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

Protein crystallography data

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

Other elements in 2fza:

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

Calcium Binding Sites:

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 2fza

Go back to Calcium Binding Sites List in 2fza
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 2fza

Go back to Calcium Binding Sites List in 2fza
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

Reference:

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
Page generated: Tue Jul 8 05:40:06 2025

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