Cobalt in PDB 6m4t: U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence

The structure of U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence, PDB code: 6m4t was solved by M.H.Hou, C.M.Chien, R.B.Satange, P.C.Wu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.73 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.204, 62.631, 29.743, 90.00, 121.29, 90.00
R / Rfree (%)	16.5 / 19

The structure of U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence also contains other interesting chemical elements:

Bromine	(Br)	4 atoms
Chlorine	(Cl)	4 atoms

The binding sites of Cobalt atom in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence (pdb code 6m4t). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence, PDB code: 6m4t:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:20.0 occ:1.00 O D:HOH211 1.9 21.6 1.0 O D:HOH208 2.0 17.1 1.0 O A:HOH215 2.0 20.1 1.0 N7 D:DG8 2.1 16.5 1.0 O A:HOH201 2.1 21.4 1.0 N7 A:DG5 2.2 27.1 1.0 C8 D:DG8 3.0 22.8 1.0 C8 A:DG5 3.1 21.4 1.0 C5 D:DG8 3.2 20.4 1.0 C5 A:DG5 3.3 28.3 1.0 O6 D:DG8 3.6 24.6 1.0 O6 A:DG5 3.7 27.6 1.0 C6 D:DG8 3.8 23.5 1.0 C6 A:DG5 3.9 28.8 1.0 NAH C:F1R101 4.1 25.2 1.0 O C:HOH235 4.3 21.5 1.0 N9 D:DG8 4.3 21.5 1.0 N4 A:DC6 4.3 26.1 1.0 N9 A:DG5 4.3 22.8 1.0 C4 D:DG8 4.4 17.4 1.0 O D:HOH228 4.4 16.4 1.0 O4' D:DT7 4.4 25.3 1.0 C4 A:DG5 4.4 25.5 1.0 NAG C:F1R101 4.5 25.3 1.0 OP1 A:DG5 4.6 27.2 1.0 CAY C:F1R101 4.6 22.5 1.0 O3' D:DT7 4.7 21.2 1.0 O D:HOH225 4.7 24.4 1.0 CAW C:F1R101 4.7 27.5 1.0 OP2 A:DG5 4.8 24.7 1.0 NAC C:F1R101 4.8 21.4 1.0 C4' D:DT7 4.9 23.9 1.0 C1' D:DT7 4.9 25.0 1.0 C5 A:DC6 4.9 21.0 1.0 O A:HOH251 4.9 22.5 1.0 C4 A:DC6 4.9 25.4 1.0

Cobalt binding site 2 out of 4 in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:17.8 occ:1.00 O A:HOH225 2.0 19.7 1.0 O D:HOH215 2.0 14.6 1.0 O D:HOH203 2.1 15.7 1.0 N7 D:DG5 2.2 17.3 1.0 O B:HOH224 2.3 13.4 1.0 N7 A:DG8 2.3 29.3 1.0 C8 A:DG8 3.0 20.2 1.0 C8 D:DG5 3.0 14.6 1.0 C5 D:DG5 3.4 18.0 1.0 C5 A:DG8 3.5 27.0 1.0 O6 D:DG5 3.8 15.9 1.0 O6 A:DG8 4.0 19.8 1.0 C6 D:DG5 4.0 14.2 1.0 OP2 D:DG5 4.0 21.9 1.0 C6 A:DG8 4.1 20.3 1.0 NAH B:F1R103 4.1 14.1 1.0 O4' A:DT7 4.3 19.0 1.0 O B:HOH235 4.3 16.2 1.0 N9 D:DG5 4.3 14.8 1.0 N9 A:DG8 4.3 22.9 1.0 O A:HOH212 4.4 22.4 1.0 O B:HOH219 4.4 20.7 1.0 OP1 D:DG5 4.4 17.1 1.0 C4 D:DG5 4.5 16.3 1.0 N4 D:DC6 4.6 20.7 1.0 C4 A:DG8 4.6 21.1 1.0 O3' A:DT7 4.6 26.8 1.0 NAG B:F1R103 4.6 16.3 1.0 CAY B:F1R103 4.6 13.1 1.0 C1' A:DT7 4.7 22.7 1.0 C4' A:DT7 4.7 20.1 1.0 P D:DG5 4.7 18.2 1.0 CAW B:F1R103 4.8 18.1 1.0 NAC B:F1R103 4.9 20.6 1.0

Cobalt binding site 3 out of 4 in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:17.0 occ:1.00 O B:HOH225 1.8 18.1 1.0 O C:HOH216 2.1 20.7 1.0 N7 B:DG5 2.2 18.9 1.0 N7 C:DG8 2.2 20.8 1.0 O B:HOH201 2.2 19.8 1.0 O D:HOH218 2.3 17.6 1.0 C8 C:DG8 2.9 21.8 1.0 C8 B:DG5 3.0 16.0 1.0 C5 B:DG5 3.4 17.1 1.0 C5 C:DG8 3.4 21.2 1.0 O6 B:DG5 3.8 13.3 1.0 C6 B:DG5 4.0 13.6 1.0 O6 C:DG8 4.0 25.1 1.0 O4' C:DT7 4.1 20.8 1.0 C6 C:DG8 4.1 20.8 1.0 N9 C:DG8 4.2 23.1 1.0 O C:HOH220 4.2 26.7 1.0 OP1 B:DG5 4.2 20.0 1.0 N9 B:DG5 4.3 18.9 1.0 NAH D:F1R101 4.3 28.5 1.0 OP2 B:DG5 4.3 19.7 1.0 O D:HOH228 4.4 16.4 1.0 C4 B:DG5 4.4 15.4 1.0 O3' C:DT7 4.4 24.2 1.0 C4 C:DG8 4.5 22.3 1.0 N4 B:DC6 4.5 21.1 1.0 C4' C:DT7 4.5 21.6 1.0 C1' C:DT7 4.5 21.4 1.0 NAC D:F1R101 4.6 26.9 1.0 CAW D:F1R101 4.7 33.9 1.0 P B:DG5 4.7 19.4 1.0 O D:HOH227 5.0 18.4 1.0

Cobalt binding site 4 out of 4 in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:19.3 occ:1.00 O B:HOH206 2.0 17.9 1.0 O C:HOH213 2.0 23.7 1.0 N7 B:DG8 2.2 29.1 1.0 O C:HOH207 2.2 26.6 1.0 N7 C:DG5 2.2 18.5 1.0 O C:HOH228 2.2 12.1 1.0 C8 C:DG5 3.1 18.7 1.0 C8 B:DG8 3.1 26.5 1.0 C5 B:DG8 3.3 27.3 1.0 C5 C:DG5 3.4 21.9 1.0 O A:HOH232 3.5 17.4 1.0 O6 B:DG8 3.6 24.3 1.0 O6 C:DG5 3.7 28.6 1.0 C6 B:DG8 3.8 23.1 1.0 C6 C:DG5 3.9 26.9 1.0 NAH A:F1R103 4.0 15.6 1.0 NAG A:F1R103 4.2 12.9 1.0 OP2 C:DG5 4.2 23.2 1.0 N9 B:DG8 4.3 24.2 1.0 N4 C:DC6 4.3 19.7 1.0 N9 C:DG5 4.4 18.2 1.0 CAY A:F1R103 4.4 13.4 1.0 O B:HOH219 4.4 20.7 1.0 C4 B:DG8 4.4 23.9 1.0 C4 C:DG5 4.5 19.6 1.0 OP1 C:DG5 4.5 25.6 1.0 O4' B:DT7 4.7 23.3 1.0 O3' B:DT7 4.7 24.8 1.0 O B:HOH207 4.8 20.4 1.0 P C:DG5 4.8 23.0 1.0 CAW A:F1R103 4.8 15.6 1.0 C5 C:DC6 4.9 19.1 1.0 O A:HOH230 4.9 21.2 1.0 C4 C:DC6 5.0 19.0 1.0 C1' B:DT7 5.0 24.7 1.0

C.M.Chien, P.C.Wu, R.Satange, C.C.Chang, Z.L.Lai, L.D.Hagler, S.C.Zimmerman, M.H.Hou. Structural Basis For Targeting T:T Mismatch with Triaminotriazine-Acridine Conjugate Induces A U-Shaped Head-to-Head Four-Way Junction in Ctg Repeat Dna. J.Am.Chem.Soc. V. 142 11165 2020.
ISSN: ESSN 1520-5126
PubMed: 32478511
DOI: 10.1021/JACS.0C03591