Magnesium in PDB 5cfg: C2 Crystal Form of APE1 with MG2+

All present enzymatic activity of C2 Crystal Form of APE1 with MG2+:
4.2.99.18;

The structure of C2 Crystal Form of APE1 with MG2+, PDB code: 5cfg was solved by S.Morera, A.Vigouroux, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.39 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	86.530, 45.120, 77.980, 90.00, 105.15, 90.00
R / Rfree (%)	18.5 / 20.4

The binding sites of Magnesium atom in the C2 Crystal Form of APE1 with MG2+ (pdb code 5cfg). 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 C2 Crystal Form of APE1 with MG2+, PDB code: 5cfg:

Magnesium binding site 1 out of 1 in the C2 Crystal Form of APE1 with MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of C2 Crystal Form of APE1 with MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:32.1 occ:1.00 O A:HOH514 1.9 29.8 1.0 OE2 A:GLU96 1.9 25.8 1.0 O A:HOH513 2.0 29.4 1.0 O A:HOH522 2.1 16.7 1.0 O A:HOH565 2.2 36.5 1.0 OD1 A:ASP70 2.2 27.7 1.0 CD A:GLU96 2.9 35.8 1.0 OE1 A:GLU96 3.1 38.6 1.0 CG A:ASP70 3.2 28.2 1.0 CB A:ASP70 3.8 21.5 1.0 CA A:ASP70 4.0 19.5 1.0 O A:HOH555 4.1 27.9 1.0 OD2 A:ASP308 4.1 25.6 1.0 OD1 A:ASP308 4.2 20.9 1.0 OD2 A:ASP70 4.2 24.9 1.0 CG A:GLU96 4.3 24.1 1.0 OD1 A:ASN68 4.3 18.8 1.0 CG A:ASP308 4.6 25.1 1.0 NZ A:LYS98 4.7 46.5 1.0 CE A:LYS98 4.7 37.3 1.0 OH A:TYR171 4.7 26.6 1.0 ND2 A:ASN68 4.8 22.8 1.0 CB A:GLU96 4.8 16.2 1.0 N A:ASP70 4.9 17.8 1.0 CG A:ASN68 5.0 24.7 1.0

M.Redrejo-Rodriguez, A.Vigouroux, A.Mursalimov, I.Grin, D.Alili, Z.Koshenov, Z.Akishev, A.Maksimenko, A.K.Bissenbaev, B.T.Matkarimov, M.Saparbaev, A.A.Ishchenko, S.Morera. Structural Comparison of Ap Endonucleases From the Exonuclease III Family Reveals New Amino Acid Residues in Human Ap Endonuclease 1 That Are Involved in Incision of Damaged Dna. Biochimie V.-129 20 2016.
ISSN: ISSN 0300-9084
PubMed: 27343627
DOI: 10.1016/J.BIOCHI.2016.06.011