Cobalt in PDB 1ub8: Crystal Structure of D(Gcgaagc), Bending Duplex with A Bulge-in Residue

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

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 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 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 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 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 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 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 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 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 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

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