Chlorine in PDB 8sv4: 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: 8sv4 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)	27.60 / 2.30
Space group	P 62
Cell size a, b, c (Å), α, β, γ (°)	92.539, 92.539, 78.896, 90, 90, 120
R / Rfree (%)	21.4 / 25.4

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

Fluorine

(F)

8 atoms

The binding sites of Chlorine atom in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex (pdb code 8sv4). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex, PDB code: 8sv4:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl7 b:47.1 occ:1.00 CL B:UCL7 0.0 47.1 1.0 C5 B:UCL7 1.8 40.8 1.0 C4 B:UCL7 2.7 42.5 1.0 C6 B:UCL7 2.7 42.6 1.0 O4 B:UCL7 2.8 43.3 1.0 C8 B:7DA6 3.7 42.8 1.0 C2' B:7DA6 3.8 48.2 1.0 N9 B:7DA6 3.8 41.8 1.0 N1 B:UCL7 4.0 45.9 1.0 N3 B:UCL7 4.0 41.3 1.0 C7 B:7DA6 4.0 39.9 1.0 C4 B:7DA6 4.3 41.6 1.0 C1' B:7DA6 4.3 46.8 1.0 C5 B:7DA6 4.4 41.0 1.0 C2 B:UCL7 4.5 46.0 1.0 CL B:UCL8 4.6 57.9 1.0 O4 B:UCL8 4.6 48.6 1.0

Chlorine binding site 2 out of 4 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl8 b:57.9 occ:1.00 CL B:UCL8 0.0 57.9 1.0 C5 B:UCL8 1.8 43.9 1.0 C6 B:UCL8 2.8 46.9 1.0 C4 B:UCL8 2.8 48.9 1.0 O4 B:UCL8 3.0 48.6 1.0 C6 B:UCL7 3.5 42.6 1.0 C2' B:UCL7 3.7 61.4 1.0 N1 B:UCL7 3.7 45.9 1.0 C5 B:UCL7 3.9 40.8 1.0 N1 B:UCL8 4.0 51.5 1.0 N3 B:UCL8 4.1 46.3 1.0 C1' B:UCL7 4.2 56.8 1.0 C2 B:UCL7 4.3 46.0 1.0 N4 B:C379 4.3 51.9 1.0 C4 B:UCL7 4.4 42.5 1.0 C2 B:UCL8 4.6 47.6 1.0 CL B:UCL7 4.6 47.1 1.0 F B:C379 4.6 49.8 1.0 N3 B:UCL7 4.6 41.3 1.0 C4 B:C379 5.0 46.9 1.0 O2 B:UCL7 5.0 52.8 1.0

Chlorine binding site 3 out of 4 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl7 b:55.3 occ:1.00 CL C:UCL7 0.0 55.3 1.0 C5 C:UCL7 1.8 43.4 1.0 C6 C:UCL7 2.7 47.5 1.0 C4 C:UCL7 2.7 50.9 1.0 O4 C:UCL7 3.0 51.0 1.0 C8 C:7DA6 3.6 45.2 1.0 C2' C:7DA6 3.6 69.9 1.0 O C:HOH106 3.7 46.7 1.0 N9 C:7DA6 3.7 52.1 1.0 N1 C:UCL7 4.0 54.0 1.0 N3 C:UCL7 4.0 46.7 1.0 C7 C:7DA6 4.0 48.1 1.0 C1' C:7DA6 4.2 65.7 1.0 C4 C:7DA6 4.3 41.2 1.0 C5 C:7DA6 4.4 42.0 1.0 C2 C:UCL7 4.5 46.9 1.0 O4 C:UCL8 4.6 41.9 1.0 CL C:UCL8 4.7 54.8 1.0 C3' C:7DA6 5.0 72.3 1.0

Chlorine binding site 4 out of 4 in the 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of 7-Deazapurines and 5-Halogenpyrimidine Dna Duplex within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl8 b:54.8 occ:1.00 CL C:UCL8 0.0 54.8 1.0 C5 C:UCL8 1.7 38.7 1.0 O C:HOH106 2.3 46.7 1.0 C6 C:UCL8 2.7 44.5 1.0 C4 C:UCL8 2.7 41.4 1.0 O4 C:UCL8 2.9 41.9 1.0 C6 C:UCL7 3.5 47.5 1.0 C2' C:UCL7 3.5 70.5 1.0 O C:HOH105 3.5 54.9 1.0 N1 C:UCL7 3.6 54.0 1.0 C5 C:UCL7 3.9 43.4 1.0 N1 C:UCL8 3.9 50.5 1.0 N3 C:UCL8 4.0 38.3 1.0 C1' C:UCL7 4.1 68.7 1.0 C2 C:UCL7 4.1 46.9 1.0 C4 C:UCL7 4.4 50.9 1.0 N4 C:C379 4.4 43.0 1.0 C2 C:UCL8 4.4 45.7 1.0 N3 C:UCL7 4.4 46.7 1.0 F C:C379 4.5 52.9 1.0 CL C:UCL7 4.7 55.3 1.0 O2 C:UCL7 4.8 46.8 1.0 C3' C:UCL7 4.9 69.6 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