Potassium 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:

Magnesium

(Mg)

2 atoms

The binding sites of Potassium atom in the Crystal Structure of HFEN1 in Apo Form (pdb code 5zod). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of HFEN1 in Apo Form, PDB code: 5zod:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 in the Crystal Structure of HFEN1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of HFEN1 in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:K403 b:71.7 occ:1.00 ND1 A:HIS208 2.6 25.0 1.0 O A:HOH544 2.7 29.2 1.0 O A:GLU206 3.0 23.3 1.0 O A:ALA17 3.3 24.4 1.0 CE1 A:HIS208 3.5 20.4 1.0 CG A:ARG19 3.6 46.2 1.0 C A:GLU206 3.6 28.1 1.0 CG A:HIS208 3.7 21.4 1.0 N A:HIS208 3.7 19.9 1.0 N A:ARG19 3.9 32.5 1.0 CB A:ARG19 3.9 36.7 1.0 C A:PHE207 3.9 19.4 1.0 CG A:GLU206 3.9 23.0 1.0 CB A:HIS208 4.0 20.5 1.0 C A:ALA17 4.0 31.1 1.0 CA A:PHE207 4.1 21.3 1.0 N A:PHE207 4.1 18.3 1.0 C A:ILE18 4.2 35.9 1.0 CB A:GLU206 4.2 25.1 1.0 CA A:ILE18 4.3 27.2 1.0 CA A:HIS208 4.4 17.9 1.0 N A:ILE18 4.5 27.5 1.0 CA A:ARG19 4.5 31.9 1.0 CD A:GLU206 4.5 26.4 1.0 CA A:GLU206 4.6 22.9 1.0 O A:PHE207 4.6 16.0 1.0 NE2 A:HIS208 4.6 22.7 1.0 OE2 A:GLU206 4.7 24.4 1.0 CD2 A:HIS208 4.7 17.3 1.0 O A:HOH639 4.9 47.9 1.0 O A:ILE18 4.9 32.7 1.0 CA A:ALA17 5.0 28.3 1.0

Potassium binding site 2 out of 4 in the Crystal Structure of HFEN1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of HFEN1 in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:K404 b:55.7 occ:1.00 O A:HOH649 2.8 43.3 1.0 CG A:GLU221 3.0 34.9 1.0 N A:GLU221 3.0 17.2 1.0 N A:GLN220 3.4 19.5 1.0 CG A:ASN219 3.4 24.1 1.0 CB A:GLU221 3.5 24.9 1.0 OD1 A:ASN219 3.7 21.0 1.0 O A:HOH578 3.7 23.1 1.0 CB A:ASN219 3.7 23.4 1.0 ND2 A:ASN219 3.8 23.9 1.0 CA A:GLU221 3.8 23.3 1.0 CD A:GLU221 3.9 47.5 1.0 CB A:GLN220 3.9 20.7 1.0 C A:GLN220 3.9 20.5 1.0 CA A:GLN220 3.9 20.5 1.0 C A:ASN219 4.2 21.8 1.0 OE1 A:GLU221 4.4 52.4 1.0 OE2 A:GLU221 4.5 53.5 1.0 CA A:ASN219 4.6 20.0 1.0 O A:ASN219 5.0 18.4 1.0

Potassium binding site 3 out of 4 in the Crystal Structure of HFEN1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of HFEN1 in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:K405 b:63.6 occ:1.00 O A:HOH603 2.8 33.4 1.0 ND1 A:HIS276 2.9 26.5 1.0 OD1 A:ASP225 3.0 25.1 1.0 O A:HOH506 3.1 36.1 1.0 CB A:HIS280 3.5 24.1 1.0 O A:HIS276 3.5 23.1 1.0 CE1 A:HIS276 3.7 30.8 1.0 ND1 A:HIS280 3.7 22.9 1.0 CG A:ASP225 3.7 28.3 1.0 CG A:HIS280 3.7 27.8 1.0 OD2 A:ASP225 3.7 25.5 1.0 C A:HIS276 3.9 24.1 1.0 OE1 A:GLU257 3.9 45.9 1.0 CG A:HIS276 4.0 25.0 1.0 OE2 A:GLU257 4.1 49.3 1.0 N A:LYS277 4.1 22.2 1.0 CA A:LYS277 4.1 27.5 1.0 CD1 A:ILE256 4.2 22.3 1.0 CB A:ILE256 4.2 27.7 1.0 CB A:HIS276 4.3 24.6 1.0 CD A:GLU257 4.4 44.4 1.0 CG1 A:ILE256 4.5 21.3 1.0 CE1 A:HIS280 4.6 28.8 1.0 O A:HOH587 4.6 32.5 1.0 CD2 A:HIS280 4.6 25.1 1.0 CD1 A:ILE228 4.7 18.8 1.0 CA A:HIS276 4.7 26.9 1.0 CG A:LYS277 4.8 28.4 1.0 NE2 A:HIS276 4.9 24.2 1.0 CA A:HIS280 4.9 23.2 1.0 CG2 A:ILE256 4.9 21.8 1.0

Potassium binding site 4 out of 4 in the Crystal Structure of HFEN1 in Apo Form


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of HFEN1 in Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:K406 b:51.4 occ:1.00 O A:HOH638 2.9 25.8 1.0 O A:LEU289 2.9 19.6 1.0 CA A:ASP290 3.6 18.6 1.0 CD A:PRO291 3.7 21.3 1.0 C A:LEU289 3.7 22.6 1.0 CG2 A:VAL288 3.7 20.0 1.0 N A:ASP290 4.0 17.4 1.0 O A:VAL288 4.2 18.1 1.0 CB A:ASP290 4.3 19.6 1.0 CG A:ASP290 4.5 21.3 1.0 N A:PRO291 4.6 18.5 1.0 C A:ASP290 4.6 19.4 1.0 C A:VAL288 4.6 21.4 1.0 OD1 A:ASP290 4.7 18.8 1.0 O A:HOH650 4.7 27.0 1.0 CG A:PRO291 4.8 23.4 1.0 O A:HOH556 4.9 27.6 1.0 CB A:VAL288 4.9 20.2 1.0 CA A:LEU289 4.9 20.5 1.0 OD2 A:ASP290 5.0 19.7 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