Strontium in PDB 1nuv: The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution
Protein crystallography data
The structure of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution, PDB code: 1nuv
was solved by
J.E.Wedekind,
D.B.Mckay,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
28.10 /
1.81
|
Space group
|
P 61
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.600,
60.600,
133.100,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
21 /
21.9
|
Other elements in 1nuv:
The structure of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution also contains other interesting chemical elements:
Strontium Binding Sites:
The binding sites of Strontium atom in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution
(pdb code 1nuv). This binding sites where shown within
5.0 Angstroms radius around Strontium atom.
In total 6 binding sites of Strontium where determined in the
The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution, PDB code: 1nuv:
Jump to Strontium binding site number:
1;
2;
3;
4;
5;
6;
Strontium binding site 1 out
of 6 in 1nuv
Go back to
Strontium Binding Sites List in 1nuv
Strontium binding site 1 out
of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Strontium with other atoms in the Sr binding
site number 1 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Sr424
b:68.9
occ:1.00
|
O
|
B:HOH466
|
2.2
|
41.3
|
1.0
|
O
|
B:HOH467
|
2.2
|
43.5
|
1.0
|
O
|
B:HOH465
|
2.3
|
38.8
|
1.0
|
O
|
B:HOH456
|
2.8
|
26.3
|
1.0
|
N7
|
B:G44
|
4.0
|
27.5
|
1.0
|
O
|
B:HOH457
|
4.1
|
28.5
|
1.0
|
N6
|
B:A45
|
4.2
|
30.3
|
1.0
|
O
|
A:HOH424
|
4.2
|
40.0
|
1.0
|
O
|
B:HOH461
|
4.3
|
49.1
|
1.0
|
O
|
A:HOH449
|
4.3
|
43.8
|
1.0
|
N3
|
A:C23
|
4.5
|
29.8
|
1.0
|
O6
|
B:G44
|
4.5
|
27.8
|
1.0
|
N7
|
B:G43
|
4.5
|
20.6
|
1.0
|
OP2
|
B:G43
|
4.6
|
26.7
|
1.0
|
N4
|
A:C23
|
4.6
|
32.2
|
1.0
|
O
|
A:HOH422
|
4.7
|
33.4
|
1.0
|
C5
|
B:G44
|
5.0
|
26.3
|
1.0
|
C8
|
B:G44
|
5.0
|
28.6
|
1.0
|
C8
|
B:G43
|
5.0
|
21.8
|
1.0
|
|
Strontium binding site 2 out
of 6 in 1nuv
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Strontium Binding Sites List in 1nuv
Strontium binding site 2 out
of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Strontium with other atoms in the Sr binding
site number 2 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Sr420
b:57.2
occ:1.00
|
O
|
C:HOH157
|
2.3
|
45.7
|
1.0
|
O
|
C:HOH147
|
2.7
|
55.5
|
1.0
|
O
|
C:HOH325
|
2.8
|
43.6
|
1.0
|
N1
|
D:A45
|
2.9
|
25.9
|
1.0
|
OP1
|
C:A25
|
2.9
|
20.9
|
1.0
|
O
|
C:HOH395
|
3.0
|
33.0
|
1.0
|
C2
|
D:A45
|
3.1
|
22.8
|
1.0
|
O2
|
C:C23
|
3.4
|
38.0
|
1.0
|
O2'
|
C:C23
|
3.8
|
37.4
|
1.0
|
P
|
C:A25
|
3.9
|
20.9
|
1.0
|
OP2
|
C:A25
|
3.9
|
21.3
|
1.0
|
C6
|
D:A45
|
4.1
|
25.4
|
1.0
|
N3
|
D:A45
|
4.4
|
26.6
|
1.0
|
C2
|
C:C23
|
4.4
|
35.1
|
1.0
|
N6
|
D:A45
|
4.5
|
26.0
|
1.0
|
O
|
C:HOH244
|
4.8
|
40.2
|
1.0
|
C1'
|
C:C23
|
4.8
|
36.0
|
1.0
|
O6
|
D:G44
|
4.8
|
26.1
|
1.0
|
C2'
|
C:C23
|
4.8
|
37.1
|
1.0
|
O5'
|
C:A25
|
4.8
|
20.0
|
1.0
|
|
Strontium binding site 3 out
of 6 in 1nuv
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Strontium Binding Sites List in 1nuv
Strontium binding site 3 out
of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Strontium with other atoms in the Sr binding
site number 3 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Sr422
b:85.1
occ:1.00
|
O
|
D:HOH123
|
2.3
|
28.3
|
1.0
|
O
|
D:HOH192
|
2.5
|
44.1
|
1.0
|
O
|
D:HOH121
|
2.6
|
48.2
|
1.0
|
O
|
D:HOH186
|
4.1
|
48.9
|
1.0
|
O
|
C:HOH197
|
4.3
|
56.3
|
1.0
|
O
|
D:HOH183
|
4.4
|
32.0
|
1.0
|
O
|
D:HOH135
|
4.6
|
42.9
|
1.0
|
O
|
D:HOH139
|
4.9
|
27.8
|
1.0
|
O6
|
D:G43
|
5.0
|
18.7
|
1.0
|
N7
|
D:G42
|
5.0
|
23.3
|
1.0
|
O6
|
D:G42
|
5.0
|
19.5
|
1.0
|
|
Strontium binding site 4 out
of 6 in 1nuv
Go back to
Strontium Binding Sites List in 1nuv
Strontium binding site 4 out
of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Strontium with other atoms in the Sr binding
site number 4 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Sr421
b:53.6
occ:1.00
|
O
|
E:HOH82
|
2.4
|
42.0
|
1.0
|
O
|
F:HOH114
|
2.5
|
50.7
|
1.0
|
N1
|
F:A45
|
2.8
|
23.8
|
1.0
|
OP1
|
E:A25
|
2.8
|
21.3
|
1.0
|
O
|
E:HOH329
|
2.9
|
46.9
|
1.0
|
O
|
E:HOH83
|
3.1
|
34.2
|
1.0
|
C2
|
F:A45
|
3.2
|
22.8
|
1.0
|
O2
|
E:C23
|
3.4
|
35.0
|
1.0
|
O2'
|
E:C23
|
3.8
|
41.3
|
1.0
|
P
|
E:A25
|
3.9
|
20.6
|
1.0
|
OP2
|
E:A25
|
3.9
|
19.4
|
1.0
|
C6
|
F:A45
|
4.0
|
22.9
|
1.0
|
N6
|
F:A45
|
4.4
|
23.4
|
1.0
|
C2
|
E:C23
|
4.4
|
32.8
|
1.0
|
N3
|
F:A45
|
4.5
|
26.8
|
1.0
|
O
|
C:HOH393
|
4.8
|
34.2
|
1.0
|
O
|
E:HOH340
|
4.8
|
35.6
|
1.0
|
O6
|
F:G44
|
4.8
|
27.1
|
1.0
|
C1'
|
E:C23
|
4.8
|
35.7
|
1.0
|
O5'
|
E:A25
|
4.8
|
18.4
|
1.0
|
C2'
|
E:C23
|
4.8
|
39.5
|
1.0
|
|
Strontium binding site 5 out
of 6 in 1nuv
Go back to
Strontium Binding Sites List in 1nuv
Strontium binding site 5 out
of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Strontium with other atoms in the Sr binding
site number 5 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Sr425
b:84.6
occ:1.00
|
O
|
F:HOH331
|
2.2
|
29.6
|
1.0
|
O
|
F:HOH330
|
2.3
|
44.4
|
1.0
|
O
|
F:HOH392
|
2.4
|
48.0
|
1.0
|
O
|
F:HOH397
|
4.2
|
58.5
|
1.0
|
O
|
F:HOH387
|
4.5
|
32.7
|
1.0
|
O
|
F:HOH92
|
4.6
|
36.1
|
1.0
|
O6
|
F:G42
|
4.9
|
19.3
|
1.0
|
O6
|
F:G43
|
4.9
|
20.3
|
1.0
|
N7
|
F:G42
|
4.9
|
24.0
|
1.0
|
O
|
F:HOH396
|
5.0
|
30.0
|
1.0
|
|
Strontium binding site 6 out
of 6 in 1nuv
Go back to
Strontium Binding Sites List in 1nuv
Strontium binding site 6 out
of 6 in the The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution
Mono view
Stereo pair view
|
A full contact list of Strontium with other atoms in the Sr binding
site number 6 of The Leadzyme Ribozyme Bound to Mg(H2O)6(II) and Sr(II) at 1.8 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Sr423
b:65.4
occ:1.00
|
O
|
H:HOH236
|
2.1
|
48.0
|
1.0
|
O
|
H:HOH243
|
2.2
|
35.2
|
1.0
|
O
|
H:HOH270
|
2.3
|
31.4
|
1.0
|
O
|
G:HOH284
|
2.4
|
31.1
|
1.0
|
O
|
H:HOH283
|
2.7
|
25.6
|
1.0
|
N7
|
H:G44
|
4.1
|
28.6
|
1.0
|
O
|
G:HOH234
|
4.2
|
39.1
|
1.0
|
N6
|
H:A45
|
4.2
|
28.5
|
1.0
|
O
|
H:HOH358
|
4.2
|
27.5
|
1.0
|
O
|
H:HOH354
|
4.3
|
49.1
|
1.0
|
O
|
G:HOH261
|
4.4
|
43.0
|
1.0
|
N3
|
G:C23
|
4.5
|
30.7
|
1.0
|
N7
|
H:G43
|
4.5
|
22.0
|
1.0
|
OP2
|
H:G43
|
4.5
|
28.7
|
1.0
|
O6
|
H:G44
|
4.6
|
28.2
|
1.0
|
N4
|
G:C23
|
4.6
|
32.6
|
1.0
|
O
|
G:HOH229
|
4.7
|
36.3
|
1.0
|
O
|
G:HOH403
|
4.9
|
51.7
|
1.0
|
C8
|
H:G43
|
4.9
|
23.0
|
1.0
|
|
Reference:
J.E.Wedekind,
D.B.Mckay.
Crystal Structure of the Leadzyme at 1.8 A Resolution: Metal Ion Binding and the Implications For Catalytic Mechanism and Allo Site Ion Regulation. Biochemistry V. 42 9554 2003.
ISSN: ISSN 0006-2960
PubMed: 12911297
DOI: 10.1021/BI0300783
Page generated: Thu Oct 10 14:04:07 2024
|