Sodium in PDB 8sv3: 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex

All present enzymatic activity of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex:
3.1.26.4;

The structure of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex, PDB code: 8sv3 was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.54 / 1.51
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.983, 89, 72.566, 90, 100.44, 90
R / Rfree (%)	17.7 / 21

The structure of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex also contains other interesting chemical elements:

Chlorine	(Cl)	5 atoms
Fluorine	(F)	10 atoms
Magnesium	(Mg)	1 atom

The binding sites of Sodium atom in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex (pdb code 8sv3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex, PDB code: 8sv3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:16.7 occ:1.00 OD1 B:ASN132 2.2 13.8 1.0 OE2 B:GLU109 2.2 15.3 1.0 OD1 B:ASP71 2.2 12.9 1.0 O B:HOH372 3.0 14.2 1.0 CD B:GLU109 3.0 14.0 1.0 CG B:ASN132 3.0 13.1 1.0 OE1 B:GLU109 3.1 15.3 1.0 CG B:ASP71 3.2 12.4 1.0 ND2 B:ASN132 3.3 13.5 1.0 OD2 B:ASP71 3.6 13.7 1.0 O B:HOH356 4.1 16.6 1.0 CB B:ASP71 4.4 13.7 1.0 CG B:GLU109 4.4 13.3 1.0 CB B:ASN132 4.4 12.3 1.0 CG1 B:VAL72 4.6 13.7 1.0 N B:ASN132 4.6 12.2 1.0 CA B:ASP71 4.7 12.3 1.0 C B:ASN132 4.7 12.3 1.0 N B:VAL72 4.7 14.0 1.0 N B:SER133 4.8 11.5 1.0 CA B:ASN132 4.8 12.3 1.0 CB B:SER133 4.9 11.6 1.0

Sodium binding site 2 out of 2 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:25.5 occ:0.80 O C:HOH303 1.8 26.8 0.6 OD1 C:ASP71 2.2 24.9 1.0 O C:HOH341 2.2 32.4 1.0 O C:HOH324 2.3 37.7 1.0 CG C:ASP71 3.2 26.8 1.0 OD2 C:ASP71 3.4 35.1 1.0 O C:VAL72 3.6 20.6 1.0 OE2 C:GLU109 3.6 24.0 1.0 N C:VAL72 4.3 16.5 1.0 CB C:ASP71 4.6 23.4 1.0 C C:VAL72 4.6 20.4 1.0 O C:HOH342 4.7 16.6 1.0 OD1 C:ASN105 4.8 27.7 1.0 CD C:GLU109 4.8 19.1 1.0 CA C:VAL72 4.9 16.3 1.0 CB C:VAL72 4.9 17.7 1.0 CA C:ASP71 4.9 18.9 1.0

P.S.Pallan, T.P.Lybrand, E.Rozners, M.Abramov, G.Schepers, E.Eremeeva, P.Herdewijn, M.Egli. Conformational Morphing By A Dna Analogue Featuring 7-Deazapurines and 5-Halogenpyrimidines and the Origins of Adenine-Tract Geometry. Biochemistry 2023.
ISSN: ISSN 0006-2960
PubMed: 37694722
DOI: 10.1021/ACS.BIOCHEM.3C00327