Cobalt in PDB 1uhy: Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex

The structure of Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex, PDB code: 1uhy was solved by J.Kondo, S.I.Umeda, K.Fujita, T.Sunami, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.87 / 1.70
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	37.000, 37.000, 65.300, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 23.9

The structure of Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex also contains other interesting chemical elements:

Bromine	(Br)	1 atom
Chlorine	(Cl)	1 atom
Sodium	(Na)	1 atom

The binding sites of Cobalt atom in the Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex (pdb code 1uhy). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex, PDB code: 1uhy:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex


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(Gcgatagc): the Base-Intercalated Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co100 b:43.3 occ:0.17 CO A:NCO100 0.0 43.3 0.2 N3 A:NCO100 1.9 44.1 0.2 N2 A:NCO100 1.9 44.1 0.2 N1 A:NCO100 2.0 44.1 0.2 N4 A:NCO100 2.0 44.2 0.2 N5 A:NCO100 2.0 44.1 0.2 N6 A:NCO100 2.0 44.1 0.2 O A:HOH41 3.8 53.0 1.0 O4 A:DT5 4.0 38.9 1.0 O A:HOH52 4.1 40.5 0.5

Cobalt binding site 2 out of 2 in the Crystal Structure of D(Gcgatagc): the Base-Intercalated Duplex


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(Gcgatagc): the Base-Intercalated Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:12.2 occ:0.33 CO A:NCO101 0.0 12.2 0.3 N1 A:NCO101 1.9 13.1 0.3 N5 A:NCO101 1.9 15.0 0.3 N4 A:NCO101 2.0 13.1 0.3 N2 A:NCO101 2.0 15.6 0.3 N6 A:NCO101 2.0 15.0 0.3 N3 A:NCO101 2.0 13.1 0.3 O6 A:DG3 4.1 18.3 1.0 O A:HOH9 4.4 19.3 1.0 N7 A:DG3 4.4 16.8 1.0 O A:HOH31 4.7 36.2 1.0 C6 A:DG3 5.0 11.4 1.0

J.Kondo, S.I.Umeda, K.Fujita, T.Sunami, A.Takenaka. X-Ray Analyses of D(Gcgaxagc) Containing G and T at X: the Base-Intercalated Duplex Is Still Stable Even in Point Mutants at the Fifth Residue. J.Synchrotron Radiat. V. 11 117 2004.
ISSN: ISSN 0909-0495
PubMed: 14646150
DOI: 10.1107/S0909049503023562