Chlorine 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:

Cobalt	(Co)	4 atoms
Bromine	(Br)	4 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the U Shaped Head to Head Four-Way Junction in D(Ttctgctgctgaa) Sequence, PDB code: 6m4t:
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) 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) Sequence within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl103 b:26.4 occ:1.00 CLA A:F1R103 0.0 26.4 1.0 CAI A:F1R103 1.7 23.6 1.0 CAN A:F1R103 2.7 17.8 1.0 CAJ A:F1R103 2.7 23.7 1.0 C6 A:DT10 3.3 22.7 1.0 C5 A:DT10 3.3 21.7 1.0 C7 A:DT10 3.5 21.5 1.0 N1 A:DT10 3.9 23.1 1.0 CAK A:F1R103 4.0 21.8 1.0 CAM A:F1R103 4.0 15.6 1.0 C4 A:DT10 4.0 21.1 1.0 C3' A:DT10 4.0 25.6 1.0 OP2 A:DG11 4.1 34.4 1.0 N7 A:DG11 4.1 23.5 1.0 O5' A:DT10 4.1 26.2 1.0 O A:HOH207 4.2 27.6 1.0 C8 A:DG11 4.3 25.7 1.0 OP2 A:DT10 4.3 28.2 1.0 C2' A:DT10 4.4 25.1 1.0 O A:HOH252 4.4 31.9 1.0 N3 A:DT10 4.5 21.6 1.0 CAL A:F1R103 4.5 19.4 1.0 C2 A:DT10 4.5 22.6 1.0 O4 A:DT10 4.6 21.6 1.0 O5' A:DG11 4.6 29.8 1.0 C1' A:DT10 4.6 24.4 1.0 C5 A:DG11 4.8 26.9 1.0 P A:DT10 4.9 28.5 1.0 P A:DG11 4.9 34.4 1.0 O4' A:DT10 4.9 24.9 1.0 C4' A:DT10 4.9 25.9 1.0 O3' A:DT10 5.0 31.2 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 B:Cl103 b:30.6 occ:1.00 CLA B:F1R103 0.0 30.6 1.0 CAI B:F1R103 1.8 26.3 1.0 CAJ B:F1R103 2.7 28.2 1.0 CAN B:F1R103 2.7 22.6 1.0 C6 B:DT10 3.4 24.7 1.0 C5 B:DT10 3.4 21.9 1.0 C7 B:DT10 3.5 21.2 1.0 CAK B:F1R103 4.0 26.5 1.0 N7 B:DG11 4.0 37.4 1.0 CAM B:F1R103 4.0 17.8 1.0 OP2 B:DT10 4.1 36.8 1.0 O B:HOH203 4.1 36.7 1.0 N1 B:DT10 4.1 28.8 1.0 C4 B:DT10 4.2 23.8 1.0 C8 B:DG11 4.2 32.7 1.0 O5' B:DT10 4.2 36.4 1.0 C3' B:DT10 4.3 37.7 1.0 OP2 B:DG11 4.4 42.5 1.0 CAL B:F1R103 4.5 19.6 1.0 C2' B:DT10 4.6 30.8 1.0 N3 B:DT10 4.7 24.4 1.0 O4 B:DT10 4.8 20.1 1.0 C2 B:DT10 4.8 30.3 1.0 C5 B:DG11 4.8 35.1 1.0 O5' B:DG11 4.8 34.1 1.0 C1' B:DT10 4.8 30.0 1.0 P B:DT10 4.8 35.8 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 C:Cl101 b:22.6 occ:1.00 CLA C:F1R101 0.0 22.6 1.0 CAI C:F1R101 1.8 25.8 1.0 CAJ C:F1R101 2.7 22.2 1.0 CAN C:F1R101 2.7 28.3 1.0 O C:HOH204 3.3 26.7 1.0 C5 C:DT10 3.6 24.5 1.0 C7 C:DT10 3.7 29.1 1.0 C6 C:DT10 3.7 25.7 1.0 N7 C:DG11 3.8 23.8 1.0 O C:HOH253 3.8 30.8 1.0 CAK C:F1R101 4.0 21.6 1.0 CAM C:F1R101 4.0 30.8 1.0 C4 C:DT10 4.1 21.3 1.0 C8 C:DG11 4.1 26.8 1.0 N1 C:DT10 4.4 23.0 1.0 OP2 C:DG11 4.4 38.8 1.0 O C:HOH217 4.4 40.8 1.0 OP2 C:DT10 4.5 31.8 1.0 CAL C:F1R101 4.5 30.1 1.0 O4 C:DT10 4.6 23.0 1.0 N3 C:DT10 4.6 24.1 1.0 C5 C:DG11 4.6 28.5 1.0 C3' C:DT10 4.7 28.0 1.0 O5' C:DT10 4.7 34.3 1.0 C2 C:DT10 4.8 22.2 1.0 C2' C:DT10 4.9 26.2 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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 D:Cl101 b:25.7 occ:1.00 CLA D:F1R101 0.0 25.7 1.0 CAI D:F1R101 1.8 24.1 1.0 CAN D:F1R101 2.8 26.1 1.0 CAJ D:F1R101 2.8 23.5 1.0 C6 D:DT10 3.4 37.3 1.0 C5 D:DT10 3.5 28.0 1.0 C7 D:DT10 3.6 30.7 1.0 N7 D:DG11 3.9 36.3 1.0 C2' D:DT10 4.0 45.7 1.0 CAK D:F1R101 4.1 26.8 1.0 N1 D:DT10 4.1 39.8 1.0 CAM D:F1R101 4.1 30.4 1.0 O D:HOH244 4.1 35.4 1.0 C4 D:DT10 4.2 25.1 1.0 C8 D:DG11 4.3 34.2 1.0 OP2 D:DT10 4.3 53.5 1.0 CAL D:F1R101 4.6 32.0 1.0 C1' D:DT10 4.7 43.4 1.0 N3 D:DT10 4.7 32.5 1.0 C2 D:DT10 4.7 37.4 1.0 C5 D:DG11 4.8 35.4 1.0 O4 D:DT10 4.8 27.6 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