Chlorine in PDB 4huf: Structure of 5-Chlorouracil Modified A:U Base Pair

All present enzymatic activity of Structure of 5-Chlorouracil Modified A:U Base Pair:
3.1.26.4;

The structure of Structure of 5-Chlorouracil Modified A:U Base Pair, PDB code: 4huf was solved by A.Patra, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.90 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.193, 64.748, 116.470, 90.00, 90.00, 90.00
R / Rfree (%)	19.2 / 22.8

The structure of Structure of 5-Chlorouracil Modified A:U Base Pair also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Chlorine atom in the Structure of 5-Chlorouracil Modified A:U Base Pair (pdb code 4huf). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of 5-Chlorouracil Modified A:U Base Pair, PDB code: 4huf:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of 5-Chlorouracil Modified A:U Base Pair


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of 5-Chlorouracil Modified A:U Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl7 b:47.4 occ:1.00 CL C:UCL7 0.0 47.4 1.0 C5 C:UCL7 1.7 36.6 1.0 C6 C:UCL7 2.7 37.9 1.0 C4 C:UCL7 2.8 35.2 1.0 O4 C:UCL7 3.0 37.9 1.0 C8 C:DA6 3.6 29.0 1.0 O C:HOH233 3.6 48.5 1.0 N7 C:DA6 3.8 30.4 1.0 N9 C:DA6 3.9 35.1 1.0 N1 C:UCL7 3.9 36.0 1.0 C2' C:DA6 4.0 45.3 1.0 N3 C:UCL7 4.0 36.4 1.0 C5 C:DA6 4.1 26.9 1.0 C4 C:DA6 4.2 30.9 1.0 C2 C:UCL7 4.5 35.8 1.0 C1' C:DA6 4.5 36.5 1.0 O4 C:DT8 4.6 40.8 1.0 C7 C:DT8 4.9 38.0 1.0 C6 C:DA6 5.0 27.7 1.0

Chlorine binding site 2 out of 4 in the Structure of 5-Chlorouracil Modified A:U Base Pair


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of 5-Chlorouracil Modified A:U Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl19 b:42.2 occ:1.00 CL D:UCL19 0.0 42.2 1.0 C5 D:UCL19 1.7 32.3 1.0 C6 D:UCL19 2.7 37.3 1.0 C4 D:UCL19 2.8 31.9 1.0 O4 D:UCL19 3.0 35.4 1.0 O D:HOH112 3.3 40.0 1.0 C8 D:DA18 3.7 41.7 1.0 C2' D:DA18 3.8 52.4 1.0 N9 D:DA18 3.9 41.2 1.0 N1 D:UCL19 3.9 36.1 1.0 N7 D:DA18 4.0 42.8 1.0 N3 D:UCL19 4.0 34.4 1.0 C4 D:DA18 4.4 37.2 1.0 C5 D:DA18 4.4 38.2 1.0 C1' D:DA18 4.4 50.4 1.0 C2 D:UCL19 4.5 33.3 1.0 O4 D:DT20 4.6 29.5 1.0 C7 D:DT20 4.6 32.4 1.0

Chlorine binding site 3 out of 4 in the Structure of 5-Chlorouracil Modified A:U Base Pair


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of 5-Chlorouracil Modified A:U Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ E:Cl7 b:60.6 occ:1.00 CL E:UCL7 0.0 60.6 1.0 C5 E:UCL7 1.7 58.9 1.0 C6 E:UCL7 2.7 61.9 1.0 C4 E:UCL7 2.8 57.9 1.0 O4 E:UCL7 3.0 59.2 1.0 C8 E:DA6 3.7 44.9 1.0 N7 E:DA6 3.9 45.3 1.0 N1 E:UCL7 3.9 63.7 1.0 N9 E:DA6 4.0 50.4 1.0 C2' E:DA6 4.0 60.0 1.0 N3 E:UCL7 4.0 58.1 1.0 C5 E:DA6 4.3 38.8 1.0 C4 E:DA6 4.4 48.4 1.0 C7 E:DT8 4.4 59.3 1.0 C2 E:UCL7 4.5 61.2 1.0 C1' E:DA6 4.6 54.8 1.0

Chlorine binding site 4 out of 4 in the Structure of 5-Chlorouracil Modified A:U Base Pair


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of 5-Chlorouracil Modified A:U Base Pair within 5.0Å range: probe atom residue distance (Å) B Occ F:Cl19 b:60.3 occ:1.00 CL F:UCL19 0.0 60.3 1.0 C5 F:UCL19 1.7 53.6 1.0 C6 F:UCL19 2.7 62.2 1.0 C4 F:UCL19 2.8 54.3 1.0 O4 F:UCL19 3.0 57.4 1.0 C2' F:DA18 3.6 72.0 1.0 N1 F:UCL19 3.9 64.5 1.0 N3 F:UCL19 4.0 51.8 1.0 C8 F:DA18 4.1 63.7 1.0 N9 F:DA18 4.3 65.8 1.0 N7 F:DA18 4.5 60.0 1.0 C2 F:UCL19 4.5 58.8 1.0 C1' F:DA18 4.6 71.3 1.0 C4 F:DA18 4.8 58.5 1.0 C3' F:DA18 4.8 76.3 1.0 C7 F:DT20 4.8 52.1 1.0 C5 F:DA18 4.9 63.4 1.0 O4 F:DT20 4.9 45.5 1.0

A.Patra, J.Harp, P.S.Pallan, L.Zhao, M.Abramov, P.Herdewijn, M.Egli. Structure, Stability and Function of 5-Chlorouracil Modified A:U and G:U Base Pairs. Nucleic Acids Res. V. 41 2689 2013.
ISSN: ISSN 0305-1048
PubMed: 23275540
DOI: 10.1093/NAR/GKS1316