Cobalt in PDB 1p24: Crystal Structure of Cobalt(II)-D(Ggcgcc)2

The structure of Crystal Structure of Cobalt(II)-D(Ggcgcc)2, PDB code: 1p24 was solved by S.L.Labiuk, L.T.Delbaere, J.S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 3.02
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	68.940, 68.940, 55.270, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 28.6

The binding sites of Cobalt atom in the Crystal Structure of Cobalt(II)-D(Ggcgcc)2 (pdb code 1p24). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Crystal Structure of Cobalt(II)-D(Ggcgcc)2, PDB code: 1p24:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Crystal Structure of Cobalt(II)-D(Ggcgcc)2


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 Cobalt(II)-D(Ggcgcc)2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:36.3 occ:1.00 N7 A:DG1 2.1 14.9 1.0 O A:HOH202 2.1 40.5 1.0 O A:HOH205 2.1 40.5 1.0 O A:HOH201 2.1 40.5 1.0 O A:HOH204 2.1 40.5 1.0 O A:HOH203 2.1 40.5 1.0 C8 A:DG1 3.0 14.9 1.0 C5 A:DG1 3.2 14.9 1.0 O6 A:DG1 3.6 14.9 1.0 C6 A:DG1 3.7 14.9 1.0 N9 A:DG1 4.3 14.9 1.0 C4 A:DG1 4.3 14.9 1.0 O6 A:DG2 4.8 21.9 1.0

Cobalt binding site 2 out of 5 in the Crystal Structure of Cobalt(II)-D(Ggcgcc)2


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 Cobalt(II)-D(Ggcgcc)2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:36.1 occ:1.00 N7 B:DG7 2.1 32.9 1.0 O B:HOH208 2.1 38.1 1.0 O B:HOH209 2.1 38.1 1.0 O B:HOH206 2.1 38.1 1.0 O B:HOH207 2.1 38.1 1.0 O B:HOH210 2.1 38.1 1.0 C8 B:DG7 3.0 32.9 1.0 C5 B:DG7 3.1 32.9 1.0 O6 B:DG7 3.5 32.9 1.0 C6 B:DG7 3.6 32.9 1.0 N9 B:DG7 4.2 32.9 1.0 C4 B:DG7 4.2 32.9 1.0 N4 A:DC6 4.7 18.4 1.0 N1 B:DG7 5.0 32.9 1.0

Cobalt binding site 3 out of 5 in the Crystal Structure of Cobalt(II)-D(Ggcgcc)2


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 Cobalt(II)-D(Ggcgcc)2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Co103 b:65.0 occ:1.00 N7 C:DG13 2.1 23.0 1.0 O C:HOH212 2.1 44.0 1.0 O C:HOH211 2.1 44.0 1.0 O C:HOH215 2.1 44.0 1.0 O C:HOH214 2.1 44.0 1.0 O C:HOH213 2.1 44.0 1.0 C5 C:DG13 3.1 23.0 1.0 C8 C:DG13 3.1 23.0 1.0 O6 C:DG13 3.3 23.0 1.0 C6 C:DG13 3.5 23.0 1.0 C4 C:DG13 4.3 23.0 1.0 N9 C:DG13 4.3 23.0 1.0 O6 C:DG14 4.7 36.8 1.0 N7 C:DG14 4.8 36.8 1.0 N1 C:DG13 4.9 23.0 1.0

Cobalt binding site 4 out of 5 in the Crystal Structure of Cobalt(II)-D(Ggcgcc)2


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 Cobalt(II)-D(Ggcgcc)2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Co104 b:43.5 occ:1.00 N7 D:DG19 2.1 21.3 1.0 O D:HOH217 2.1 40.0 1.0 O D:HOH216 2.1 40.0 1.0 O D:HOH220 2.1 40.0 1.0 O D:HOH219 2.1 40.0 1.0 O D:HOH218 2.1 40.0 1.0 C8 D:DG19 2.9 21.3 1.0 C5 D:DG19 3.1 21.3 1.0 O6 D:DG19 3.7 21.3 1.0 C6 D:DG19 3.7 21.3 1.0 N9 D:DG19 4.0 21.3 1.0 C4 D:DG19 4.1 21.3 1.0 O6 D:DG20 4.5 15.5 1.0 N7 D:DG20 4.9 15.5 1.0

Cobalt binding site 5 out of 5 in the Crystal Structure of Cobalt(II)-D(Ggcgcc)2


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 Cobalt(II)-D(Ggcgcc)2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Co105 b:67.6 occ:1.00 O E:HOH224 2.1 36.2 1.0 O E:HOH225 2.1 36.2 1.0 O E:HOH223 2.1 36.2 1.0 O E:HOH221 2.1 36.2 1.0 O E:HOH222 2.1 36.2 1.0 N7 E:DG25 2.2 23.7 1.0 C8 E:DG25 3.1 23.7 1.0 C5 E:DG25 3.3 23.7 1.0 O6 E:DG25 3.7 23.7 1.0 C6 E:DG25 3.9 23.7 1.0 N9 E:DG25 4.3 23.7 1.0 C4 E:DG25 4.4 23.7 1.0

S.L.Labiuk, L.T.Delbaere, J.S.Lee. Cobalt(II), Nickel(II) and Zinc(II) Do Not Bind to Intra-Helical N(7) Guanine Positions in the B-Form Crystal Structure of D(Ggcgcc) J.Biol.Inorg.Chem. V. 8 715 2003.
ISSN: ISSN 0949-8257
PubMed: 14505075
DOI: 10.1007/S00775-003-0473-4