Magnesium 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:

Chlorine

(Cl)

4 atoms

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of 5-Chlorouracil Modified A:U Base Pair, PDB code: 4huf:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of 5-Chlorouracil Modified A:U Base Pair


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 A:Mg202 b:14.8 occ:0.49 OE2 A:GLU109 1.9 19.7 1.0 O A:HOH384 2.0 26.1 1.0 O A:HOH338 2.0 29.8 1.0 O A:HOH394 2.1 20.8 0.3 O A:HOH346 2.1 26.8 1.0 OD1 A:ASP71 2.3 15.5 1.0 CD A:GLU109 3.1 20.0 1.0 CG A:ASP71 3.5 17.5 1.0 OD1 A:ASN132 3.5 20.8 0.5 OE1 A:GLU109 3.8 15.8 1.0 O A:HOH374 3.8 26.3 1.0 OD1 A:ASN105 3.9 17.1 1.0 OD2 A:ASP71 4.0 21.4 1.0 N A:VAL72 4.0 11.5 1.0 O A:HOH387 4.1 33.8 1.0 O A:VAL72 4.2 12.9 1.0 ND2 A:ASN105 4.2 16.1 1.0 CG A:GLU109 4.2 13.2 1.0 ND2 A:ASN132 4.2 18.5 0.5 CG A:ASN132 4.3 17.0 0.5 O A:HOH308 4.4 15.9 1.0 CB A:VAL72 4.4 11.3 1.0 O B:HOH257 4.5 25.9 1.0 CG A:ASN105 4.5 13.4 1.0 OE2 B:GLU175 4.5 29.7 1.0 CA A:VAL72 4.7 9.4 1.0 CB A:ASP71 4.7 14.0 1.0 CA A:ASP71 4.8 10.9 1.0 C A:VAL72 4.9 13.7 1.0 O A:HOH313 4.9 22.8 1.0 C A:ASP71 5.0 11.1 1.0

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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 E:Mg101 b:19.5 occ:0.59 O E:HOH212 2.1 32.8 1.0 O E:HOH216 2.1 34.4 1.0 OP2 E:DG2 2.1 20.1 1.0 O E:HOH217 2.1 34.8 1.0 O E:HOH213 2.1 32.0 1.0 O E:HOH205 2.1 26.0 1.0 O E:HOH218 2.8 34.9 1.0 O E:HOH219 3.4 37.2 1.0 P E:DG2 3.5 19.2 1.0 O F:HOH204 3.9 33.2 1.0 C3' E:DC1 3.9 19.3 1.0 O3' E:DC1 4.1 17.5 1.0 O E:HOH222 4.1 41.0 1.0 C8 E:DG2 4.1 17.0 1.0 O E:HOH224 4.2 40.5 1.0 O5' E:DC1 4.2 23.2 1.0 N7 E:DG2 4.2 16.6 1.0 O5' E:DG2 4.3 18.2 1.0 O E:HOH214 4.4 32.6 1.0 OP1 E:DG2 4.5 21.9 1.0 O1 F:EDO102 4.6 34.2 1.0 C2' E:DC1 4.8 19.0 1.0 C5' E:DC1 5.0 20.2 1.0 C4' E:DC1 5.0 16.5 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