Sodium in PDB 7kz1: Human MBD4 Glycosylase Domain Bound to Dna Containing An Abasic Site

The structure of Human MBD4 Glycosylase Domain Bound to Dna Containing An Abasic Site, PDB code: 7kz1 was solved by L.S.Pidugu, H.Bright, E.Pozharski, A.C.Drohat, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.61 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	40.669, 54.292, 98.767, 90, 90, 90
R / Rfree (%)	18.2 / 20.5

The binding sites of Sodium atom in the Human MBD4 Glycosylase Domain Bound to Dna Containing An Abasic Site (pdb code 7kz1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Human MBD4 Glycosylase Domain Bound to Dna Containing An Abasic Site, PDB code: 7kz1:

Sodium binding site 1 out of 1 in the Human MBD4 Glycosylase Domain Bound to Dna Containing An Abasic Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human MBD4 Glycosylase Domain Bound to Dna Containing An Abasic Site within 5.0Å range: probe atom residue distance (Å) B Occ A:Na703 b:22.6 occ:1.00 O A:HOH866 2.3 35.3 1.0 O A:LEU534 2.3 19.7 1.0 O A:ILE537 2.4 17.5 1.0 O A:ILE532 2.4 21.1 1.0 O C:HOH109 2.6 39.4 1.0 OP1 C:DA10 2.7 24.4 1.0 C A:LEU534 3.4 24.9 1.0 C A:ILE532 3.4 19.4 1.0 C A:ILE537 3.5 21.8 1.0 P C:DA10 3.7 24.1 1.0 N A:LEU534 3.8 17.7 1.0 OP2 C:DA10 3.8 23.0 1.0 N A:ILE537 3.9 17.2 1.0 O C:HOH118 4.0 57.4 1.0 O A:HOH858 4.0 23.8 0.4 CA A:ILE532 4.1 20.4 1.0 CA A:ILE537 4.2 16.2 1.0 C A:GLU533 4.2 20.3 1.0 CA A:LEU534 4.2 18.5 1.0 N A:HIS535 4.2 21.1 1.0 N A:GLY536 4.2 19.0 1.0 CA A:HIS535 4.4 19.1 1.0 O A:PRO531 4.4 19.8 1.0 N A:GLU533 4.4 21.2 1.0 CG1 A:ILE532 4.5 23.1 1.0 O A:HOH858 4.5 34.9 0.6 N A:GLY538 4.5 18.4 1.0 C A:HIS535 4.6 25.2 1.0 O3' C:DC9 4.6 20.8 1.0 CB A:ILE537 4.6 16.4 1.0 CA A:GLU533 4.7 19.8 1.0 O A:GLU533 4.7 24.3 1.0 CA A:GLY538 4.8 16.4 1.0 C A:GLY536 4.9 19.3 1.0 O5' C:DA10 4.9 27.5 1.0 CB A:ILE532 5.0 21.3 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