Manganese in PDB 8w76: Crystal Structure of D(Cgtatacg)2 Duplex

The structure of Crystal Structure of D(Cgtatacg)2 Duplex, PDB code: 8w76 was solved by R.B.Satange, C.L.Peng, M.H.Hou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.07 / 2.71
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	37.614, 37.614, 77.994, 90, 90, 90
R / Rfree (%)	22.1 / 26.8

The binding sites of Manganese atom in the Crystal Structure of D(Cgtatacg)2 Duplex (pdb code 8w76). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of D(Cgtatacg)2 Duplex, PDB code: 8w76:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Crystal Structure of D(Cgtatacg)2 Duplex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of D(Cgtatacg)2 Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn101 b:23.5 occ:0.52 N7 C:DG8 1.8 40.8 1.0 OP2 C:DG8 2.0 32.4 1.0 O C:HOH201 2.1 34.3 1.0 C8 C:DG8 2.6 37.8 1.0 C5 C:DG8 2.9 30.0 1.0 P C:DG8 3.3 31.9 1.0 O5' C:DG8 3.5 46.8 1.0 C6 C:DG8 3.6 28.9 1.0 O6 C:DG8 3.7 58.3 1.0 N9 C:DG8 3.8 33.8 1.0 C4 C:DG8 3.9 32.5 1.0 C3' C:DC7 4.0 38.1 1.0 O3' C:DC7 4.2 38.0 1.0 OP1 C:DG8 4.4 34.2 1.0 C2' C:DC7 4.8 61.4 1.0 N1 C:DG8 4.9 33.3 1.0 C5' C:DG8 5.0 22.7 1.0

Manganese binding site 2 out of 4 in the Crystal Structure of D(Cgtatacg)2 Duplex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of D(Cgtatacg)2 Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn101 b:67.1 occ:1.00 O D:HOH202 2.1 48.6 1.0 O D:HOH204 2.2 68.4 1.0 N7 D:DG8 2.3 54.7 1.0 O D:HOH201 2.3 66.8 1.0 O D:HOH203 2.6 40.6 1.0 C5 D:DG8 3.3 30.9 1.0 C8 D:DG8 3.3 49.5 1.0 O6 D:DG8 3.4 49.9 1.0 C6 D:DG8 3.7 30.0 1.0 OP2 D:DG8 4.4 50.9 1.0 N9 D:DG8 4.5 32.5 1.0 C4 D:DG8 4.5 32.3 1.0

Manganese binding site 3 out of 4 in the Crystal Structure of D(Cgtatacg)2 Duplex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of D(Cgtatacg)2 Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn102 b:70.5 occ:1.00 OP1 D:DG8 2.1 74.5 1.0 P D:DG8 3.4 63.4 1.0 O3' D:DC7 3.7 52.6 1.0 O5' D:DG8 4.4 32.6 1.0 OP2 D:DG8 4.4 50.9 1.0 C5' D:DG8 4.5 42.8 1.0 C3' D:DC7 5.0 50.8 1.0

Manganese binding site 4 out of 4 in the Crystal Structure of D(Cgtatacg)2 Duplex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of D(Cgtatacg)2 Duplex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn103 b:90.3 occ:1.00 O3' D:DG8 2.8 50.2 1.0 C3' D:DG8 3.8 43.5 1.0 C2' D:DG8 3.9 49.8 1.0 C4' D:DG8 4.7 43.2 1.0

S.C.Huang, C.W.Chen, R.Satange, C.C.Hsieh, C.C.Chang, S.C.Wang, C.L.Peng, T.L.Chen, M.H.Chiang, Y.C.Horng, M.H.Hou. Targeting Dna Junction Sites By Bis-Intercalators Induces Topological Changes with Potent Antitumor Effects. Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
PubMed: 39036959
DOI: 10.1093/NAR/GKAE643