Cobalt in PDB 4fep: Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Protein crystallography data
The structure of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine, PDB code: 4fep
was solved by
C.D.Stoddard,
J.J.Trausch,
J.Widmann,
J.Marcano,
R.Knight,
R.T.Batey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.00 /
1.65
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
133.071,
35.252,
41.855,
90.00,
91.40,
90.00
|
R / Rfree (%)
|
17.9 /
22.9
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
(pdb code 4fep). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 9 binding sites of Cobalt where determined in the
Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine, PDB code: 4fep:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Cobalt binding site 1 out
of 9 in 4fep
Go back to
Cobalt Binding Sites List in 4fep
Cobalt binding site 1 out
of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 1 of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co102
b:14.8
occ:1.00
|
CO
|
B:NCO102
|
0.0
|
14.8
|
1.0
|
N1
|
B:NCO102
|
2.0
|
16.4
|
1.0
|
N2
|
B:NCO102
|
2.0
|
17.6
|
1.0
|
N3
|
B:NCO102
|
2.0
|
15.3
|
1.0
|
N4
|
B:NCO102
|
2.0
|
18.4
|
1.0
|
N6
|
B:NCO102
|
2.0
|
16.4
|
1.0
|
N5
|
B:NCO102
|
2.0
|
15.1
|
1.0
|
O
|
B:HOH850
|
3.5
|
31.2
|
1.0
|
O
|
B:HOH856
|
3.8
|
30.3
|
1.0
|
O
|
B:HOH677
|
3.8
|
15.9
|
1.0
|
O
|
B:HOH655
|
3.9
|
18.9
|
1.0
|
O
|
B:HOH681
|
4.0
|
20.2
|
1.0
|
O
|
B:HOH982
|
4.0
|
1.0
|
1.0
|
OP1
|
B:U67
|
4.1
|
11.7
|
1.0
|
O
|
B:HOH1031
|
4.3
|
0.1
|
1.0
|
O3'
|
B:A66
|
4.4
|
11.1
|
1.0
|
O
|
B:HOH836
|
4.5
|
40.7
|
1.0
|
O
|
B:HOH744
|
4.6
|
20.6
|
1.0
|
P
|
B:U67
|
4.9
|
10.9
|
1.0
|
O2'
|
B:A66
|
5.0
|
10.7
|
1.0
|
|
Cobalt binding site 2 out
of 9 in 4fep
Go back to
Cobalt Binding Sites List in 4fep
Cobalt binding site 2 out
of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 2 of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co103
b:25.3
occ:1.00
|
CO
|
B:NCO103
|
0.0
|
25.3
|
1.0
|
N4
|
B:NCO103
|
2.0
|
26.2
|
1.0
|
N3
|
B:NCO103
|
2.0
|
24.9
|
1.0
|
N2
|
B:NCO103
|
2.0
|
24.9
|
1.0
|
N6
|
B:NCO103
|
2.0
|
24.9
|
1.0
|
N5
|
B:NCO103
|
2.0
|
26.3
|
1.0
|
N1
|
B:NCO103
|
2.0
|
24.8
|
1.0
|
O
|
B:HOH1025
|
3.8
|
32.2
|
1.0
|
O
|
B:HOH848
|
3.8
|
36.4
|
1.0
|
O
|
B:HOH658
|
3.9
|
23.6
|
1.0
|
O
|
B:HOH927
|
3.9
|
23.6
|
1.0
|
O
|
B:HOH756
|
3.9
|
32.4
|
1.0
|
OP1
|
B:G38
|
4.1
|
11.8
|
1.0
|
OP1
|
B:G56
|
4.2
|
18.5
|
1.0
|
O
|
B:HOH912
|
4.5
|
48.8
|
1.0
|
O
|
B:HOH998
|
4.7
|
0.1
|
1.0
|
O
|
B:HOH746
|
4.8
|
34.2
|
1.0
|
OP2
|
B:G56
|
4.9
|
18.6
|
1.0
|
O
|
B:HOH771
|
4.9
|
30.2
|
1.0
|
O
|
B:HOH811
|
4.9
|
33.2
|
1.0
|
|
Cobalt binding site 3 out
of 9 in 4fep
Go back to
Cobalt Binding Sites List in 4fep
Cobalt binding site 3 out
of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 3 of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co104
b:15.5
occ:1.00
|
CO
|
B:NCO104
|
0.0
|
15.5
|
1.0
|
N6
|
B:NCO104
|
2.0
|
18.0
|
1.0
|
N3
|
B:NCO104
|
2.0
|
16.8
|
1.0
|
N1
|
B:NCO104
|
2.0
|
18.2
|
1.0
|
N4
|
B:NCO104
|
2.0
|
19.8
|
1.0
|
N2
|
B:NCO104
|
2.0
|
17.3
|
1.0
|
N5
|
B:NCO104
|
2.0
|
15.5
|
1.0
|
O
|
B:HOH1135
|
3.6
|
57.4
|
1.0
|
O4
|
B:U69
|
4.0
|
8.9
|
1.0
|
O
|
B:HOH720
|
4.1
|
25.3
|
1.0
|
O
|
B:HOH763
|
4.1
|
32.1
|
1.0
|
O6
|
B:G56
|
4.1
|
14.0
|
1.0
|
O
|
B:HOH698
|
4.2
|
25.6
|
1.0
|
O
|
B:HOH697
|
4.3
|
27.2
|
1.0
|
O
|
B:HOH617
|
4.4
|
17.5
|
1.0
|
O
|
B:HOH726
|
4.4
|
20.6
|
1.0
|
OP2
|
B:C39
|
4.4
|
15.1
|
1.0
|
O
|
B:HOH683
|
4.4
|
19.4
|
1.0
|
OP1
|
B:C39
|
4.5
|
14.2
|
1.0
|
N7
|
B:G56
|
4.7
|
13.7
|
1.0
|
O6
|
B:G68
|
4.9
|
10.1
|
1.0
|
C6
|
B:G56
|
5.0
|
13.1
|
1.0
|
|
Cobalt binding site 4 out
of 9 in 4fep
Go back to
Cobalt Binding Sites List in 4fep
Cobalt binding site 4 out
of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 4 of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co105
b:11.7
occ:1.00
|
CO
|
B:NCO105
|
0.0
|
11.7
|
1.0
|
N6
|
B:NCO105
|
2.0
|
12.7
|
1.0
|
N5
|
B:NCO105
|
2.0
|
14.4
|
1.0
|
N1
|
B:NCO105
|
2.0
|
14.4
|
1.0
|
N2
|
B:NCO105
|
2.0
|
12.1
|
1.0
|
N3
|
B:NCO105
|
2.0
|
11.2
|
1.0
|
N4
|
B:NCO105
|
2.0
|
9.2
|
1.0
|
O
|
B:HOH607
|
3.9
|
14.7
|
1.0
|
OP2
|
B:A66
|
3.9
|
17.3
|
1.0
|
O6
|
B:G32
|
4.0
|
11.2
|
1.0
|
O
|
B:HOH643
|
4.1
|
19.2
|
1.0
|
O6
|
B:G31
|
4.1
|
8.6
|
1.0
|
O
|
B:HOH638
|
4.1
|
16.4
|
1.0
|
O
|
B:HOH727
|
4.2
|
24.8
|
1.0
|
O
|
B:HOH641
|
4.2
|
19.4
|
1.0
|
O
|
B:HOH624
|
4.3
|
18.8
|
1.0
|
O
|
B:HOH646
|
4.3
|
13.5
|
1.0
|
O
|
B:HOH610
|
4.3
|
18.3
|
1.0
|
N7
|
B:G31
|
4.4
|
10.7
|
1.0
|
C6
|
B:G31
|
4.9
|
10.2
|
1.0
|
O
|
B:HOH950
|
4.9
|
37.2
|
1.0
|
|
Cobalt binding site 5 out
of 9 in 4fep
Go back to
Cobalt Binding Sites List in 4fep
Cobalt binding site 5 out
of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 5 of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co106
b:37.9
occ:1.00
|
CO
|
B:NCO106
|
0.0
|
37.9
|
1.0
|
N5
|
B:NCO106
|
2.0
|
39.0
|
1.0
|
N1
|
B:NCO106
|
2.0
|
37.6
|
1.0
|
N2
|
B:NCO106
|
2.0
|
38.0
|
1.0
|
N6
|
B:NCO106
|
2.0
|
37.8
|
1.0
|
N4
|
B:NCO106
|
2.0
|
38.4
|
1.0
|
N3
|
B:NCO106
|
2.0
|
38.0
|
1.0
|
O
|
B:HOH1132
|
3.7
|
41.7
|
1.0
|
O
|
B:HOH715
|
3.8
|
33.3
|
1.0
|
OP2
|
B:G37
|
4.0
|
11.3
|
1.0
|
O
|
B:HOH629
|
4.0
|
19.9
|
1.0
|
O
|
B:HOH827
|
4.2
|
33.3
|
1.0
|
O6
|
B:G38
|
4.3
|
8.1
|
1.0
|
O
|
B:HOH694
|
4.4
|
25.4
|
1.0
|
N7
|
B:G38
|
4.4
|
8.6
|
1.0
|
O
|
B:HOH886
|
4.5
|
33.6
|
1.0
|
O
|
B:HOH967
|
4.6
|
29.0
|
1.0
|
N7
|
B:G37
|
4.6
|
11.0
|
1.0
|
O
|
B:HOH703
|
5.0
|
28.6
|
1.0
|
|
Cobalt binding site 6 out
of 9 in 4fep
Go back to
Cobalt Binding Sites List in 4fep
Cobalt binding site 6 out
of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 6 of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co107
b:29.0
occ:1.00
|
CO
|
B:NCO107
|
0.0
|
29.0
|
1.0
|
N1
|
B:NCO107
|
2.0
|
29.1
|
1.0
|
N6
|
B:NCO107
|
2.0
|
28.6
|
1.0
|
N5
|
B:NCO107
|
2.0
|
28.0
|
1.0
|
N2
|
B:NCO107
|
2.0
|
28.8
|
1.0
|
N3
|
B:NCO107
|
2.0
|
28.7
|
1.0
|
N4
|
B:NCO107
|
2.0
|
28.1
|
1.0
|
O
|
B:HOH674
|
3.7
|
27.3
|
1.0
|
O
|
B:HOH614
|
3.9
|
19.6
|
1.0
|
O
|
B:HOH881
|
3.9
|
43.1
|
1.0
|
OP1
|
B:C54
|
4.0
|
23.2
|
1.0
|
O
|
B:HOH1023
|
4.0
|
41.0
|
1.0
|
OP2
|
B:C41
|
4.1
|
14.2
|
1.0
|
O
|
B:HOH858
|
4.3
|
31.5
|
1.0
|
O
|
B:HOH602
|
4.4
|
14.1
|
1.0
|
OP2
|
B:G42
|
4.5
|
10.8
|
1.0
|
O5'
|
B:C54
|
4.7
|
19.6
|
1.0
|
O
|
B:HOH883
|
4.8
|
43.9
|
1.0
|
P
|
B:C54
|
4.9
|
22.4
|
1.0
|
|
Cobalt binding site 7 out
of 9 in 4fep
Go back to
Cobalt Binding Sites List in 4fep
Cobalt binding site 7 out
of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 7 of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co108
b:26.7
occ:1.00
|
CO
|
B:NCO108
|
0.0
|
26.7
|
1.0
|
N4
|
B:NCO108
|
2.0
|
27.9
|
1.0
|
N2
|
B:NCO108
|
2.0
|
26.4
|
1.0
|
N3
|
B:NCO108
|
2.0
|
27.2
|
1.0
|
N5
|
B:NCO108
|
2.0
|
26.9
|
1.0
|
N1
|
B:NCO108
|
2.0
|
26.3
|
1.0
|
N6
|
B:NCO108
|
2.0
|
25.9
|
1.0
|
O
|
B:HOH676
|
3.4
|
96.1
|
1.0
|
O
|
B:HOH1004
|
3.7
|
50.5
|
1.0
|
O
|
B:HOH1059
|
3.8
|
41.5
|
1.0
|
O
|
B:HOH1157
|
3.9
|
46.4
|
1.0
|
O
|
B:HOH859
|
3.9
|
36.9
|
1.0
|
O4
|
B:U47
|
4.2
|
18.2
|
1.0
|
O
|
B:HOH894
|
4.2
|
28.6
|
1.0
|
O6
|
B:G46
|
4.2
|
14.6
|
1.0
|
N7
|
B:G46
|
4.5
|
15.8
|
1.0
|
O
|
B:HOH806
|
4.5
|
29.7
|
1.0
|
O
|
B:HOH721
|
4.5
|
24.3
|
1.0
|
O
|
B:HOH776
|
4.8
|
25.1
|
1.0
|
O
|
B:HOH754
|
4.8
|
27.9
|
1.0
|
|
Cobalt binding site 8 out
of 9 in 4fep
Go back to
Cobalt Binding Sites List in 4fep
Cobalt binding site 8 out
of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 8 of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co109
b:0.5
occ:1.00
|
CO
|
B:NCO109
|
0.0
|
0.5
|
1.0
|
N1
|
B:NCO109
|
2.0
|
0.3
|
1.0
|
N6
|
B:NCO109
|
2.0
|
0.2
|
1.0
|
N5
|
B:NCO109
|
2.0
|
0.2
|
1.0
|
N4
|
B:NCO109
|
2.0
|
0.2
|
1.0
|
N3
|
B:NCO109
|
2.0
|
0.2
|
1.0
|
N2
|
B:NCO109
|
2.0
|
0.3
|
1.0
|
OP1
|
B:A21
|
3.7
|
23.4
|
1.0
|
OP2
|
B:U22
|
3.9
|
21.1
|
1.0
|
O
|
B:HOH1166
|
4.5
|
65.3
|
1.0
|
O
|
B:HOH1130
|
4.5
|
62.0
|
1.0
|
P
|
B:A21
|
4.8
|
24.5
|
1.0
|
O
|
B:HOH951
|
4.9
|
61.8
|
1.0
|
O
|
B:HOH817
|
5.0
|
32.6
|
1.0
|
|
Cobalt binding site 9 out
of 9 in 4fep
Go back to
Cobalt Binding Sites List in 4fep
Cobalt binding site 9 out
of 9 in the Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine
Mono view
Stereo pair view
|
A full contact list of Cobalt with other atoms in the Co binding
site number 9 of Crystal Structure of the A24U/U25A/A46G/C74U Mutant Xpt-Pbux Guanine Riboswitch Aptamer Domain in Complex with 2,6-Diaminopurine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co110
b:15.8
occ:0.64
|
CO
|
B:NCO110
|
0.0
|
15.8
|
0.6
|
N5
|
B:NCO110
|
2.0
|
16.2
|
0.6
|
N2
|
B:NCO110
|
2.0
|
17.1
|
0.6
|
N1
|
B:NCO110
|
2.0
|
18.1
|
0.6
|
N3
|
B:NCO110
|
2.0
|
18.2
|
0.6
|
N6
|
B:NCO110
|
2.0
|
15.9
|
0.6
|
N4
|
B:NCO110
|
2.0
|
15.9
|
0.6
|
O
|
B:HOH875
|
4.0
|
48.1
|
1.0
|
OP1
|
B:G72
|
4.2
|
12.1
|
1.0
|
O
|
B:HOH888
|
4.2
|
36.1
|
1.0
|
OP1
|
B:A73
|
4.2
|
23.0
|
1.0
|
O
|
B:HOH1078
|
4.4
|
61.6
|
1.0
|
O
|
B:HOH675
|
4.5
|
22.2
|
1.0
|
OP2
|
B:A73
|
4.9
|
26.5
|
1.0
|
|
Reference:
C.D.Stoddard,
J.Widmann,
J.J.Trausch,
J.G.Marcano-Velazquez,
R.Knight,
R.T.Batey.
Nucleotides Adjacent to the Ligand-Binding Pocket Are Linked to Activity Tuning in the Purine Riboswitch. J.Mol.Biol. V. 425 1596 2013.
ISSN: ISSN 0022-2836
PubMed: 23485418
DOI: 10.1016/J.JMB.2013.02.023
Page generated: Tue Jul 30 17:04:35 2024
|