Chlorine 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:

Cobalt

(Co)

4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa/Ttctgcagctgaa) Sequence, PDB code: 6m5j:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl103 b:30.7 occ:1.00 CLA A:F1R103 0.0 30.7 1.0 CAI A:F1R103 1.8 27.6 1.0 CAN A:F1R103 2.7 27.1 1.0 CAJ A:F1R103 2.7 28.1 1.0 O A:HOH204 3.2 31.6 1.0 C7 A:DT10 3.6 25.6 1.0 N7 A:DG11 3.8 29.3 1.0 C5 A:DT10 4.0 25.6 1.0 CAK A:F1R103 4.0 25.7 1.0 CAM A:F1R103 4.0 27.3 1.0 C8 A:DG11 4.1 30.9 1.0 C6 A:DT10 4.4 27.4 1.0 O A:HOH208 4.4 30.1 1.0 CAL A:F1R103 4.5 28.3 1.0 C5 A:DG11 4.5 28.4 1.0 OP2 A:DT10 4.6 34.7 1.0 C4 A:DT10 4.6 23.9 1.0 O A:HOH210 4.9 28.2 1.0 O4 A:DT10 4.9 24.3 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 B:Cl103 b:32.0 occ:1.00 CLA B:F1R103 0.0 32.0 1.0 CAI B:F1R103 1.8 30.1 1.0 CAN B:F1R103 2.7 27.8 1.0 CAJ B:F1R103 2.8 29.9 1.0 C5 B:DT10 3.5 25.8 1.0 C7 B:DT10 3.5 24.9 1.0 C6 B:DT10 3.6 26.4 1.0 N7 B:DG11 3.9 32.1 1.0 C8 B:DG11 4.0 32.8 1.0 CAM B:F1R103 4.0 28.9 1.0 CAK B:F1R103 4.1 28.6 1.0 C4 B:DT10 4.1 24.1 1.0 N1 B:DT10 4.3 26.6 1.0 C5 B:DG11 4.5 30.6 1.0 C3' B:DT10 4.6 26.8 1.0 CAL B:F1R103 4.6 29.4 1.0 O4 B:DT10 4.6 24.5 1.0 O5' B:DT10 4.6 30.7 1.0 O5' B:DG11 4.7 34.5 1.0 N3 B:DT10 4.7 25.3 1.0 O B:HOH242 4.7 38.7 1.0 OP2 B:DT10 4.7 35.3 1.0 N9 B:DG11 4.7 30.4 1.0 C2' B:DT10 4.7 26.2 1.0 OP2 B:DG11 4.8 32.5 1.0 C2 B:DT10 4.8 26.2 1.0 O B:HOH219 4.9 40.0 1.0 C4 B:DG11 5.0 31.4 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 C:Cl101 b:29.5 occ:1.00 CLA C:F1R101 0.0 29.5 1.0 CAI C:F1R101 1.8 27.4 1.0 CAJ C:F1R101 2.7 27.0 1.0 CAN C:F1R101 2.7 25.0 1.0 O C:HOH212 3.3 33.2 1.0 C5 C:DT10 3.4 23.8 1.0 C7 C:DT10 3.6 24.9 1.0 C6 C:DT10 3.6 24.7 1.0 N7 C:DG11 3.9 31.5 1.0 CAK C:F1R101 4.0 25.1 1.0 C4 C:DT10 4.0 21.7 1.0 CAM C:F1R101 4.1 25.1 1.0 N1 C:DT10 4.3 24.2 1.0 C8 C:DG11 4.3 29.9 1.0 O C:HOH222 4.4 30.8 1.0 OP2 C:DG11 4.5 32.7 1.0 O4 C:DT10 4.5 22.0 1.0 CAL C:F1R101 4.5 26.0 1.0 C3' C:DT10 4.6 29.6 1.0 N3 C:DT10 4.6 22.9 1.0 OP2 C:DT10 4.7 34.6 1.0 C2' C:DT10 4.7 27.6 1.0 O5' C:DT10 4.7 31.0 1.0 C2 C:DT10 4.8 22.4 1.0 C5 C:DG11 4.8 28.7 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 D:Cl101 b:30.6 occ:1.00 CLA D:F1R101 0.0 30.6 1.0 CAI D:F1R101 1.8 27.8 1.0 CAJ D:F1R101 2.7 28.2 1.0 CAN D:F1R101 2.8 25.3 1.0 C6 D:DT10 3.1 23.9 1.0 C5 D:DT10 3.2 23.5 1.0 N1 D:DT10 3.5 23.6 1.0 C7 D:DT10 3.7 23.2 1.0 C4 D:DT10 3.7 21.5 1.0 C2' D:DT10 3.8 28.3 1.0 C3' D:DT10 3.8 29.8 1.0 OP2 D:DG11 4.0 34.2 1.0 C2 D:DT10 4.0 23.1 1.0 N7 D:DG11 4.0 30.1 1.0 CAK D:F1R101 4.0 27.0 1.0 N3 D:DT10 4.1 24.1 1.0 CAM D:F1R101 4.1 26.3 1.0 C1' D:DT10 4.2 26.7 1.0 C8 D:DG11 4.2 30.9 1.0 O5' D:DT10 4.4 29.0 1.0 O4 D:DT10 4.5 21.4 1.0 CAL D:F1R101 4.6 26.8 1.0 O5' D:DG11 4.6 33.1 1.0 O4' D:DT10 4.7 25.2 1.0 P D:DG11 4.7 34.0 1.0 C5 D:DG11 4.8 29.4 1.0 O3' D:DT10 4.8 30.4 1.0 OP2 D:DT10 4.8 33.6 1.0 C4' D:DT10 4.8 27.8 1.0 O2 D:DT10 4.9 24.9 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