Magnesium in PDB 3zdb: Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium

The structure of Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium, PDB code: 3zdb was solved by G.R.Hemsworth, C.S.Anstey-Gilbert, C.S.Flemming, M.R.G.Hodskinson, J.Zhang, S.E.Sedelnikova, T.J.Stillman, J.R.Sayers, P.J.Artymiuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.67 / 1.47
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	66.238, 152.302, 34.522, 90.00, 90.00, 90.00
R / Rfree (%)	20.287 / 23.054

The structure of Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Magnesium atom in the Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium (pdb code 3zdb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium, PDB code: 3zdb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1252 b:20.6 occ:0.60 K A:K1251 1.5 19.8 0.4 OP2 X:DC10 1.9 25.7 1.0 O A:HOH2151 2.0 21.4 0.6 O A:HOH2149 2.2 29.0 1.0 O A:ALA172 2.2 22.8 1.0 O A:HOH2148 2.3 32.5 1.0 O A:ILE185 2.4 24.2 1.0 C A:ALA172 3.2 22.6 1.0 P X:DC10 3.3 27.3 1.0 C A:ILE185 3.6 21.6 1.0 CA A:ALA172 3.8 18.3 1.0 OP1 X:DC10 3.9 28.9 1.0 CA A:GLY186 4.0 17.9 1.0 O5' X:DC10 4.1 24.7 1.0 O A:PRO180 4.1 23.6 1.0 O A:VAL182 4.2 22.8 1.0 N A:GLY186 4.2 18.5 1.0 N A:GLY173 4.3 17.9 1.0 O A:HOH2150 4.4 35.0 1.0 O3' X:DA9 4.4 25.9 1.0 O A:LEU171 4.4 21.1 1.0 O A:HOH2060 4.5 29.9 1.0 O A:HOH2153 4.6 36.8 1.0 N A:ILE185 4.6 24.9 1.0 CA A:GLY173 4.6 21.0 1.0 C3' X:DA9 4.6 19.6 1.0 CB A:ALA172 4.6 18.3 1.0 CA A:ILE185 4.7 23.9 1.0 N A:ALA172 5.0 18.8 1.0

Magnesium binding site 2 out of 3 in the Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1253 b:28.9 occ:1.00 O A:HOH2010 1.9 22.8 1.0 O A:HOH2196 2.0 32.4 1.0 O A:HOH2066 2.1 37.0 1.0 O A:HOH2011 2.1 32.6 1.0 OD1 A:ASP104 2.1 21.6 1.0 O A:HOH2046 2.4 39.7 1.0 MG A:MG1255 2.5 31.9 1.0 CG A:ASP104 2.8 28.8 1.0 OD2 A:ASP104 2.8 33.2 1.0 O A:HOH2009 3.4 29.5 1.0 OD2 A:ASP9 4.2 24.7 1.0 O A:HOH2045 4.3 38.5 1.0 CB A:ASP104 4.3 21.9 1.0 O A:HOH2067 4.4 45.4 1.0 OE2 A:GLU102 4.5 81.2 1.0 OD2 A:ASP127 4.6 36.0 1.0 NZ A:LYS67 4.6 29.9 1.0 OD1 A:ASP9 4.6 18.9 1.0 N A:ASP104 4.6 15.6 1.0 CG A:ASP9 4.8 20.5 1.0 OH A:TYR130 4.8 20.1 1.0 CA A:ASP104 4.9 15.6 1.0 CB A:GLU102 4.9 59.8 1.0 CD A:GLU102 5.0 57.3 1.0

Magnesium binding site 3 out of 3 in the Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of E. Coli Exoix in Complex with the Palindromic 5OV4 Dna Oligonucleotide, Di-Magnesium and Potassium within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1255 b:31.9 occ:1.00 O A:HOH2046 2.0 39.7 1.0 O A:HOH2010 2.0 22.8 1.0 O A:HOH2009 2.0 29.5 1.0 O A:HOH2045 2.1 38.5 1.0 O A:HOH2196 2.2 32.4 1.0 MG A:MG1253 2.5 28.9 1.0 O A:HOH2011 3.9 32.6 1.0 OD2 A:ASP50 4.0 26.1 1.0 OD1 A:ASP104 4.0 21.6 1.0 OD1 A:ASP50 4.1 31.6 1.0 OD1 A:ASP9 4.1 18.9 1.0 O A:HOH2067 4.2 45.4 1.0 O A:HOH2066 4.2 37.0 1.0 O A:HOH2008 4.3 16.4 1.0 CG A:ASP50 4.4 0.0 1.0 CB A:LEU11 4.7 15.9 1.0 OE2 A:GLU102 4.8 81.2 1.0 OD2 A:ASP9 4.9 24.7 1.0 CB A:ALA103 4.9 19.9 1.0 CG A:ASP9 4.9 20.5 1.0

C.S.Anstey-Gilbert, G.R.Hemsworth, C.S.Flemming, M.R.G.Hodskinson, J.Zhang, S.E.Sedelnikova, T.J.Stillman, J.R.Sayers, P.J.Artymiuk. The Structure of E. Coli Exoix - Implications For Dna Binding and Catalysis in Flap Endonucleases Nucleic Acids Res. V. 41 8357 2013.
ISSN: ISSN 0305-1048
PubMed: 23821668
DOI: 10.1093/NAR/GKT591