Sodium in PDB 5u8g: Dna Polymerase Beta Crystallized in Peg 400

All present enzymatic activity of Dna Polymerase Beta Crystallized in Peg 400:
2.7.7.7;

The structure of Dna Polymerase Beta Crystallized in Peg 400, PDB code: 5u8g was solved by B.E.Eckenroth, S.Doublie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	13.68 / 2.17
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.104, 78.659, 54.721, 90.00, 104.25, 90.00
R / Rfree (%)	17.9 / 22.5

The structure of Dna Polymerase Beta Crystallized in Peg 400 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Beta Crystallized in Peg 400 (pdb code 5u8g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta Crystallized in Peg 400, PDB code: 5u8g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta Crystallized in Peg 400


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta Crystallized in Peg 400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:31.4 occ:1.00 O A:VAL65 2.4 23.9 1.0 O A:LEU62 2.5 34.9 1.0 O A:LYS60 2.5 42.2 1.0 O A:HOH600 2.5 31.6 1.0 OP1 D:DC3 2.7 32.8 1.0 O A:HOH596 2.8 35.9 1.0 C A:LEU62 3.4 31.2 1.0 C A:VAL65 3.5 21.9 1.0 C A:LYS60 3.6 35.0 1.0 P D:DC3 3.7 29.7 1.0 N A:VAL65 3.8 31.0 1.0 OP2 D:DC3 3.9 30.4 1.0 CA A:VAL65 4.1 25.6 1.0 CA A:PRO63 4.1 31.8 1.0 N A:LEU62 4.2 33.4 1.0 N A:PRO63 4.2 33.2 1.0 C A:LYS61 4.2 40.7 1.0 N A:GLY64 4.2 25.0 1.0 CA A:LYS60 4.3 28.9 1.0 O A:LYS61 4.4 37.6 1.0 CD A:LYS60 4.4 38.5 1.0 CB A:VAL65 4.4 33.6 1.0 CA A:LEU62 4.4 36.0 1.0 O A:HOH678 4.4 60.1 1.0 N A:LYS61 4.5 35.8 1.0 N A:GLY66 4.5 24.8 1.0 C A:PRO63 4.6 31.4 1.0 O3' D:DT2 4.6 26.1 1.0 CA A:LYS61 4.6 34.0 1.0 NZ A:LYS60 4.8 39.6 1.0 O A:ALA59 4.8 29.5 1.0 CG A:LYS60 4.8 37.5 1.0 CA A:GLY66 4.8 21.9 1.0 C A:GLY64 4.9 30.9 1.0 CE A:LYS60 5.0 41.5 1.0 O5' D:DC3 5.0 29.3 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta Crystallized in Peg 400


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta Crystallized in Peg 400 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:25.2 occ:1.00 OP1 P:DG9 2.3 26.6 1.0 O A:THR101 2.3 29.9 1.0 O A:ILE106 2.5 17.8 1.0 O A:VAL103 2.5 26.0 1.0 O A:HOH644 2.6 33.1 1.0 O P:HOH117 2.6 22.1 1.0 C A:THR101 3.3 24.0 1.0 C A:ILE106 3.4 20.1 1.0 C A:VAL103 3.4 29.0 1.0 P P:DG9 3.4 25.4 1.0 O A:HOH538 3.6 39.8 1.0 OP2 P:DG9 3.6 28.2 1.0 N A:ILE106 3.7 18.7 1.0 CA A:THR101 3.9 18.9 1.0 N A:GLY105 3.9 20.2 1.0 CA A:SER104 4.0 23.0 1.0 N A:SER104 4.1 30.2 1.0 CA A:ILE106 4.1 23.0 1.0 N A:VAL103 4.2 20.4 1.0 N A:GLY107 4.3 21.5 1.0 C A:SER104 4.4 29.4 1.0 N A:ARG102 4.4 20.4 1.0 CB A:THR101 4.4 21.2 1.0 O3' P:DC8 4.4 24.7 1.0 C A:ARG102 4.4 30.2 1.0 CA A:VAL103 4.4 26.2 1.0 CB A:ILE106 4.5 23.9 1.0 O5' P:DG9 4.6 25.3 1.0 C A:GLY105 4.6 19.0 1.0 CA A:GLY107 4.6 17.9 1.0 CA A:ARG102 4.7 25.4 1.0 CA A:GLY105 4.9 19.2 1.0 O A:ARG102 4.9 27.3 1.0 O A:LEU100 5.0 21.8 1.0 O A:HOH552 5.0 31.6 1.0

B.E.Eckenroth, J.B.Towle-Weicksel, A.A.Nemec, D.L.Murphy, J.B.Sweasy, S.Doublie. Remote Mutations Induce Functional Changes in Active Site Residues of Human Dna Polymerase Beta. Biochemistry V. 56 2363 2017.
ISSN: ISSN 1520-4995
PubMed: 28402631
DOI: 10.1021/ACS.BIOCHEM.6B01287