Magnesium in PDB 5zod: Crystal Structure of HFEN1 in Apo Form

The structure of Crystal Structure of HFEN1 in Apo Form, PDB code: 5zod was solved by W.Han, Y.Hua, Y.Zhao, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.43 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.950, 61.070, 110.450, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 22.6

The structure of Crystal Structure of HFEN1 in Apo Form also contains other interesting chemical elements:

Potassium

(K)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of HFEN1 in Apo Form (pdb code 5zod). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of HFEN1 in Apo Form, PDB code: 5zod:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of HFEN1 in Apo Form


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 HFEN1 in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:27.3 occ:1.00 O A:HOH633 2.2 25.7 1.0 O A:HOH513 2.2 28.2 1.0 O A:HOH542 2.3 20.8 1.0 O A:HOH512 2.3 23.5 1.0 O A:HOH504 2.3 26.3 1.0 OG A:SER36 3.8 42.5 1.0 OE1 A:GLU160 3.9 19.2 1.0 OD2 A:ASP86 4.0 30.6 1.0 OD2 A:ASP179 4.1 21.2 1.0 OD2 A:ASP34 4.1 20.6 1.0 MG A:MG402 4.1 10.3 1.0 OD1 A:ASP86 4.3 24.3 1.0 OD1 A:ASP34 4.4 24.7 1.0 CG A:MET37 4.5 45.3 1.0 OE1 A:GLU158 4.5 30.8 1.0 CD A:GLU160 4.5 21.4 1.0 OE2 A:GLU160 4.5 19.9 1.0 CG A:ASP86 4.6 27.2 1.0 O A:HOH520 4.7 30.4 1.0 CG A:ASP34 4.7 25.3 1.0 CE A:MET37 4.7 52.0 1.0 CB A:SER36 4.9 38.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of HFEN1 in Apo Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of HFEN1 in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:10.3 occ:1.00 OE2 A:GLU160 2.7 19.9 1.0 OD2 A:ASP179 2.7 21.2 1.0 OD2 A:ASP181 2.8 17.9 1.0 OD2 A:ASP233 2.8 20.7 1.0 O A:HOH542 2.9 20.8 1.0 OH A:TYR234 3.0 21.2 1.0 O A:HOH633 3.2 25.7 1.0 CG A:ASP181 3.7 20.3 1.0 CG A:ASP179 3.7 20.2 1.0 CD A:GLU160 3.8 21.4 1.0 OD1 A:ASP181 3.8 16.6 1.0 CG A:ASP233 3.9 23.9 1.0 CZ A:TYR234 3.9 23.8 1.0 O A:HOH520 4.0 30.4 1.0 OE2 A:GLU158 4.0 27.7 1.0 O A:HOH512 4.1 23.5 1.0 OD1 A:ASP179 4.1 18.5 1.0 MG A:MG401 4.1 27.3 1.0 OE1 A:GLU160 4.2 19.2 1.0 N A:GLY2 4.4 19.7 1.0 CE2 A:TYR234 4.5 21.8 1.0 O A:HOH543 4.5 16.7 1.0 CD A:GLU158 4.5 30.4 1.0 CB A:ASP233 4.5 20.6 1.0 OD1 A:ASP233 4.7 21.8 1.0 CE1 A:TYR234 4.8 23.9 1.0 OE1 A:GLU158 4.9 30.8 1.0 CE2 A:PHE185 5.0 14.8 1.0 CG A:GLU160 5.0 16.1 1.0

H.Xu, R.Shi, W.Han, J.Cheng, X.Xu, K.Cheng, L.Wang, B.Tian, L.Zheng, B.Shen, Y.Hua, Y.Zhao. Structural Basis of 5' Flap Recognition and Protein-Protein Interactions of Human Flap Endonuclease 1. Nucleic Acids Res. V. 46 11315 2018.
ISSN: ESSN 1362-4962
PubMed: 30295841
DOI: 10.1093/NAR/GKY911