Potassium in PDB 7kz0: Human MBD4 Glycosylase Domain Bound to Dna Containing Substrate Analog 2'-Deoxy-Pseudouridine

The structure of Human MBD4 Glycosylase Domain Bound to Dna Containing Substrate Analog 2'-Deoxy-Pseudouridine, PDB code: 7kz0 was solved by L.S.Pidugu, E.Pozharski, A.C.Drohat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.65 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.361, 56.86, 105.416, 90, 90, 90
R / Rfree (%)	18.8 / 21.5

The binding sites of Potassium atom in the Human MBD4 Glycosylase Domain Bound to Dna Containing Substrate Analog 2'-Deoxy-Pseudouridine (pdb code 7kz0). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total only one binding site of Potassium was determined in the Human MBD4 Glycosylase Domain Bound to Dna Containing Substrate Analog 2'-Deoxy-Pseudouridine, PDB code: 7kz0:

Potassium binding site 1 out of 1 in the Human MBD4 Glycosylase Domain Bound to Dna Containing Substrate Analog 2'-Deoxy-Pseudouridine


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Human MBD4 Glycosylase Domain Bound to Dna Containing Substrate Analog 2'-Deoxy-Pseudouridine within 5.0Å range: probe atom residue distance (Å) B Occ A:K602 b:22.7 occ:1.00 O A:LEU534 2.6 20.6 1.0 O A:ILE537 2.6 17.3 1.0 O A:ILE532 2.7 21.8 1.0 O C:HOH110 2.7 34.8 1.0 O A:HOH834 2.8 39.3 1.0 OP1 C:DA10 2.8 22.6 1.0 C A:LEU534 3.5 25.1 1.0 C A:ILE532 3.6 20.3 1.0 C A:ILE537 3.7 18.4 1.0 P C:DA10 3.8 19.7 1.0 OP2 C:DA10 3.9 19.4 1.0 O C:HOH123 3.9 27.6 1.0 N A:LEU534 4.0 19.6 1.0 O A:HOH786 4.0 56.5 1.0 N A:ILE537 4.1 15.9 1.0 CA A:ILE532 4.2 18.6 1.0 N A:HIS535 4.4 21.3 1.0 N A:GLY536 4.4 17.2 1.0 CA A:LEU534 4.4 22.7 1.0 CA A:ILE537 4.4 17.0 1.0 C A:GLU533 4.4 19.5 1.0 CA A:HIS535 4.4 20.0 0.3 CA A:HIS535 4.4 19.7 0.7 CG1 A:ILE532 4.5 18.6 1.0 O C:HOH146 4.5 29.6 0.4 N A:GLU533 4.6 21.0 1.0 O A:PRO531 4.7 19.0 1.0 O3' C:DC9 4.7 20.2 1.0 C A:HIS535 4.7 23.9 1.0 N A:GLY538 4.7 14.9 1.0 O C:HOH146 4.7 29.1 0.6 CB A:ILE537 4.8 15.1 1.0 CA A:GLU533 4.8 18.1 1.0 CA A:GLY538 5.0 15.7 1.0 O A:GLU533 5.0 20.5 1.0 CB A:ILE532 5.0 22.9 1.0

L.S.Pidugu, H.Bright, W.J.Lin, C.Majumdar, R.P.Van Ostrand, S.S.David, E.Pozharski, A.C.Drohat. Structural Insights Into the Mechanism of Base Excision By MBD4. J.Mol.Biol. V. 433 67097 2021.
ISSN: ESSN 1089-8638
PubMed: 34107280
DOI: 10.1016/J.JMB.2021.167097