Cobalt in PDB 6m5j: U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa/Ttctgcagctgaa) Sequence

The structure of U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa/Ttctgcagctgaa) Sequence, PDB code: 6m5j was solved by M.H.Hou, C.M.Chien, R.B.Satange, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.22 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	57.630, 62.086, 30.747, 90.00, 121.84, 90.00
R / Rfree (%)	18.7 / 20.8

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

Chlorine

(Cl)

4 atoms

The binding sites of Cobalt atom in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa/Ttctgcagctgaa) Sequence (pdb code 6m5j). 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/Ttctgcagctgaa) Sequence, PDB code: 6m5j:
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/Ttctgcagctgaa) 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/Ttctgcagctgaa) Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Co101 b:21.7 occ:1.00 O A:HOH216 1.6 19.3 1.0 O D:HOH224 2.0 19.6 1.0 O A:HOH205 2.2 19.5 1.0 N7 D:DG8 2.3 22.4 1.0 N7 A:DG5 2.3 21.9 1.0 O C:HOH224 2.4 19.3 1.0 C8 D:DG8 3.2 20.4 1.0 C8 A:DG5 3.2 18.2 1.0 C5 D:DG8 3.4 21.7 1.0 C5 A:DG5 3.4 19.3 1.0 O6 D:DG8 3.7 23.7 1.0 O6 A:DG5 3.7 21.2 1.0 C6 D:DG8 3.9 22.5 1.0 C6 A:DG5 3.9 22.0 1.0 O C:HOH218 4.0 19.5 1.0 OP2 A:DG5 4.1 24.9 1.0 NAH C:F1R101 4.2 21.6 1.0 O D:HOH225 4.2 24.9 1.0 O D:HOH216 4.3 24.5 1.0 O4' D:DT7 4.3 22.9 1.0 N9 D:DG8 4.4 21.9 1.0 N9 A:DG5 4.4 18.7 1.0 C4 D:DG8 4.5 21.3 1.0 C4 A:DG5 4.5 20.6 1.0 NAG C:F1R101 4.5 20.6 1.0 C1' D:DT7 4.6 22.9 1.0 O3' D:DT7 4.7 25.0 1.0 CAY C:F1R101 4.7 20.9 1.0 OP1 A:DG5 4.7 25.6 1.0 C4' D:DT7 4.7 21.4 1.0 N4 A:DC6 4.9 23.2 1.0 P A:DG5 4.9 23.7 1.0 CAW C:F1R101 5.0 21.6 1.0

Cobalt binding site 2 out of 4 in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa/Ttctgcagctgaa) 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/Ttctgcagctgaa) Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Co102 b:22.8 occ:1.00 O D:HOH205 1.7 23.3 1.0 O D:HOH207 2.0 20.0 1.0 O D:HOH208 2.0 19.8 1.0 N7 D:DG5 2.1 20.1 1.0 N7 A:DG8 2.2 22.4 1.0 O A:HOH213 2.2 19.2 1.0 C8 D:DG5 2.9 21.4 1.0 C8 A:DG8 3.0 23.1 1.0 C5 D:DG5 3.3 22.6 1.0 C5 A:DG8 3.3 24.0 1.0 O6 A:DG8 3.9 22.5 1.0 O6 D:DG5 3.9 23.0 1.0 C6 A:DG8 4.0 22.5 1.0 C6 D:DG5 4.0 21.4 1.0 NAH B:F1R103 4.1 23.3 1.0 N4 D:DC6 4.2 21.4 1.0 N9 D:DG5 4.2 21.1 1.0 N9 A:DG8 4.2 25.7 1.0 OP1 D:DG5 4.3 20.8 1.0 C4 D:DG5 4.4 21.6 1.0 O A:HOH202 4.4 26.1 1.0 C4 A:DG8 4.4 21.5 1.0 O C:HOH215 4.4 22.2 1.0 O B:HOH221 4.5 23.6 1.0 OP2 D:DG5 4.5 23.0 1.0 O4' A:DT7 4.6 25.2 1.0 CAY B:F1R103 4.6 24.8 1.0 NAG B:F1R103 4.6 25.9 1.0 C5 D:DC6 4.7 20.8 1.0 CAW B:F1R103 4.7 24.4 1.0 O D:HOH238 4.7 24.6 1.0 NAC B:F1R103 4.7 22.9 1.0 C4 D:DC6 4.8 20.5 1.0 C4' A:DT7 4.8 26.6 1.0 O3' A:DT7 4.8 29.2 1.0 P D:DG5 4.8 22.8 1.0 C1' A:DT7 4.9 26.7 1.0 C5' A:DG8 4.9 30.4 1.0

Cobalt binding site 3 out of 4 in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa/Ttctgcagctgaa) 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/Ttctgcagctgaa) Sequence within 5.0Å range: probe atom residue distance (Å) B Occ B:Co101 b:20.7 occ:1.00 O C:HOH208 1.8 22.2 1.0 O B:HOH204 2.0 20.1 1.0 N7 C:DG8 2.2 23.4 1.0 O B:HOH216 2.2 19.6 1.0 O C:HOH206 2.3 21.5 1.0 N7 B:DG5 2.4 21.5 1.0 C8 C:DG8 2.8 24.5 1.0 C8 B:DG5 3.3 18.0 1.0 C5 B:DG5 3.4 19.7 1.0 C5 C:DG8 3.4 23.5 1.0 O6 B:DG5 3.6 22.3 1.0 C6 B:DG5 3.8 22.8 1.0 OP2 B:DG5 3.9 28.5 1.0 O6 C:DG8 4.1 24.0 1.0 O4' C:DT7 4.1 26.6 1.0 O3' C:DT7 4.1 27.7 1.0 O C:HOH204 4.1 26.8 1.0 N9 C:DG8 4.2 24.6 1.0 C6 C:DG8 4.2 23.4 1.0 NAH D:F1R101 4.3 24.3 1.0 C4 C:DG8 4.4 21.3 1.0 N9 B:DG5 4.4 18.3 1.0 C1' C:DT7 4.5 28.7 1.0 C4 B:DG5 4.5 20.8 1.0 O5' C:DG8 4.6 28.7 1.0 OP1 B:DG5 4.6 25.6 1.0 NAG D:F1R101 4.6 22.4 1.0 P B:DG5 4.7 24.1 1.0 CAY D:F1R101 4.7 23.5 1.0 O D:HOH225 4.8 24.9 1.0 C4' C:DT7 4.8 29.4 1.0 O D:HOH230 4.9 23.5 1.0 CAW D:F1R101 4.9 23.6 1.0 C3' C:DT7 5.0 30.9 1.0

Cobalt binding site 4 out of 4 in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa/Ttctgcagctgaa) 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/Ttctgcagctgaa) Sequence within 5.0Å range: probe atom residue distance (Å) B Occ B:Co102 b:19.7 occ:1.00 O B:HOH218 1.8 20.1 1.0 O A:HOH220 2.0 20.5 1.0 N7 B:DG8 2.3 22.9 1.0 O C:HOH214 2.3 19.5 1.0 O C:HOH202 2.3 21.2 1.0 N7 C:DG5 2.3 21.1 1.0 C8 C:DG5 3.1 18.7 1.0 C8 B:DG8 3.2 20.1 1.0 C5 B:DG8 3.3 24.1 1.0 O A:HOH209 3.3 20.9 1.0 C5 C:DG5 3.5 20.7 1.0 O6 B:DG8 3.6 24.8 1.0 C6 B:DG8 3.8 24.7 1.0 N4 C:DC6 3.9 21.4 1.0 NAH A:F1R103 4.0 23.4 1.0 O6 C:DG5 4.1 23.6 1.0 O C:HOH215 4.1 22.2 1.0 C6 C:DG5 4.2 21.9 1.0 N9 C:DG5 4.3 19.4 1.0 OP1 C:DG5 4.4 22.6 1.0 NAG A:F1R103 4.4 26.1 1.0 C5 C:DC6 4.4 20.8 1.0 N9 B:DG8 4.4 23.8 1.0 C4 B:DG8 4.5 23.6 1.0 CAY A:F1R103 4.5 24.5 1.0 O4' B:DA7 4.5 24.3 1.0 C4 C:DC6 4.5 21.9 1.0 C4 C:DG5 4.6 19.3 1.0 OP2 C:DG5 4.7 21.9 1.0 O B:HOH230 4.7 24.8 1.0 CAW A:F1R103 4.7 24.4 1.0 NAC A:F1R103 4.9 22.5 1.0 P C:DG5 4.9 22.8 1.0 C1' B:DA7 4.9 23.2 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