Cobalt in PDB 5yze: Crystal Structure of the [CO2+-(Chromomycin A3)2]-D(Ccg)3 Complex

The structure of Crystal Structure of the [CO2+-(Chromomycin A3)2]-D(Ccg)3 Complex, PDB code: 5yze was solved by M.H.Hou, Y.W.Chen, P.C.Wu, R.B.Satange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.18 / 1.87
Space group	P 32 1 2
Cell size a, b, c (Å), α, β, γ (°)	46.401, 46.401, 73.822, 90.00, 90.00, 120.00
R / Rfree (%)	19.4 / 25.2

The binding sites of Cobalt atom in the Crystal Structure of the [CO2+-(Chromomycin A3)2]-D(Ccg)3 Complex (pdb code 5yze). 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 the [CO2+-(Chromomycin A3)2]-D(Ccg)3 Complex, PDB code: 5yze:
Jump to Cobalt binding site number: 1; 2; 3;

Cobalt binding site 1 out of 3 in the Crystal Structure of the [CO2+-(Chromomycin A3)2]-D(Ccg)3 Complex


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 the [CO2+-(Chromomycin A3)2]-D(Ccg)3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co107 b:28.9 occ:1.00 O9 B:CPH103 2.0 25.5 1.0 O9 A:CPH106 2.0 25.1 1.0 O1 B:CPH103 2.0 26.4 1.0 O1 A:CPH106 2.0 27.9 1.0 O B:HOH208 2.1 24.4 1.0 O A:HOH202 2.1 23.4 1.0 C1 B:CPH103 3.0 28.7 1.0 C1 A:CPH106 3.0 27.4 1.0 C9 B:CPH103 3.1 29.6 1.0 C9 A:CPH106 3.1 28.7 1.0 C9A B:CPH103 3.5 26.2 1.0 C9A A:CPH106 3.5 26.7 1.0 O8 A:CPH106 4.0 25.4 1.0 O8 B:CPH103 4.0 26.2 1.0 C8A B:CPH103 4.3 23.3 1.0 C8A A:CPH106 4.3 22.4 1.0 O2 B:DC19 4.3 26.3 1.0 O4' B:DC20 4.3 34.0 1.0 O2 A:DC8 4.3 30.1 1.0 O4' A:DC9 4.4 35.1 1.0 C2 B:CPH103 4.4 33.9 1.0 C2 A:CPH106 4.4 32.6 1.0 C1 B:CDR104 4.5 34.7 1.0 OGL A:CDR101 4.5 30.5 1.0 C1 A:CDR101 4.5 34.8 1.0 OGL B:CDR104 4.6 29.7 1.0 C8 A:CPH106 4.6 23.8 1.0 C8 B:CPH103 4.6 22.9 1.0 C2 B:CDR104 4.8 32.4 1.0 C2' B:DC19 4.8 22.6 1.0 C2 A:CDR101 4.8 31.3 1.0 C1' B:DC19 4.8 23.6 1.0 C2' A:DC8 4.8 23.5 1.0 C4' B:DC20 4.8 33.4 1.0 C1' A:DC8 4.9 25.1 1.0 C4A B:CPH103 4.9 25.3 1.0 C4' A:DC9 4.9 31.6 1.0 C4A A:CPH106 4.9 27.7 1.0 N2 B:DG18 5.0 28.8 1.0 N2 A:DG7 5.0 31.5 1.0

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


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 the [CO2+-(Chromomycin A3)2]-D(Ccg)3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Co108 b:48.0 occ:1.00 O A:HOH203 2.0 37.2 1.0 O A:HOH221 2.0 45.3 1.0 O A:HOH229 2.2 47.8 1.0 N7 A:DG7 2.2 39.3 1.0 O A:HOH217 2.2 43.2 1.0 O A:HOH201 2.2 45.0 1.0 C8 A:DG7 3.1 39.9 1.0 C5 A:DG7 3.3 38.7 1.0 O6 A:DG7 3.7 43.3 1.0 C6 A:DG7 3.9 38.1 1.0 N7 A:DG4 4.1 50.0 1.0 O6 A:DG4 4.3 44.7 1.0 OP1 A:DG7 4.3 42.9 1.0 N9 A:DG7 4.3 35.7 1.0 C4 A:DG7 4.4 33.5 1.0 OP2 A:DG7 4.5 35.8 1.0 C5 A:DG4 4.8 41.8 1.0 P A:DG7 4.8 44.9 1.0 C6 A:DG4 4.9 41.6 1.0 O A:HOH222 5.0 67.1 1.0

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


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 the [CO2+-(Chromomycin A3)2]-D(Ccg)3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Co107 b:47.9 occ:1.00 O B:HOH220 1.9 45.1 1.0 O B:HOH206 2.0 36.9 1.0 O B:HOH216 2.2 41.2 1.0 N7 B:DG18 2.2 35.9 1.0 O B:HOH235 2.2 46.4 1.0 O B:HOH202 2.2 43.0 1.0 C8 B:DG18 3.0 39.1 1.0 C5 B:DG18 3.3 35.3 1.0 O6 B:DG18 3.7 42.1 1.0 C6 B:DG18 3.9 37.8 1.0 N7 B:DG15 4.1 47.6 1.0 O6 B:DG15 4.3 43.4 1.0 N9 B:DG18 4.3 35.5 1.0 OP1 B:DG18 4.3 44.6 1.0 C4 B:DG18 4.4 32.5 1.0 OP2 B:DG18 4.5 35.0 1.0 C5 B:DG15 4.8 43.0 1.0 C6 B:DG15 4.8 40.8 1.0 P B:DG18 4.9 42.6 1.0

Y.W.Chen, R.Satange, P.C.Wu, C.R.Jhan, C.K.Chang, K.R.Chung, M.J.Waring, S.W.Lin, L.C.Hsieh, M.H.Hou. Coii(Chromomycin)2 Complex Induces A Conformational Change of Ccg Repeats From I-Motif to Base-Extruded Dna Duplex Int J Mol Sci V. 19 2018.
ISSN: ESSN 1422-0067
PubMed: 30227633
DOI: 10.3390/IJMS19092796