Cobalt in PDB 6j0i: Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex

The structure of Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex, PDB code: 6j0i was solved by R.B.Satange, C.Y.Chuang, M.H.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	16.12 / 2.50
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	47.826, 48.096, 96.725, 90.00, 90.00, 90.00
R / Rfree (%)	25.7 / 29

The binding sites of Cobalt atom in the Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex (pdb code 6j0i). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 7 binding sites of Cobalt where determined in the Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex, PDB code: 6j0i:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6; 7;

Cobalt binding site 1 out of 7 in the Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co110 b:32.1 occ:0.92 O9 B:CRH103 1.9 31.6 1.0 O9 A:CRH103 2.1 30.9 1.0 O1 A:CRH103 2.2 30.4 1.0 O1 B:CRH103 2.5 31.2 1.0 C9 B:CRH103 3.2 30.7 1.0 C9 A:CRH103 3.3 31.7 1.0 C1 A:CRH103 3.4 31.8 1.0 C1 B:CRH103 3.6 33.5 1.0 O8 B:CRH103 3.6 29.9 1.0 O2 A:DC5 3.8 25.5 1.0 C13 A:CRH103 3.8 31.2 1.0 C13 B:CRH103 3.9 31.9 1.0 C2' B:DC13 3.9 34.8 1.0 C2' A:DC5 4.0 32.1 1.0 O8 A:CRH103 4.0 30.6 1.0 O2 B:DC13 4.3 24.4 1.0 C12 B:CRH103 4.3 29.6 1.0 C1' A:DC5 4.3 30.3 1.0 N2 A:DG4 4.4 25.2 1.0 C8 B:CRH103 4.5 31.4 1.0 C12 A:CRH103 4.5 32.0 1.0 O4' A:DG6 4.6 36.8 1.0 C1' B:DC13 4.7 32.8 1.0 OGL A:CDR104 4.7 31.4 1.0 C2 A:CRH103 4.7 33.4 1.0 C8 A:CRH103 4.8 33.9 1.0 N2 B:DG12 4.8 29.0 1.0 C1 A:CDR104 4.8 30.4 1.0 C2 A:DC5 4.9 26.2 1.0 C2 B:CRH103 4.9 33.6 1.0 C1' A:DG6 4.9 35.4 1.0

Cobalt binding site 2 out of 7 in the Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co111 b:30.4 occ:0.90 N7 A:DG4 2.4 30.7 1.0 O A:HOH210 2.5 19.1 1.0 C8 A:DG4 3.1 32.1 1.0 O A:HOH228 3.4 36.1 1.0 C5 A:DG4 3.6 29.2 1.0 N2 A:DG3 3.8 41.0 1.0 O6 A:DG4 4.1 30.5 1.0 C6 A:DG4 4.3 29.0 1.0 C2 A:DG3 4.3 40.3 1.0 N9 A:DG4 4.4 33.2 1.0 C4 A:DG4 4.7 29.1 1.0 N1 A:DG3 4.8 37.6 1.0 N3 A:DG3 4.8 39.9 1.0

Cobalt binding site 3 out of 7 in the Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Co110 b:25.3 occ:0.92 O9 D:CRH103 1.9 33.5 1.0 O1 C:CRH103 2.1 34.3 1.0 O9 C:CRH103 2.3 31.6 1.0 O1 D:CRH103 2.3 33.2 1.0 C1 C:CRH103 3.2 34.0 1.0 C9 D:CRH103 3.2 33.3 1.0 C1 D:CRH103 3.5 33.8 1.0 C9 C:CRH103 3.5 31.8 1.0 O2 C:DC5 3.7 23.9 1.0 O8 D:CRH103 3.8 23.6 1.0 C13 D:CRH103 3.9 33.8 1.0 C13 C:CRH103 3.9 32.7 1.0 C2' C:DC5 4.2 30.3 1.0 O2 D:DC13 4.2 22.1 1.0 O4' C:DG6 4.2 33.6 1.0 O8 C:CRH103 4.4 34.5 1.0 C12 D:CRH103 4.4 32.5 1.0 C1 C:CDR104 4.4 32.2 1.0 C1' C:DC5 4.4 28.8 1.0 C2 C:CRH103 4.5 32.6 1.0 C8 D:CRH103 4.6 31.4 1.0 OGL C:CDR104 4.6 32.2 1.0 C12 C:CRH103 4.7 31.2 1.0 C2 C:DC5 4.7 23.8 1.0 C2 D:CRH103 4.8 36.3 1.0 OGL C:CDR107 4.8 35.1 1.0 C1 C:CDR107 4.9 36.1 1.0 C1' D:DC13 4.9 31.8 1.0 N2 C:DG4 4.9 33.3 1.0 C2 C:CDR104 5.0 32.0 1.0 N2 D:DG12 5.0 29.3 1.0 O4' D:DG14 5.0 34.6 1.0

Cobalt binding site 4 out of 7 in the Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Co111 b:48.2 occ:0.90 O C:HOH205 2.2 42.7 1.0 O C:HOH216 2.2 49.5 1.0 N7 C:DG3 2.8 46.5 1.0 N7 C:DG4 3.4 34.7 1.0 C8 C:DG3 3.5 47.7 1.0 C5 C:DG3 3.7 45.4 1.0 O C:HOH246 4.1 46.9 1.0 C8 C:DG4 4.2 34.9 1.0 O6 C:DG3 4.2 41.5 1.0 C6 C:DG3 4.3 43.8 1.0 C5 C:DG4 4.5 34.7 1.0 N9 C:DG3 4.6 48.0 1.0 O6 C:DG4 4.6 33.8 1.0 C4 C:DG3 4.7 46.2 1.0 C6 C:DG4 5.0 34.4 1.0

Cobalt binding site 5 out of 7 in the Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Co104 b:38.8 occ:1.00 N7 D:DG12 2.3 29.3 1.0 O D:HOH204 2.9 27.5 1.0 O D:HOH217 3.2 29.0 1.0 C8 D:DG12 3.3 29.8 1.0 C5 D:DG12 3.3 30.2 1.0 O6 D:DG12 3.4 29.3 1.0 O D:HOH221 3.5 31.0 1.0 C6 D:DG12 3.7 29.5 1.0 N1 D:DG11 4.3 31.4 1.0 N9 D:DG12 4.5 31.9 1.0 C4 D:DG12 4.5 31.0 1.0 C2 D:DG11 4.6 33.0 1.0 N2 D:DG11 4.7 34.3 1.0 C6 D:DG11 4.7 31.1 1.0 O6 D:DG11 4.9 31.6 1.0

Cobalt binding site 6 out of 7 in the Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Co110 b:38.8 occ:0.92 O1 E:CRH103 2.0 34.6 1.0 O9 E:CRH103 2.0 33.2 1.0 O9 F:CRH103 2.1 36.3 1.0 O1 F:CRH103 2.4 38.6 1.0 C1 E:CRH103 3.2 35.9 1.0 C9 E:CRH103 3.3 34.8 1.0 C9 F:CRH103 3.4 37.6 1.0 C1 F:CRH103 3.5 39.0 1.0 C13 E:CRH103 3.7 34.9 1.0 O2 F:DC13 3.9 18.4 1.0 C13 F:CRH103 3.9 38.9 1.0 O8 F:CRH103 4.0 33.2 1.0 O4' E:DG6 4.0 31.7 1.0 O8 E:CRH103 4.1 36.3 1.0 O2 E:DC5 4.1 18.0 1.0 C2' F:DC13 4.3 30.7 1.0 C2 E:CRH103 4.5 37.6 1.0 C12 E:CRH103 4.5 34.3 1.0 C2' E:DC5 4.5 31.6 1.0 C12 F:CRH103 4.6 37.0 1.0 O4' F:DG14 4.6 36.0 1.0 C1' F:DC13 4.6 27.3 1.0 OGL E:CDR107 4.7 43.1 1.0 C8 F:CRH103 4.8 36.1 1.0 OGL E:CDR104 4.8 40.3 1.0 N2 F:DG12 4.8 28.4 1.0 C8 E:CRH103 4.8 34.1 1.0 C1 E:CDR104 4.8 39.5 1.0 C2 F:CRH103 4.8 41.5 1.0 C4' E:DG6 4.8 32.5 1.0 C1 E:CDR107 4.9 41.4 1.0 C1' E:DC5 5.0 26.1 1.0

Cobalt binding site 7 out of 7 in the Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 7 of Structure of [CO2+-(Chromomycin A3)2]-D(Ttggcgaa)2 Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Co104 b:44.7 occ:1.00 O F:HOH214 2.4 26.7 1.0 N7 F:DG12 2.5 24.9 1.0 O F:HOH247 2.5 26.0 1.0 O F:HOH227 2.8 26.5 1.0 C8 F:DG12 3.3 26.8 1.0 C5 F:DG12 3.6 24.4 1.0 O6 F:DG12 4.0 18.8 1.0 N1 F:DG11 4.1 35.8 1.0 C6 F:DG12 4.2 23.3 1.0 O F:HOH204 4.2 24.4 1.0 C2 F:DG11 4.4 37.5 1.0 N2 F:DG11 4.5 36.4 1.0 N9 F:DG12 4.5 26.9 1.0 C6 F:DG11 4.6 32.5 1.0 C4 F:DG12 4.7 24.9 1.0 O E:HOH229 4.9 33.7 1.0 O6 F:DG11 4.9 28.6 1.0

R.Satange, C.Y.Chuang, S.Neidle, M.H.Hou. Polymorphic G:G Mismatches Act As Hotspots For Inducing Right-Handed Z Dna By Dna Intercalation. Nucleic Acids Res. V. 47 8899 2019.
ISSN: ESSN 1362-4962
PubMed: 31361900
DOI: 10.1093/NAR/GKZ653