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Sodium in PDB 1d39: Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2

Protein crystallography data

The structure of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2, PDB code: 1d39 was solved by T.F.Kagawa, B.H.Geierstanger, A.H.-J.Wang, P.S.Ho, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) N/A / 1.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 18.010, 31.030, 44.800, 90.00, 90.00, 90.00
R / Rfree (%) n/a / n/a

Other elements in 1d39:

The structure of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 also contains other interesting chemical elements:

Copper (Cu) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 (pdb code 1d39). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2, PDB code: 1d39:

Sodium binding site 1 out of 1 in 1d39

Go back to Sodium Binding Sites List in 1d39
Sodium binding site 1 out of 1 in the Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Covalent Modification of Guanine Bases in Double Stranded Dna: the 1.2 Angstroms Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na16

b:35.9
occ:1.00
O B:HOH26 2.6 34.9 1.0
C8 B:DG10 3.3 11.9 1.0
C2' B:DG10 3.4 13.2 1.0
O B:HOH73 3.4 33.7 1.0
N9 B:DG10 3.5 11.2 1.0
C5 B:DC11 3.6 7.2 1.0
C1' B:DG10 3.6 12.0 1.0
O B:HOH77 3.9 38.4 1.0
N7 B:DG10 3.9 10.7 1.0
C4 B:DG10 4.3 10.7 1.0
N4 B:DC11 4.3 7.1 1.0
C4 B:DC11 4.4 7.4 1.0
C5 B:DG10 4.4 10.6 1.0
C6 B:DC11 4.5 7.8 1.0
O A:HOH42 4.5 5.8 1.0
N4 A:DC1 4.8 8.2 1.0
C3' B:DG10 4.9 15.4 1.0

Reference:

T.F.Kagawa, B.H.Geierstanger, A.H.Wang, P.S.Ho. Covalent Modification of Guanine Bases in Double-Stranded Dna. the 1.2-A Z-Dna Structure of D(Cgcgcg) in the Presence of CUCL2. J.Biol.Chem. V. 266 20175 1991.
ISSN: ISSN 0021-9258
PubMed: 1939078
Page generated: Tue Dec 15 05:22:51 2020

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