Cobalt in PDB 1xcu: Oligonucleotid/Drug Complex

The structure of Oligonucleotid/Drug Complex, PDB code: 1xcu was solved by N.Valls, R.A.Steiner, G.Wright, G.N.Murshudov, J.A.Subirana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.00
Space group	C 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	29.056, 52.856, 40.084, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 25.2

The structure of Oligonucleotid/Drug Complex also contains other interesting chemical elements:

Barium	(Ba)	1 atom
Sodium	(Na)	1 atom

The binding sites of Cobalt atom in the Oligonucleotid/Drug Complex (pdb code 1xcu). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 3 binding sites of Cobalt where determined in the Oligonucleotid/Drug Complex, PDB code: 1xcu:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Oligonucleotid/Drug Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Oligonucleotid/Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co33 b:53.4 occ:1.00 O A:HOH43 2.2 52.0 1.0 O A:HOH49 2.2 49.7 1.0 O A:HOH52 2.2 52.4 1.0 O A:HOH48 2.2 51.9 1.0 O A:HOH51 2.2 53.6 1.0 N7 A:DG2 2.3 33.6 1.0 C8 A:DG2 3.2 36.9 1.0 C5 A:DG2 3.3 36.4 1.0 O6 A:DG2 3.6 33.8 1.0 C6 A:DG2 3.8 35.6 1.0 O A:HOH42 4.0 42.5 1.0 O3' A:DC1 4.3 60.4 1.0 N9 A:DG2 4.4 36.3 1.0 C4 A:DG2 4.5 36.5 1.0 O4 A:DT3 4.5 36.1 1.0 C7 A:DT3 4.6 44.3 1.0 OP1 A:DG2 4.7 58.3 1.0

Cobalt binding site 2 out of 3 in the Oligonucleotid/Drug Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Oligonucleotid/Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co35 b:40.4 occ:0.25 O A:HOH53 1.9 39.1 0.2 OP1 A:DG6 2.1 50.1 1.0 P A:DG6 3.3 52.5 1.0 O3' A:DC5 3.4 46.5 1.0 O5' A:DG6 4.0 49.5 1.0 O A:HOH44 4.0 33.7 0.5 C3' A:DC5 4.4 44.9 1.0 OP2 A:DG6 4.6 50.7 1.0 C4' A:DC5 4.7 43.8 1.0 O A:HOH44 4.8 37.8 0.5

Cobalt binding site 3 out of 3 in the Oligonucleotid/Drug Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Oligonucleotid/Drug Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co32 b:35.9 occ:0.50 O B:HOH49 2.0 38.0 1.0 O B:HOH46 2.1 37.7 1.0 N7 B:DG12 2.2 32.9 1.0 C8 B:DG12 3.1 34.5 1.0 C5 B:DG12 3.4 37.4 1.0 O6 B:DG12 3.8 36.5 1.0 C6 B:DG12 4.0 40.1 1.0 OP2 B:DG12 4.0 35.2 1.0 BA B:BA34 4.2 37.7 0.2 O B:HOH48 4.3 47.4 1.0 N9 B:DG12 4.3 33.3 1.0 O B:HOH55 4.4 43.5 1.0 C4 B:DG12 4.5 33.9 1.0 P B:DG12 5.0 37.2 1.0

N.Valls, R.A.Steiner, G.Wright, G.N.Murshudov, J.A.Subirana. Variable Role of Ions in Two Drug Intercalation Complexes of Dna J.Biol.Inorg.Chem. V. 10 476 2005.
ISSN: ISSN 0949-8257
PubMed: 15926069
DOI: 10.1007/S00775-005-0655-3