Cobalt in PDB 3ges: Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
Protein crystallography data
The structure of Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine, PDB code: 3ges
was solved by
S.D.Gilbert,
R.T.Batey,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.44 /
2.15
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
130.940,
35.040,
42.190,
90.00,
89.61,
90.00
|
R / Rfree (%)
|
23.8 /
28.3
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
(pdb code 3ges). This binding sites where shown within
5.0 Angstroms radius around Cobalt atom.
In total 8 binding sites of Cobalt where determined in the
Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine, PDB code: 3ges:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Cobalt binding site 1 out
of 8 in 3ges
Go back to
Cobalt Binding Sites List in 3ges
Cobalt binding site 1 out
of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co101
b:28.3
occ:1.00
|
CO
|
A:NCO101
|
0.0
|
28.3
|
1.0
|
N4
|
A:NCO101
|
2.0
|
27.3
|
1.0
|
N2
|
A:NCO101
|
2.0
|
22.8
|
1.0
|
N6
|
A:NCO101
|
2.0
|
25.1
|
1.0
|
N1
|
A:NCO101
|
2.0
|
24.0
|
1.0
|
N5
|
A:NCO101
|
2.0
|
25.6
|
1.0
|
N3
|
A:NCO101
|
2.0
|
25.8
|
1.0
|
O
|
A:HOH410
|
3.7
|
40.6
|
1.0
|
OP1
|
A:U67
|
4.2
|
19.4
|
1.0
|
O3'
|
A:A66
|
4.4
|
20.3
|
1.0
|
OP2
|
A:C28
|
4.6
|
52.1
|
1.0
|
OP1
|
A:G27
|
4.8
|
55.6
|
1.0
|
OP1
|
A:C28
|
4.8
|
48.5
|
1.0
|
O2'
|
A:A66
|
4.9
|
28.5
|
1.0
|
P
|
A:U67
|
5.0
|
20.7
|
1.0
|
|
Cobalt binding site 2 out
of 8 in 3ges
Go back to
Cobalt Binding Sites List in 3ges
Cobalt binding site 2 out
of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co102
b:45.0
occ:1.00
|
CO
|
A:NCO102
|
0.0
|
45.0
|
1.0
|
N2
|
A:NCO102
|
2.0
|
46.9
|
1.0
|
N5
|
A:NCO102
|
2.0
|
45.5
|
1.0
|
N4
|
A:NCO102
|
2.0
|
45.6
|
1.0
|
N6
|
A:NCO102
|
2.0
|
45.5
|
1.0
|
N3
|
A:NCO102
|
2.0
|
45.3
|
1.0
|
N1
|
A:NCO102
|
2.0
|
44.5
|
1.0
|
OP1
|
A:G56
|
3.9
|
34.1
|
1.0
|
OP1
|
A:G38
|
4.0
|
20.2
|
1.0
|
O
|
A:HOH333
|
4.0
|
27.7
|
1.0
|
OP2
|
A:G56
|
4.7
|
32.1
|
1.0
|
O
|
A:HOH336
|
4.8
|
33.4
|
1.0
|
C5'
|
A:C39
|
4.8
|
30.2
|
1.0
|
P
|
A:G56
|
4.8
|
32.0
|
1.0
|
O
|
A:HOH360
|
4.9
|
34.5
|
1.0
|
|
Cobalt binding site 3 out
of 8 in 3ges
Go back to
Cobalt Binding Sites List in 3ges
Cobalt binding site 3 out
of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co103
b:35.5
occ:1.00
|
CO
|
A:NCO103
|
0.0
|
35.5
|
1.0
|
N1
|
A:NCO103
|
2.0
|
33.0
|
1.0
|
N3
|
A:NCO103
|
2.0
|
32.6
|
1.0
|
N2
|
A:NCO103
|
2.0
|
33.7
|
1.0
|
N6
|
A:NCO103
|
2.0
|
35.6
|
1.0
|
N4
|
A:NCO103
|
2.0
|
34.5
|
1.0
|
N5
|
A:NCO103
|
2.0
|
34.3
|
1.0
|
O6
|
A:G56
|
3.9
|
30.7
|
1.0
|
O4
|
A:U69
|
3.9
|
24.5
|
1.0
|
O
|
A:HOH339
|
4.4
|
24.7
|
1.0
|
N7
|
A:G56
|
4.4
|
28.5
|
1.0
|
OP2
|
A:C39
|
4.5
|
28.6
|
1.0
|
OP1
|
A:C39
|
4.7
|
26.3
|
1.0
|
C6
|
A:G56
|
4.7
|
30.4
|
1.0
|
O6
|
A:G68
|
4.9
|
17.2
|
1.0
|
C5
|
A:G56
|
5.0
|
29.2
|
1.0
|
|
Cobalt binding site 4 out
of 8 in 3ges
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Cobalt Binding Sites List in 3ges
Cobalt binding site 4 out
of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co104
b:33.0
occ:1.00
|
CO
|
A:NCO104
|
0.0
|
33.0
|
1.0
|
N3
|
A:NCO104
|
2.0
|
30.2
|
1.0
|
N1
|
A:NCO104
|
2.0
|
28.6
|
1.0
|
N6
|
A:NCO104
|
2.0
|
29.5
|
1.0
|
N5
|
A:NCO104
|
2.0
|
31.3
|
1.0
|
N2
|
A:NCO104
|
2.0
|
30.0
|
1.0
|
N4
|
A:NCO104
|
2.0
|
28.0
|
1.0
|
O
|
A:HOH305
|
3.7
|
23.5
|
1.0
|
O6
|
A:G32
|
3.9
|
22.7
|
1.0
|
OP2
|
A:A66
|
3.9
|
31.5
|
1.0
|
O
|
A:HOH328
|
4.0
|
29.2
|
1.0
|
O
|
A:HOH312
|
4.1
|
16.3
|
1.0
|
O
|
A:HOH300
|
4.1
|
20.2
|
1.0
|
O6
|
A:G31
|
4.2
|
20.1
|
1.0
|
N7
|
A:G31
|
4.4
|
22.6
|
1.0
|
O
|
A:HOH316
|
4.6
|
18.2
|
1.0
|
O
|
A:HOH322
|
4.8
|
21.6
|
1.0
|
C6
|
A:G32
|
4.9
|
22.8
|
1.0
|
C6
|
A:G31
|
4.9
|
22.1
|
1.0
|
O
|
A:HOH330
|
4.9
|
35.4
|
1.0
|
|
Cobalt binding site 5 out
of 8 in 3ges
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Cobalt Binding Sites List in 3ges
Cobalt binding site 5 out
of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co105
b:80.3
occ:1.00
|
CO
|
A:NCO105
|
0.0
|
80.3
|
1.0
|
N6
|
A:NCO105
|
2.0
|
80.4
|
1.0
|
N2
|
A:NCO105
|
2.0
|
80.9
|
1.0
|
N3
|
A:NCO105
|
2.0
|
80.6
|
1.0
|
N1
|
A:NCO105
|
2.0
|
81.2
|
1.0
|
N5
|
A:NCO105
|
2.0
|
80.0
|
1.0
|
N4
|
A:NCO105
|
2.0
|
80.5
|
1.0
|
O
|
A:HOH396
|
3.6
|
62.1
|
1.0
|
O
|
A:HOH365
|
3.9
|
67.4
|
1.0
|
OP2
|
A:G37
|
3.9
|
28.7
|
1.0
|
O6
|
A:G38
|
4.3
|
28.5
|
1.0
|
N7
|
A:G38
|
4.3
|
25.8
|
1.0
|
O
|
A:HOH398
|
4.4
|
37.1
|
1.0
|
O
|
A:HOH311
|
4.4
|
36.0
|
1.0
|
O
|
A:HOH320
|
4.5
|
31.5
|
1.0
|
N7
|
A:G37
|
4.7
|
23.4
|
1.0
|
|
Cobalt binding site 6 out
of 8 in 3ges
Go back to
Cobalt Binding Sites List in 3ges
Cobalt binding site 6 out
of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co108
b:76.5
occ:1.00
|
CO
|
A:NCO108
|
0.0
|
76.5
|
1.0
|
N3
|
A:NCO108
|
2.0
|
76.3
|
1.0
|
N5
|
A:NCO108
|
2.0
|
76.4
|
1.0
|
N4
|
A:NCO108
|
2.0
|
76.0
|
1.0
|
N2
|
A:NCO108
|
2.0
|
75.9
|
1.0
|
N1
|
A:NCO108
|
2.0
|
76.0
|
1.0
|
N6
|
A:NCO108
|
2.0
|
76.0
|
1.0
|
O
|
A:HOH382
|
3.2
|
40.3
|
1.0
|
O4
|
A:U47
|
3.7
|
45.2
|
1.0
|
O6
|
A:G46
|
4.3
|
35.1
|
1.0
|
C4
|
A:U47
|
4.6
|
43.4
|
1.0
|
N7
|
A:G46
|
4.7
|
39.2
|
1.0
|
OP2
|
A:C50
|
4.9
|
46.6
|
1.0
|
|
Cobalt binding site 7 out
of 8 in 3ges
Go back to
Cobalt Binding Sites List in 3ges
Cobalt binding site 7 out
of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co109
b:88.7
occ:1.00
|
CO
|
A:NCO109
|
0.0
|
88.7
|
1.0
|
N1
|
A:NCO109
|
2.0
|
88.6
|
1.0
|
N4
|
A:NCO109
|
2.0
|
88.4
|
1.0
|
N6
|
A:NCO109
|
2.0
|
88.5
|
1.0
|
N5
|
A:NCO109
|
2.0
|
88.6
|
1.0
|
N2
|
A:NCO109
|
2.0
|
88.1
|
1.0
|
N3
|
A:NCO109
|
2.0
|
88.0
|
1.0
|
O
|
A:HOH307
|
3.9
|
51.8
|
1.0
|
OP2
|
A:C71
|
4.0
|
28.0
|
1.0
|
OP1
|
A:A24
|
4.0
|
37.0
|
1.0
|
|
Cobalt binding site 8 out
of 8 in 3ges
Go back to
Cobalt Binding Sites List in 3ges
Cobalt binding site 8 out
of 8 in the Crystal Structure of the Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine
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 Guanine Riboswitch C74U Mutant Bound to 6-O-Methylguanine within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co112
b:50.2
occ:0.64
|
CO
|
A:NCO112
|
0.0
|
50.2
|
0.6
|
N2
|
A:NCO112
|
2.0
|
49.3
|
0.6
|
N6
|
A:NCO112
|
2.0
|
49.5
|
0.6
|
N3
|
A:NCO112
|
2.0
|
49.6
|
0.6
|
N4
|
A:NCO112
|
2.0
|
48.7
|
0.6
|
N1
|
A:NCO112
|
2.0
|
49.8
|
0.6
|
N5
|
A:NCO112
|
2.0
|
49.4
|
0.6
|
O
|
A:HOH353
|
3.1
|
51.2
|
1.0
|
OP1
|
A:G72
|
4.0
|
20.5
|
1.0
|
O
|
A:HOH413
|
4.3
|
63.0
|
1.0
|
OP2
|
A:A73
|
5.0
|
35.7
|
1.0
|
|
Reference:
S.D.Gilbert,
F.E.Reyes,
A.L.Edwards,
R.T.Batey.
Adaptive Ligand Binding By the Purine Riboswitch in the Recognition of Guanine and Adenine Analogs Structure V. 17 857 2009.
ISSN: ISSN 0969-2126
PubMed: 19523903
DOI: 10.1016/J.STR.2009.04.009
Page generated: Tue Jul 30 16:04:16 2024
|