Sodium 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
Calcium	(Ca)	2 atoms

The binding sites of Sodium 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 Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex, PDB code: 2fza:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na13 b:93.4 occ:0.33 O6 A:DG4 3.1 92.9 1.0 C6 A:DG4 4.3 92.7 1.0 O6 B:DG5 4.5 92.9 1.0 CA A:CA11 4.8 93.4 0.3 O6 A:DG3 4.9 88.2 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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 A:Na15 b:69.9 occ:0.33 O6 B:DG5 2.8 92.9 1.0 O6 A:DG5 2.8 92.7 1.0 C6 B:DG5 3.8 92.5 1.0 C6 A:DG5 3.8 92.5 1.0 N1 A:DG5 4.4 91.4 1.0 N1 B:DG5 4.4 91.9 1.0 C5 B:DG5 4.9 92.0 1.0 C5 A:DG5 4.9 92.3 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na21 b:0.6 occ:1.00 N7 A:DG7 2.9 90.7 1.0 O6 A:DG7 3.8 88.5 1.0 C8 A:DG7 3.8 92.1 1.0 C5 A:DG7 3.9 90.1 1.0 C6 A:DG7 4.2 89.5 1.0 C8 A:DA6 4.3 92.9 1.0 N7 A:DA6 4.7 92.2 1.0 OP2 A:DA6 4.9 93.3 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na14 b:93.4 occ:0.33 O6 B:DG4 3.1 92.5 1.0 C6 B:DG4 4.3 92.7 1.0 O6 A:DG5 4.5 92.7 1.0 CA B:CA12 4.8 93.4 0.3 O6 B:DG3 4.8 88.3 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of D(Gcgggagc): the Base-Intercalated Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na22 b:0.7 occ:1.00 N7 B:DG7 2.9 90.6 1.0 O6 B:DG7 3.8 89.2 1.0 C8 B:DG7 3.8 92.1 1.0 C5 B:DG7 3.9 90.5 1.0 C6 B:DG7 4.2 90.0 1.0 C8 B:DA6 4.2 93.1 1.0 N7 B:DA6 4.7 92.7 1.0 OP2 B:DA6 4.9 93.8 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