Cobalt in PDB 2dpc: Crystal Structure of D(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine

The structure of Crystal Structure of D(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine, PDB code: 2dpc was solved by E.C.M.Juan, J.Kondo, T.Kurihara, T.Ito, Y.Ueno, A.Matsuda, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.55
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	25.214, 40.533, 63.887, 90.00, 90.00, 90.00
R / Rfree (%)	21.5 / 26.6

The structure of Crystal Structure of D(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Cobalt atom in the Crystal Structure of D(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine (pdb code 2dpc). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Crystal Structure of D(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine, PDB code: 2dpc:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of D(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine


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(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co13 b:27.7 occ:1.00 O A:HOH241 1.9 23.8 1.0 O A:HOH157 2.1 27.3 1.0 O A:HOH138 2.1 25.8 1.0 O A:HOH150 2.4 50.5 1.0 O A:HOH178 4.1 34.7 1.0 O A:HOH219 4.1 46.1 1.0 O A:HOH154 4.2 40.9 1.0 OP1 A:DC9 4.2 31.7 1.0 OP2 A:DC9 4.3 28.9 1.0 O A:HOH254 4.4 50.3 1.0 O A:HOH166 4.5 43.8 1.0 P A:DC9 4.8 27.2 1.0 O A:HOH212 4.9 97.1 1.0 O A:HOH133 4.9 24.4 1.0

Cobalt binding site 2 out of 3 in the Crystal Structure of D(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine


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(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co14 b:36.3 occ:1.00 O A:HOH227 2.0 35.0 1.0 O A:HOH192 2.1 31.5 1.0 O A:HOH146 2.1 32.8 1.0 O A:HOH202 2.2 36.6 1.0 O A:HOH142 2.7 33.2 1.0 O A:HOH215 3.0 58.0 1.0 O A:HOH207 3.1 39.5 1.0 O A:HOH161 4.0 31.4 1.0 O A:HOH143 4.0 27.9 1.0 O A:HOH198 4.0 44.8 1.0 O A:HOH158 4.1 50.8 1.0 O6 A:DG12 4.2 18.0 1.0 O A:HOH194 4.2 78.0 1.0 N7 A:DG12 4.3 17.2 1.0 O A:HOH149 4.5 42.7 1.0 O A:HOH214 4.5 50.4 1.0 O A:HOH221 4.8 52.3 1.0 C6 A:DG12 4.9 16.5 1.0 O A:HOH240 5.0 34.4 1.0 C5 A:DG12 5.0 16.2 1.0

Cobalt binding site 3 out of 3 in the Crystal Structure of D(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine


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(Cgcgaatxcgcg) Where X Is 5-(N- Aminohexyl)Carbamoyl-2'-O-Methyluridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co3 b:39.8 occ:1.00 O A:HOH187 2.2 34.4 1.0 O B:HOH182 2.3 30.8 1.0 O B:HOH181 2.4 58.1 1.0 O A:HOH109 2.4 13.7 1.0 O A:HOH189 2.6 56.0 1.0 O B:HOH173 2.6 53.4 1.0 O A:HOH204 4.0 48.0 1.0 O B:HOH196 4.1 48.7 1.0 O B:HOH162 4.1 30.0 1.0 O A:HOH141 4.2 34.7 1.0 O6 B:DG14 4.2 17.7 1.0 N7 B:DG14 4.3 16.7 1.0 O6 A:DG10 4.4 14.8 1.0 O B:HOH190 4.7 59.9 1.0 O A:HOH200 4.9 39.5 1.0 O B:HOH159 5.0 44.5 1.0 O A:HOH218 5.0 52.6 1.0

E.C.M.Juan, J.Kondo, T.Kurihara, T.Ito, Y.Ueno, A.Matsuda, A.Takenaka. Crystal Structures of Dna:Dna and Dna:Rna Duplexes Containing 5-(N-Aminohexyl)Carbamoyl-Modified Uracils Reveal the Basis For Properties As Antigene and Antisense Molecules Nucleic Acids Res. V. 35 1969 2007.
ISSN: ISSN 0305-1048
PubMed: 17341465
DOI: 10.1093/NAR/GKL821