Sodium in PDB 8f6b: Crystal Structure of Murine POLG2 Hexamer Bound to Dna

The structure of Crystal Structure of Murine POLG2 Hexamer Bound to Dna, PDB code: 8f6b was solved by J.L.Wojtaszek, K.E.Hoff, R.S.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.04 / 2.75
Space group	P 32
Cell size a, b, c (Å), α, β, γ (°)	116.224, 116.224, 250.938, 90, 90, 120
R / Rfree (%)	19.6 / 22.2

The binding sites of Sodium atom in the Crystal Structure of Murine POLG2 Hexamer Bound to Dna (pdb code 8f6b). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Murine POLG2 Hexamer Bound to Dna, PDB code: 8f6b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Murine POLG2 Hexamer Bound to Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Murine POLG2 Hexamer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ H:Na101 b:178.8 occ:1.00 O4' H:DA14 2.3 115.0 1.0 O H:HOH202 2.3 106.3 1.0 O G:HOH101 2.4 109.3 1.0 O H:HOH204 2.4 99.0 1.0 O H:HOH203 2.4 103.0 1.0 O2 H:DT13 2.5 91.9 1.0 C4' H:DA14 2.7 89.9 1.0 C5' H:DA14 3.3 95.2 1.0 C1' H:DA14 3.4 87.4 1.0 C2 H:DT13 3.6 85.4 1.0 C1' H:DT13 4.0 96.0 1.0 C3' H:DA14 4.1 100.9 1.0 N9 H:DA14 4.1 87.0 1.0 N3 H:DA14 4.2 87.9 1.0 N1 H:DT13 4.3 95.6 1.0 O3' H:DA14 4.4 91.5 1.0 C4 H:DA14 4.4 91.9 1.0 C2' H:DA14 4.5 88.2 1.0 N3 H:DT13 4.6 86.1 1.0 O5' H:DA14 4.6 89.0 1.0 O4' H:DC15 4.7 99.0 1.0 C2' H:DT13 4.8 93.5 1.0 C2 G:DA6 4.8 89.2 1.0 O3' H:DT13 4.9 87.1 1.0 O4' G:DG8 5.0 83.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Murine POLG2 Hexamer Bound to Dna


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Murine POLG2 Hexamer Bound to Dna within 5.0Å range: probe atom residue distance (Å) B Occ I:Na101 b:215.5 occ:1.00 O4' I:DA14 2.2 105.5 1.0 O2 I:DT13 2.4 92.2 1.0 O I:HOH205 2.4 106.8 1.0 O I:HOH206 2.5 92.7 1.0 O I:HOH204 2.5 106.5 1.0 O I:HOH203 2.6 93.2 1.0 C4' I:DA14 2.9 89.6 1.0 C1' I:DA14 3.1 84.1 1.0 C2 I:DT13 3.5 80.2 1.0 C5' I:DA14 3.7 86.0 1.0 N9 I:DA14 3.8 93.1 1.0 N3 I:DA14 3.8 86.0 1.0 C4 I:DA14 4.0 96.4 1.0 C3' I:DA14 4.1 90.3 1.0 C1' I:DT13 4.2 91.6 1.0 N1 I:DT13 4.3 99.4 1.0 O3' I:DA14 4.3 88.5 1.0 C2' I:DA14 4.3 84.7 1.0 N3 I:DT13 4.4 83.8 1.0 C2 J:DA6 4.5 77.0 1.0 O4' I:DC15 4.7 98.6 1.0 C8 I:DA14 4.8 87.6 1.0 C2 I:DA14 4.9 85.3 1.0 C2' I:DT13 4.9 86.7 1.0 O5' I:DA14 4.9 88.4 1.0

J.L.Wojtaszek, K.E.Hoff, M.J.Longley, P.Kaur, S.N.Andres, H.Wang, R.S.Williams, W.C.Copeland. Structure-Specific Roles For POLG2-Dna Complexes in Maintenance and Replication of Mitochondrial Dna Nucleic Acids Res. 2023.
ISSN: ESSN 1362-4962