Bromine in PDB 2fza: Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex

The structure of Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex, PDB code: 2fza was solved by J.Kondo, T.Ciengshin, E.C.M.Juan, K.Mitomi, A.Takenaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 3.60
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	36.368, 36.368, 62.826, 90.00, 90.00, 120.00
R / Rfree (%)	29.4 / 32.9

The structure of Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex also contains other interesting chemical elements:

Calcium	(Ca)	2 atoms
Sodium	(Na)	5 atoms

The binding sites of Bromine atom in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex (pdb code 2fza). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 2 binding sites of Bromine where determined in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex, PDB code: 2fza:
Jump to Bromine binding site number: 1; 2;

Bromine binding site 1 out of 2 in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Br2 b:0.2 occ:1.00 BR A:CBR2 0.0 0.2 1.0 C5 A:CBR2 1.9 0.7 1.0 C6 A:CBR2 2.8 0.7 1.0 C4 A:CBR2 2.8 0.6 1.0 N4 A:CBR2 3.0 0.3 1.0 O6 A:DG3 3.3 88.2 1.0 C8 A:DG1 3.3 93.8 1.0 C6 A:DG3 3.4 90.3 1.0 N7 A:DG1 3.5 92.1 1.0 N1 A:DG3 3.7 90.3 1.0 N9 A:DG1 3.9 94.6 1.0 C5 A:DG3 4.1 90.9 1.0 N3 A:CBR2 4.1 0.1 1.0 N1 A:CBR2 4.1 0.4 1.0 C5 A:DG1 4.2 90.0 1.0 C2' A:DG1 4.3 97.7 1.0 C4 A:DG1 4.4 91.3 1.0 C2 A:DG3 4.5 90.4 1.0 C2 A:CBR2 4.6 0.4 1.0 C1' A:DG1 4.6 96.7 1.0 N7 A:DG3 4.7 90.8 1.0 C4 A:DG3 4.7 90.9 1.0 CA A:CA11 4.9 93.4 0.3 N3 A:DG3 5.0 90.4 1.0

Bromine binding site 2 out of 2 in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Br2 b:0.7 occ:1.00 BR B:CBR2 0.0 0.7 1.0 C5 B:CBR2 1.9 0.3 1.0 C6 B:CBR2 2.8 0.2 1.0 C4 B:CBR2 2.9 0.2 1.0 N4 B:CBR2 3.0 0.6 1.0 C8 B:DG1 3.3 94.0 1.0 O6 B:DG3 3.3 88.3 1.0 C6 B:DG3 3.4 90.2 1.0 N7 B:DG1 3.5 92.4 1.0 N1 B:DG3 3.7 89.9 1.0 N9 B:DG1 3.9 94.9 1.0 C5 B:DG3 4.1 91.1 1.0 N1 B:CBR2 4.1 0.3 1.0 N3 B:CBR2 4.1 0.3 1.0 C5 B:DG1 4.2 90.1 1.0 C2' B:DG1 4.3 98.3 1.0 C4 B:DG1 4.4 91.6 1.0 C2 B:DG3 4.5 89.9 1.0 C1' B:DG1 4.6 97.3 1.0 C2 B:CBR2 4.6 0.5 1.0 N7 B:DG3 4.7 91.4 1.0 C4 B:DG3 4.7 90.9 1.0 CA B:CA12 4.9 93.4 0.3

J.Kondo, T.Ciengshin, E.C.M.Juan, Y.Sato, K.Mitomi, S.Shimizu, A.Takenaka. Crystal Structure of D(Gcgxgagc) with X=G: A Mutation at X Is Possible to Occur in A Base-Intercalated Duplex For Multiplex Formation Nucleosides Nucleotides V. 25 693 2006NUCLEIC Acids.
ISSN: ISSN 1525-7770
PubMed: 16838856
DOI: 10.1080/15257770600686543