Magnesium 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
Sodium	(Na)	2 atoms

The binding sites of Magnesium atom in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex (pdb code 8sv3). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex, PDB code: 8sv3:

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:17.8 occ:0.70 O D:HOH342 2.0 32.5 1.0 O A:HOH337 2.1 34.1 1.0 OD2 A:ASP71 2.1 25.3 1.0 O D:HOH318 2.2 33.7 1.0 OD1 A:ASP192 2.2 27.3 1.0 O A:HOH321 2.3 21.4 1.0 CG A:ASP71 3.1 21.9 1.0 CG A:ASP192 3.4 22.2 1.0 OD1 A:ASP71 3.5 19.2 1.0 CB A:ASP192 3.9 22.2 1.0 O A:VAL72 4.0 18.3 1.0 O1P D:C3711 4.0 33.8 0.5 O1P D:C3711 4.1 15.0 0.5 CA A:ASP192 4.1 22.5 1.0 ND2 A:ASN132 4.2 25.1 1.0 OE2 A:GLU188 4.4 35.6 1.0 OP1 D:7GU12 4.4 14.7 0.5 O D:HOH302 4.4 17.6 0.5 OD2 A:ASP192 4.4 28.8 1.0 N A:TYR193 4.4 22.1 1.0 CB A:ASP71 4.5 17.6 1.0 OP1 D:7GU12 4.7 36.5 0.5 C A:ASP192 4.8 23.7 1.0 O D:HOH304 4.8 26.1 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