|
4.1
|
39.7
|
1.0
|
N9
|
A:G50
|
4.2
|
38.0
|
1.0
|
N6
|
A:A60
|
4.4
|
42.6
|
1.0
|
OP1
|
A:G50
|
4.5
|
48.1
|
1.0
|
O2'
|
A:U40
|
4.5
|
36.2
|
1.0
|
N1
|
A:G50
|
4.6
|
46.7
|
1.0
|
O3'
|
A:U40
|
4.7
|
43.1
|
1.0
|
|
Cadmium binding site 3 out
of 8 in 488d
Go back to
Cadmium Binding Sites List in 488d
Cadmium binding site 3 out
of 8 in the Catalytic Rna Enzyme-Product Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 3 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd3
b:26.7
occ:1.00
|
N7
|
B:G164
|
2.0
|
19.3
|
0.4
|
N7
|
D:G164
|
2.0
|
13.3
|
0.6
|
C5
|
B:G164
|
2.9
|
20.0
|
0.4
|
C5
|
D:G164
|
2.9
|
14.7
|
0.6
|
O6
|
B:G164
|
3.0
|
29.4
|
0.4
|
O6
|
D:G164
|
3.0
|
29.2
|
0.6
|
C8
|
B:G164
|
3.0
|
23.1
|
0.4
|
C8
|
D:G164
|
3.0
|
19.5
|
0.6
|
C6
|
B:G164
|
3.3
|
23.1
|
0.4
|
C6
|
D:G164
|
3.3
|
19.8
|
0.6
|
C4
|
B:G164
|
4.1
|
21.6
|
0.4
|
C4
|
D:G164
|
4.1
|
17.6
|
0.6
|
N9
|
B:G164
|
4.2
|
23.9
|
0.4
|
N9
|
D:G164
|
4.2
|
21.2
|
0.6
|
OP2
|
B:A34L
|
4.4
|
37.6
|
0.4
|
OP2
|
D:A34L
|
4.4
|
40.7
|
0.6
|
N1
|
B:G164
|
4.7
|
23.1
|
0.4
|
N1
|
D:G164
|
4.7
|
20.1
|
0.6
|
OP1
|
B:A34L
|
4.7
|
39.0
|
0.4
|
OP1
|
D:A34L
|
4.7
|
42.8
|
0.6
|
N7
|
B:A163
|
4.7
|
23.0
|
0.4
|
N7
|
D:A163
|
4.7
|
21.3
|
0.6
|
P
|
B:A34L
|
4.9
|
40.2
|
0.4
|
P
|
D:A34L
|
4.9
|
44.2
|
0.6
|
|
Cadmium binding site 4 out
of 8 in 488d
Go back to
Cadmium Binding Sites List in 488d
Cadmium binding site 4 out
of 8 in the Catalytic Rna Enzyme-Product Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 4 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd4
b:25.8
occ:1.00
|
N7
|
B:G114
|
2.0
|
57.8
|
0.4
|
N7
|
D:G114
|
2.0
|
58.7
|
0.6
|
C5
|
B:G114
|
2.8
|
59.8
|
0.4
|
C5
|
D:G114
|
2.8
|
61.8
|
0.6
|
O6
|
B:G114
|
2.9
|
62.5
|
0.4
|
O6
|
D:G114
|
2.9
|
65.2
|
0.6
|
C8
|
B:G114
|
3.1
|
59.4
|
0.4
|
C8
|
D:G114
|
3.1
|
61.5
|
0.6
|
C6
|
B:G114
|
3.2
|
60.6
|
0.4
|
C6
|
D:G114
|
3.2
|
62.7
|
0.6
|
C4
|
B:G114
|
4.1
|
59.9
|
0.4
|
C4
|
D:G114
|
4.1
|
61.9
|
0.6
|
N9
|
B:G114
|
4.2
|
59.8
|
0.4
|
N9
|
D:G114
|
4.2
|
62.3
|
0.6
|
N1
|
B:G114
|
4.6
|
59.6
|
0.4
|
N1
|
D:G114
|
4.6
|
61.2
|
0.6
|
O6
|
B:G113
|
4.8
|
43.2
|
0.4
|
O6
|
D:G113
|
4.8
|
41.5
|
0.6
|
|
Cadmium binding site 5 out
of 8 in 488d
Go back to
Cadmium Binding Sites List in 488d
Cadmium binding site 5 out
of 8 in the Catalytic Rna Enzyme-Product Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 5 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd5
b:44.7
occ:1.00
|
N7
|
B:G120
|
2.2
|
31.0
|
0.4
|
N7
|
D:G120
|
2.2
|
27.5
|
0.6
|
O6
|
B:G120
|
3.1
|
36.5
|
0.4
|
O6
|
D:G120
|
3.1
|
36.6
|
0.6
|
C5
|
B:G120
|
3.1
|
32.4
|
0.4
|
C5
|
D:G120
|
3.1
|
29.6
|
0.6
|
C8
|
B:G120
|
3.3
|
33.9
|
0.4
|
C8
|
D:G120
|
3.3
|
31.9
|
0.6
|
C6
|
B:G120
|
3.4
|
33.0
|
0.4
|
C6
|
D:G120
|
3.4
|
31.1
|
0.6
|
OP2
|
B:C111
|
4.2
|
44.8
|
0.4
|
OP2
|
D:C111
|
4.2
|
48.2
|
0.6
|
C4
|
B:G120
|
4.3
|
32.6
|
0.4
|
C4
|
D:G120
|
4.3
|
30.4
|
0.6
|
N9
|
B:G120
|
4.4
|
35.6
|
0.4
|
N9
|
D:G120
|
4.4
|
34.5
|
0.6
|
C5
|
B:C111
|
4.6
|
32.2
|
0.4
|
C5
|
D:C111
|
4.6
|
29.6
|
0.6
|
O6
|
A:G80
|
4.7
|
31.9
|
1.0
|
N1
|
B:G120
|
4.8
|
30.0
|
0.4
|
N1
|
D:G120
|
4.8
|
26.4
|
0.6
|
|
Cadmium binding site 6 out
of 8 in 488d
Go back to
Cadmium Binding Sites List in 488d
Cadmium binding site 6 out
of 8 in the Catalytic Rna Enzyme-Product Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 6 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd6
b:46.6
occ:1.00
|
N7
|
A:G25
|
2.0
|
35.7
|
1.0
|
C5
|
A:G25
|
2.6
|
41.9
|
1.0
|
C8
|
A:G25
|
2.9
|
45.3
|
1.0
|
O6
|
A:G25
|
3.0
|
44.8
|
1.0
|
C6
|
A:G25
|
3.1
|
43.3
|
1.0
|
C4
|
A:G25
|
3.7
|
48.1
|
1.0
|
N9
|
A:G25
|
3.9
|
49.2
|
1.0
|
N1
|
A:G25
|
4.3
|
45.8
|
1.0
|
N3
|
A:G25
|
4.9
|
47.3
|
1.0
|
O4
|
A:U24
|
5.0
|
33.3
|
1.0
|
|
Cadmium binding site 7 out
of 8 in 488d
Go back to
Cadmium Binding Sites List in 488d
Cadmium binding site 7 out
of 8 in the Catalytic Rna Enzyme-Product Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 7 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cd7
b:22.6
occ:1.00
|
N7
|
B:G162
|
2.0
|
24.6
|
0.4
|
N7
|
D:G162
|
2.0
|
25.2
|
0.6
|
C5
|
B:G162
|
2.9
|
26.2
|
0.4
|
C5
|
D:G162
|
2.9
|
27.7
|
0.6
|
O6
|
B:G162
|
3.0
|
35.7
|
0.4
|
O6
|
D:G162
|
3.0
|
40.6
|
0.6
|
C8
|
B:G162
|
3.1
|
25.6
|
0.4
|
C8
|
D:G162
|
3.1
|
26.6
|
0.6
|
C6
|
B:G162
|
3.3
|
30.0
|
0.4
|
C6
|
D:G162
|
3.3
|
32.7
|
0.6
|
OP2
|
B:G162
|
4.0
|
28.7
|
0.4
|
OP2
|
D:G162
|
4.0
|
30.5
|
0.6
|
C4
|
B:G162
|
4.2
|
26.1
|
0.4
|
C4
|
D:G162
|
4.2
|
26.9
|
0.6
|
N9
|
B:G162
|
4.3
|
27.2
|
0.4
|
N9
|
D:G162
|
4.3
|
29.1
|
0.6
|
O4
|
D:U161
|
4.5
|
40.4
|
0.6
|
N1
|
B:G162
|
4.7
|
29.6
|
0.4
|
N1
|
D:G162
|
4.7
|
32.0
|
0.6
|
N7
|
B:A163
|
4.7
|
23.0
|
0.4
|
N7
|
D:A163
|
4.7
|
21.3
|
0.6
|
C5
|
B:A163
|
4.9
|
20.4
|
0.4
|
C5
|
D:A163
|
4.9
|
17.4
|
0.6
|
C8
|
B:A163
|
4.9
|
23.8
|
0.4
|
C8
|
D:A163
|
4.9
|
22.9
|
0.6
|
|
Cadmium binding site 8 out
of 8 in 488d
Go back to
Cadmium Binding Sites List in 488d
Cadmium binding site 8 out
of 8 in the Catalytic Rna Enzyme-Product Complex
Mono view
Stereo pair view
|
A full contact list of Cadmium with other atoms in the Cd binding
site number 8 of Catalytic Rna Enzyme-Product Complex within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cd8
b:20.3
occ:1.00
|
N7
|
A:G101
|
1.9
|
42.9
|
1.0
|
OP2
|
A:A90
|
2.2
|
59.7
|
1.0
|
C5
|
A:G101
|
2.8
|
46.1
|
1.0
|
O6
|
A:G101
|
3.0
|
46.1
|
1.0
|
C8
|
A:G101
|
3.0
|
49.7
|
1.0
|
C6
|
A:G101
|
3.2
|
46.6
|
1.0
|
P
|
A:A90
|
3.6
|
59.0
|
1.0
|
O3'
|
A:G80
|
4.0
|
56.2
|
1.0
|
C4
|
A:G101
|
4.0
|
47.4
|
1.0
|
N9
|
A:G101
|
4.1
|
50.2
|
1.0
|
O2'
|
A:G80
|
4.2
|
60.5
|
1.0
|
OP1
|
A:A90
|
4.5
|
59.0
|
1.0
|
N1
|
A:G101
|
4.6
|
45.3
|
1.0
|
O3'
|
A:A90
|
4.7
|
51.0
|
1.0
|
O5'
|
A:A90
|
4.7
|
58.5
|
1.0
|
N2
|
B:G120
|
4.9
|
29.2
|
0.4
|
N2
|
D:G120
|
4.9
|
24.9
|
0.6
|
C3'
|
A:G80
|
4.9
|
54.3
|
1.0
|
N7
|
A:G102
|
5.0
|
33.6
|
1.0
|
|
Reference:
J.B.Murray,
H.Szoke,
A.Szoke,
W.G.Scott.
Capture and Visualization of A Catalytic Rna Enzyme-Product Complex Using Crystal Lattice Trapping and X-Ray Holographic Reconstruction. Mol.Cell V. 5 279 2000.
ISSN: ISSN 1097-2765
PubMed: 10882069
DOI: 10.1016/S1097-2765(00)80423-2
Page generated: Fri Jul 19 16:53:40 2024
|