Sodium in PDB 7kzg: Human MBD4 Glycosylase Domain Bound to Dna Containing Oxacarbenium-Ion Analog 1-Aza-2'-Deoxyribose

The structure of Human MBD4 Glycosylase Domain Bound to Dna Containing Oxacarbenium-Ion Analog 1-Aza-2'-Deoxyribose, PDB code: 7kzg 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)	37.98 / 1.68
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.465, 56.414, 102.733, 90, 90, 90
R / Rfree (%)	16.8 / 20.5

The structure of Human MBD4 Glycosylase Domain Bound to Dna Containing Oxacarbenium-Ion Analog 1-Aza-2'-Deoxyribose also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Human MBD4 Glycosylase Domain Bound to Dna Containing Oxacarbenium-Ion Analog 1-Aza-2'-Deoxyribose (pdb code 7kzg). 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 Oxacarbenium-Ion Analog 1-Aza-2'-Deoxyribose, PDB code: 7kzg:

Sodium binding site 1 out of 1 in the Human MBD4 Glycosylase Domain Bound to Dna Containing Oxacarbenium-Ion Analog 1-Aza-2'-Deoxyribose


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 Oxacarbenium-Ion Analog 1-Aza-2'-Deoxyribose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na705 b:15.9 occ:1.00 O A:ILE537 2.4 13.2 1.0 O A:LEU534 2.4 14.5 1.0 O A:ILE532 2.4 16.8 1.0 O C:HOH211 2.4 21.8 1.0 O A:HOH927 2.6 23.4 1.0 OP1 C:DA10 2.7 15.4 1.0 C A:ILE532 3.4 18.5 1.0 C A:LEU534 3.4 16.7 1.0 C A:ILE537 3.5 12.8 1.0 P C:DA10 3.7 16.8 1.0 O C:HOH210 3.8 38.1 1.0 N A:LEU534 3.8 15.3 1.0 N A:ILE537 3.9 12.1 1.0 OP2 C:DA10 3.9 17.9 1.0 CA A:ILE532 4.0 15.6 1.0 O A:HOH876 4.1 25.4 0.6 CA A:ILE537 4.2 11.8 1.0 C A:GLU533 4.2 13.3 1.0 O A:HOH876 4.2 33.2 0.4 CA A:LEU534 4.2 15.1 1.0 N A:HIS535 4.3 13.5 1.0 N A:GLY536 4.3 15.0 1.0 O A:PRO531 4.3 13.2 1.0 N A:GLU533 4.4 15.6 1.0 CA A:HIS535 4.4 15.0 1.0 CG1 A:ILE532 4.4 18.3 1.0 CB A:ILE537 4.5 10.8 1.0 N A:GLY538 4.6 12.5 1.0 O3' C:DC9 4.6 14.5 1.0 CA A:GLU533 4.6 13.7 1.0 C A:HIS535 4.6 17.5 1.0 O A:GLU533 4.8 17.3 1.0 CA A:GLY538 4.8 11.2 1.0 O A:HOH953 4.9 61.9 1.0 C A:GLY536 4.9 13.2 1.0 CB A:ILE532 4.9 14.7 1.0 O5' C:DA10 5.0 17.4 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