Magnesium in PDB 7n3z: Crystal Structure of Saccharomyces Cerevisiae APN2 Catalytic Domain

The structure of Crystal Structure of Saccharomyces Cerevisiae APN2 Catalytic Domain, PDB code: 7n3z was solved by J.L.Wojtaszek, B.D.Wallace, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.67 / 1.99
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	171.412, 46.948, 51.532, 90, 104.21, 90
R / Rfree (%)	16.3 / 19.8

The structure of Crystal Structure of Saccharomyces Cerevisiae APN2 Catalytic Domain also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Crystal Structure of Saccharomyces Cerevisiae APN2 Catalytic Domain (pdb code 7n3z). 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 Crystal Structure of Saccharomyces Cerevisiae APN2 Catalytic Domain, PDB code: 7n3z:

Magnesium binding site 1 out of 1 in the Crystal Structure of Saccharomyces Cerevisiae APN2 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Saccharomyces Cerevisiae APN2 Catalytic Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:36.1 occ:1.00 O A:HOH709 2.0 41.9 1.0 O A:HOH622 2.0 33.9 1.0 O A:HOH610 2.1 28.1 1.0 O A:HOH725 2.2 29.4 1.0 OD1 A:ASN25 2.4 39.7 1.0 OE1 A:GLU59 2.5 35.2 1.0 HZ1 A:LYS61 3.1 40.5 1.0 CD A:GLU59 3.2 33.4 1.0 CG A:ASN25 3.3 32.0 1.0 OE2 A:GLU59 3.3 34.0 1.0 HA A:ASN25 3.5 31.9 1.0 HE3 A:LYS61 3.8 38.9 1.0 NZ A:LYS61 3.9 33.8 1.0 HB2 A:ASN25 4.0 36.4 1.0 O A:HOH674 4.0 38.6 1.0 OD2 A:ASP353 4.0 31.0 1.0 CB A:ASN25 4.1 30.4 1.0 HE2 A:LYS61 4.1 38.9 1.0 CE A:LYS61 4.2 32.4 1.0 ND2 A:ASN25 4.2 32.4 1.0 CA A:ASN25 4.2 26.6 1.0 OD1 A:ASP353 4.3 27.3 1.0 HD21 A:ASN25 4.3 38.9 1.0 HZ2 A:LYS61 4.3 40.5 1.0 O A:HOH759 4.3 40.1 1.0 HZ3 A:LYS61 4.5 40.5 1.0 CG A:ASP353 4.5 32.8 1.0 HB3 A:GLU59 4.7 33.7 1.0 HD21 A:ASN23 4.7 27.2 1.0 CG A:GLU59 4.7 26.8 1.0 OD1 A:ASN23 4.7 25.5 1.0 HD22 A:ASN25 4.9 38.9 1.0 HB3 A:ASN25 5.0 36.4 1.0

J.S.Williams, J.L.Wojtaszek, D.C.Appel, J.Krahn, B.D.Wallace, E.Walsh, T.A.Kunkel, R.S.Williams. Molecular Basis For Processing of Topoisomerase 1-Triggered Dna Damage By APN2/APE2. Cell Rep V. 41 11448 2022.
ISSN: ESSN 2211-1247
PubMed: 36198268
DOI: 10.1016/J.CELREP.2022.111448