Calcium 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:

Bromine	(Br)	2 atoms
Sodium	(Na)	5 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex, PDB code: 2fza:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca11 b:93.4 occ:0.33 O6 A:DG3 3.7 88.2 1.0 NA A:NA13 4.8 93.4 0.3 C6 A:DG3 4.9 90.3 1.0 BR A:CBR2 4.9 0.2 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca12 b:93.4 occ:0.33 O6 B:DG3 3.7 88.3 1.0 NA B:NA14 4.8 93.4 0.3 C6 B:DG3 4.9 90.2 1.0 BR B:CBR2 4.9 0.7 1.0

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