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Cobalt in PDB 5jev: Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine

Protein crystallography data

The structure of Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine, PDB code: 5jev was solved by J.P.Hall, C.J.Cardin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.90 / 0.99
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 48.720, 48.720, 29.960, 90.00, 90.00, 90.00
R / Rfree (%) 12.3 / 14.1

Other elements in 5jev:

The structure of Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine also contains other interesting chemical elements:

Ruthenium (Ru) 2 atoms

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine (pdb code 5jev). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total only one binding site of Cobalt was determined in the Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine, PDB code: 5jev:

Cobalt binding site 1 out of 1 in 5jev

Go back to Cobalt Binding Sites List in 5jev
Cobalt binding site 1 out of 1 in the Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Del-[Ru(Phen)2(Dppz]2+ Bound to D(Tcggcgccga) with Cobalt Hexammine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co103

b:16.7
occ:0.45
CO A:NCO103 0.0 16.7 0.5
N3 A:NCO103 2.0 18.8 0.5
N1 A:NCO103 2.0 18.6 0.5
N5 A:NCO103 2.0 18.0 0.5
N6 A:NCO103 2.0 17.1 0.5
N4 A:NCO103 2.0 17.9 0.5
N2 A:NCO103 2.0 15.5 0.5
O A:HOH201 2.4 29.6 0.6
O A:HOH202 2.5 30.0 0.6
OP2 A:DC2 3.9 22.5 1.0
O6 A:DG4 4.1 15.5 1.0
O A:HOH227 4.2 27.4 1.0
N7 A:DG3 4.3 17.0 1.0
O A:HOH235 4.3 29.2 1.0
H42 A:DC5 4.8 24.4 1.0
H41 A:DC5 4.8 24.4 1.0
O6 A:DG3 4.8 15.8 1.0

Reference:

J.P.Hall, P.M.Keane, H.Beer, K.Buchner, G.Winter, T.L.Sorensen, D.J.Cardin, J.A.Brazier, C.J.Cardin. Delta Chirality Ruthenium 'Light-Switch' Complexes Can Bind in the Minor Groove of Dna with Five Different Binding Modes. Nucleic Acids Res. V. 44 9472 2016.
ISSN: ESSN 1362-4962
PubMed: 27599841
DOI: 10.1093/NAR/GKW753
Page generated: Sun Dec 13 10:47:45 2020

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