Cobalt in PDB 1ub8: Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
Protein crystallography data
The structure of Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue, PDB code: 1ub8
was solved by
T.Sunami,
J.Kondo,
I.Hirao,
K.Watanabe,
K.Miura,
A.Takenaka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
24.00 /
1.60
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.675,
48.856,
63.761,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
19.4 /
23.2
|
Cobalt Binding Sites:
The binding sites of Cobalt atom in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
(pdb code 1ub8). 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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue, PDB code: 1ub8:
Jump to Cobalt binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Cobalt binding site 1 out
of 9 in 1ub8
Go back to
Cobalt Binding Sites List in 1ub8
Cobalt binding site 1 out
of 9 in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Co1401
b:16.8
occ:1.00
|
CO
|
A:NCO1401
|
0.0
|
16.8
|
1.0
|
N4
|
A:NCO1401
|
1.9
|
18.9
|
1.0
|
N5
|
A:NCO1401
|
1.9
|
18.3
|
1.0
|
N6
|
A:NCO1401
|
1.9
|
16.5
|
1.0
|
N3
|
A:NCO1401
|
1.9
|
15.8
|
1.0
|
N2
|
A:NCO1401
|
1.9
|
17.5
|
1.0
|
N1
|
A:NCO1401
|
2.0
|
15.4
|
1.0
|
O
|
A:HOH1456
|
3.6
|
45.1
|
1.0
|
O
|
A:HOH1405
|
3.6
|
21.6
|
1.0
|
OP1
|
D:DA5
|
3.9
|
22.9
|
1.0
|
O
|
A:HOH1443
|
4.0
|
29.7
|
1.0
|
O6
|
B:DG3
|
4.1
|
12.3
|
1.0
|
N7
|
A:DG3
|
4.1
|
14.7
|
1.0
|
O
|
A:HOH1433
|
4.1
|
20.0
|
1.0
|
O
|
A:HOH1434
|
4.1
|
26.5
|
1.0
|
OP2
|
A:DC2
|
4.2
|
17.9
|
1.0
|
O6
|
A:DG3
|
4.3
|
14.1
|
1.0
|
OP2
|
D:DA5
|
4.4
|
22.6
|
1.0
|
O
|
A:HOH1441
|
4.6
|
40.3
|
1.0
|
P
|
D:DA5
|
4.6
|
22.7
|
1.0
|
C5
|
A:DG3
|
4.9
|
11.9
|
1.0
|
C6
|
A:DG3
|
5.0
|
11.6
|
1.0
|
|
Cobalt binding site 2 out
of 9 in 1ub8
Go back to
Cobalt Binding Sites List in 1ub8
Cobalt binding site 2 out
of 9 in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co404
b:12.0
occ:1.00
|
CO
|
B:NCO404
|
0.0
|
12.0
|
1.0
|
N4
|
B:NCO404
|
1.9
|
13.6
|
1.0
|
N5
|
B:NCO404
|
1.9
|
14.9
|
1.0
|
N6
|
B:NCO404
|
1.9
|
14.9
|
1.0
|
N3
|
B:NCO404
|
2.0
|
13.5
|
1.0
|
N2
|
B:NCO404
|
2.0
|
12.8
|
1.0
|
N1
|
B:NCO404
|
2.0
|
15.7
|
1.0
|
O
|
A:HOH1406
|
3.7
|
16.2
|
1.0
|
O
|
B:HOH36
|
3.9
|
14.0
|
1.0
|
O6
|
B:DG6
|
3.9
|
10.6
|
1.0
|
O
|
B:HOH157
|
4.0
|
31.7
|
1.0
|
OP2
|
E:DC7
|
4.2
|
13.8
|
1.0
|
O
|
B:HOH27
|
4.2
|
11.9
|
1.0
|
OP1
|
E:DC7
|
4.2
|
14.2
|
1.0
|
N7
|
B:DG6
|
4.3
|
11.6
|
1.0
|
O
|
B:HOH40
|
4.6
|
13.7
|
1.0
|
P
|
E:DC7
|
4.7
|
12.5
|
1.0
|
C6
|
B:DG6
|
4.8
|
10.4
|
1.0
|
C5
|
B:DG6
|
4.9
|
10.3
|
1.0
|
|
Cobalt binding site 3 out
of 9 in 1ub8
Go back to
Cobalt Binding Sites List in 1ub8
Cobalt binding site 3 out
of 9 in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Co406
b:33.3
occ:1.00
|
CO
|
B:NCO406
|
0.0
|
33.3
|
1.0
|
N4
|
B:NCO406
|
1.9
|
36.2
|
1.0
|
N5
|
B:NCO406
|
1.9
|
35.9
|
1.0
|
N3
|
B:NCO406
|
1.9
|
35.8
|
1.0
|
N6
|
B:NCO406
|
1.9
|
35.1
|
1.0
|
N2
|
B:NCO406
|
2.0
|
36.1
|
1.0
|
N1
|
B:NCO406
|
2.0
|
36.2
|
1.0
|
OP1
|
B:DA5
|
3.8
|
18.8
|
1.0
|
O
|
B:HOH303
|
4.0
|
36.9
|
1.0
|
|
Cobalt binding site 4 out
of 9 in 1ub8
Go back to
Cobalt Binding Sites List in 1ub8
Cobalt binding site 4 out
of 9 in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co407
b:60.8
occ:1.00
|
CO
|
C:NCO407
|
0.0
|
60.8
|
1.0
|
N4
|
C:NCO407
|
1.9
|
60.4
|
1.0
|
N5
|
C:NCO407
|
1.9
|
60.4
|
1.0
|
N6
|
C:NCO407
|
1.9
|
60.7
|
1.0
|
N3
|
C:NCO407
|
1.9
|
60.7
|
1.0
|
N2
|
C:NCO407
|
1.9
|
60.4
|
1.0
|
N1
|
C:NCO407
|
2.0
|
60.6
|
1.0
|
O6
|
C:DG6
|
3.9
|
28.3
|
1.0
|
O
|
C:HOH174
|
4.0
|
42.7
|
1.0
|
N7
|
C:DG6
|
4.3
|
31.3
|
1.0
|
C6
|
C:DG6
|
4.7
|
28.6
|
1.0
|
O
|
C:HOH52
|
4.8
|
37.6
|
1.0
|
C5
|
C:DG6
|
4.9
|
30.8
|
1.0
|
O
|
C:HOH54
|
5.0
|
35.1
|
1.0
|
|
Cobalt binding site 5 out
of 9 in 1ub8
Go back to
Cobalt Binding Sites List in 1ub8
Cobalt binding site 5 out
of 9 in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Co408
b:59.6
occ:1.00
|
CO
|
C:NCO408
|
0.0
|
59.6
|
1.0
|
N4
|
C:NCO408
|
1.9
|
58.4
|
1.0
|
N5
|
C:NCO408
|
1.9
|
58.5
|
1.0
|
N6
|
C:NCO408
|
1.9
|
59.0
|
1.0
|
N3
|
C:NCO408
|
1.9
|
58.0
|
1.0
|
N2
|
C:NCO408
|
1.9
|
58.2
|
1.0
|
N1
|
C:NCO408
|
2.0
|
58.7
|
1.0
|
O6
|
D:DG3
|
4.0
|
26.7
|
1.0
|
O
|
C:HOH291
|
4.0
|
41.1
|
1.0
|
N7
|
C:DG3
|
4.1
|
25.0
|
1.0
|
O
|
C:HOH194
|
4.4
|
42.7
|
1.0
|
OP2
|
C:DC2
|
4.6
|
42.1
|
1.0
|
O6
|
C:DG3
|
4.9
|
26.0
|
1.0
|
C8
|
C:DG3
|
4.9
|
26.2
|
1.0
|
|
Cobalt binding site 6 out
of 9 in 1ub8
Go back to
Cobalt Binding Sites List in 1ub8
Cobalt binding site 6 out
of 9 in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co400
b:23.6
occ:1.00
|
CO
|
D:NCO400
|
0.0
|
23.6
|
1.0
|
N4
|
D:NCO400
|
1.9
|
24.8
|
1.0
|
N5
|
D:NCO400
|
1.9
|
21.4
|
1.0
|
N2
|
D:NCO400
|
1.9
|
23.2
|
1.0
|
N6
|
D:NCO400
|
1.9
|
24.8
|
1.0
|
N3
|
D:NCO400
|
1.9
|
23.5
|
1.0
|
N1
|
D:NCO400
|
2.0
|
23.6
|
1.0
|
|
Cobalt binding site 7 out
of 9 in 1ub8
Go back to
Cobalt Binding Sites List in 1ub8
Cobalt binding site 7 out
of 9 in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Co402
b:20.0
occ:1.00
|
CO
|
D:NCO402
|
0.0
|
20.0
|
1.0
|
N4
|
D:NCO402
|
1.9
|
21.1
|
1.0
|
N6
|
D:NCO402
|
1.9
|
20.8
|
1.0
|
N5
|
D:NCO402
|
1.9
|
21.3
|
1.0
|
N3
|
D:NCO402
|
2.0
|
21.7
|
1.0
|
N2
|
D:NCO402
|
2.0
|
22.9
|
1.0
|
N1
|
D:NCO402
|
2.0
|
21.8
|
1.0
|
O6
|
D:DG6
|
3.8
|
18.1
|
1.0
|
O
|
D:HOH68
|
3.9
|
26.3
|
1.0
|
OP1
|
A:DG3
|
3.9
|
21.6
|
1.0
|
O
|
C:HOH254
|
4.0
|
42.2
|
1.0
|
O
|
D:HOH209
|
4.1
|
43.2
|
1.0
|
O
|
D:HOH377
|
4.2
|
47.7
|
1.0
|
OP2
|
A:DG3
|
4.2
|
19.5
|
1.0
|
O
|
D:HOH69
|
4.2
|
29.0
|
1.0
|
O
|
D:HOH215
|
4.2
|
37.9
|
1.0
|
O
|
D:HOH65
|
4.2
|
36.4
|
1.0
|
N7
|
D:DG6
|
4.3
|
19.2
|
1.0
|
O
|
D:HOH59
|
4.3
|
18.5
|
1.0
|
P
|
A:DG3
|
4.6
|
18.7
|
1.0
|
C6
|
D:DG6
|
4.7
|
17.9
|
1.0
|
O
|
D:HOH210
|
4.8
|
37.8
|
1.0
|
C5
|
D:DG6
|
4.9
|
18.8
|
1.0
|
N7
|
D:DA5
|
5.0
|
18.5
|
1.0
|
|
Cobalt binding site 8 out
of 9 in 1ub8
Go back to
Cobalt Binding Sites List in 1ub8
Cobalt binding site 8 out
of 9 in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Co403
b:15.1
occ:1.00
|
CO
|
E:NCO403
|
0.0
|
15.1
|
1.0
|
N5
|
E:NCO403
|
1.9
|
14.9
|
1.0
|
N4
|
E:NCO403
|
1.9
|
15.6
|
1.0
|
N6
|
E:NCO403
|
1.9
|
17.5
|
1.0
|
N2
|
E:NCO403
|
1.9
|
17.0
|
1.0
|
N3
|
E:NCO403
|
2.0
|
16.4
|
1.0
|
N1
|
E:NCO403
|
2.0
|
18.8
|
1.0
|
OP2
|
B:DG3
|
3.9
|
18.0
|
1.0
|
O
|
F:HOH110
|
3.9
|
21.6
|
1.0
|
O
|
E:HOH94
|
4.0
|
22.5
|
1.0
|
O6
|
E:DG6
|
4.0
|
13.4
|
1.0
|
O
|
E:HOH87
|
4.0
|
19.3
|
1.0
|
O
|
E:HOH93
|
4.0
|
30.4
|
1.0
|
O
|
E:HOH31
|
4.2
|
19.3
|
1.0
|
N7
|
E:DG6
|
4.2
|
11.7
|
1.0
|
OP1
|
B:DG3
|
4.3
|
19.1
|
1.0
|
O
|
E:HOH39
|
4.5
|
29.4
|
1.0
|
P
|
B:DG3
|
4.6
|
16.1
|
1.0
|
O
|
E:HOH158
|
4.7
|
44.9
|
1.0
|
O
|
B:HOH224
|
4.7
|
29.3
|
1.0
|
C6
|
E:DG6
|
4.8
|
10.4
|
1.0
|
C5
|
E:DG6
|
4.9
|
10.6
|
1.0
|
N4
|
E:DC7
|
4.9
|
15.8
|
1.0
|
|
Cobalt binding site 9 out
of 9 in 1ub8
Go back to
Cobalt Binding Sites List in 1ub8
Cobalt binding site 9 out
of 9 in the Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue
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 D(Gcgaagc), Bending Duplex with A Bulge-in Residue within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Co405
b:30.9
occ:1.00
|
CO
|
F:NCO405
|
0.0
|
30.9
|
1.0
|
N5
|
F:NCO405
|
1.9
|
30.8
|
1.0
|
N4
|
F:NCO405
|
1.9
|
30.7
|
1.0
|
N2
|
F:NCO405
|
1.9
|
31.2
|
1.0
|
N6
|
F:NCO405
|
1.9
|
30.7
|
1.0
|
N3
|
F:NCO405
|
1.9
|
30.5
|
1.0
|
N1
|
F:NCO405
|
2.0
|
31.4
|
1.0
|
O
|
F:HOH187
|
4.3
|
27.5
|
1.0
|
|
Reference:
T.Sunami,
J.Kondo,
I.Hirao,
K.Watanabe,
K.Miura,
A.Takenaka.
Structures of D(Gcgaagc) and D(Gcgaaagc) (Tetragonal Form): A Switching of Partners of the Sheared G.A Pairs to Form A Functional G.Axa.G Crossing. Acta Crystallogr.,Sect.D V. 60 422 2004.
ISSN: ISSN 0907-4449
PubMed: 14993665
DOI: 10.1107/S0907444903028415
Page generated: Tue Jul 30 14:39:18 2024
|