Sodium in PDB 7s9k: Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da

All present enzymatic activity of Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da:
2.7.7.7;

The structure of Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da, PDB code: 7s9k was solved by B.D.Freudenthal, B.J.Ryan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.85 / 1.97
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.28, 79.125, 54.882, 90, 105.33, 90
R / Rfree (%)	17.2 / 22.4

The binding sites of Sodium atom in the Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da (pdb code 7s9k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da, PDB code: 7s9k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da


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 Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:17.2 occ:1.00 O A:THR101 2.3 22.1 1.0 OP1 P:DG9 2.3 17.4 1.0 O A:ILE106 2.3 19.8 1.0 O A:VAL103 2.4 21.2 1.0 O P:HOH105 2.5 18.8 1.0 O A:HOH702 2.6 22.2 1.0 NA A:NA403 3.3 34.9 1.0 C A:THR101 3.3 21.9 1.0 C A:ILE106 3.4 15.9 1.0 C A:VAL103 3.4 19.5 1.0 P P:DG9 3.4 21.2 1.0 OP2 P:DG9 3.6 18.4 1.0 N A:ILE106 3.8 18.2 1.0 O P:HOH125 3.9 38.7 1.0 CA A:THR101 3.9 18.9 1.0 CA A:SER104 3.9 18.7 1.0 N A:SER104 4.1 16.7 1.0 N A:GLY105 4.1 16.8 1.0 CA A:ILE106 4.1 14.2 1.0 N A:VAL103 4.3 17.1 1.0 N A:GLY107 4.3 16.3 1.0 CB A:THR101 4.3 21.8 1.0 C A:SER104 4.3 16.9 1.0 C A:ARG102 4.3 18.4 1.0 N A:ARG102 4.4 21.3 1.0 O P:HOH127 4.4 46.0 1.0 O3' P:DC8 4.5 16.8 1.0 CA A:VAL103 4.5 16.6 1.0 O5' P:DG9 4.5 17.0 1.0 CB A:ILE106 4.5 16.4 1.0 CA A:GLY107 4.6 19.4 1.0 CA A:ARG102 4.6 18.2 1.0 C A:GLY105 4.7 17.9 1.0 O A:ARG102 4.8 21.5 1.0 O A:HOH518 4.9 33.4 1.0 CA A:GLY105 4.9 18.4 1.0 O A:HOH733 5.0 42.9 1.0 O A:LEU100 5.0 21.3 1.0

Sodium binding site 2 out of 4 in the Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da


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 Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:28.6 occ:1.00 O D:HOH110 2.2 24.9 1.0 O A:VAL65 2.3 27.8 1.0 O A:LYS60 2.4 29.6 1.0 O A:LEU62 2.5 30.6 1.0 O A:HOH693 2.6 30.1 1.0 OP1 D:DC3 2.7 28.5 1.0 C A:VAL65 3.4 23.9 1.0 C A:LYS60 3.5 30.2 1.0 C A:LEU62 3.6 26.1 1.0 P D:DC3 3.6 23.3 1.0 OP2 D:DC3 3.7 18.6 1.0 N A:VAL65 3.8 24.0 1.0 O D:HOH107 3.8 35.5 1.0 CA A:VAL65 4.1 19.4 1.0 N A:LEU62 4.2 24.3 1.0 CA A:LYS60 4.2 23.7 1.0 N A:GLY64 4.2 30.4 1.0 CA A:PRO63 4.2 29.2 1.0 C A:LYS61 4.3 32.4 1.0 N A:PRO63 4.3 27.4 1.0 CG A:LYS60 4.4 28.7 1.0 CB A:VAL65 4.5 21.0 1.0 N A:GLY66 4.5 21.5 1.0 N A:LYS61 4.5 27.7 1.0 O3' D:DT2 4.5 22.2 1.0 CA A:LEU62 4.6 29.2 1.0 O A:LYS61 4.6 34.0 1.0 C A:PRO63 4.6 29.2 1.0 CA A:LYS61 4.7 28.2 1.0 CA A:GLY66 4.7 20.2 1.0 C A:GLY64 4.8 27.1 1.0 O5' D:DC3 4.9 20.8 1.0 CB A:LYS60 4.9 25.4 1.0 O A:ALA59 4.9 25.3 1.0

Sodium binding site 3 out of 4 in the Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:34.9 occ:1.00 O P:HOH127 2.2 46.0 1.0 O P:HOH105 2.5 18.8 1.0 O A:HOH614 2.6 25.1 1.0 O A:HOH750 2.7 34.5 1.0 O A:THR101 2.7 22.1 1.0 O A:HOH702 3.1 22.2 1.0 O P:HOH125 3.1 38.7 1.0 NA A:NA401 3.3 17.2 1.0 O A:HOH711 3.5 42.2 1.0 C A:THR101 3.7 21.9 1.0 O A:HOH518 4.1 33.4 1.0 CA A:ARG102 4.2 18.2 1.0 N A:ARG102 4.3 21.3 1.0 O A:HOH733 4.5 42.9 1.0 O A:HOH748 4.5 31.7 1.0 OG1 A:THR101 4.5 21.6 1.0 CB A:THR101 4.6 21.8 1.0 C A:ARG102 4.7 18.4 1.0 OP1 P:DG9 4.8 17.4 1.0 CA A:THR101 4.8 18.9 1.0 O A:HOH559 4.8 29.5 1.0 OP2 P:DG9 4.8 18.4 1.0 O A:ARG102 4.9 21.5 1.0 O A:HOH655 4.9 33.5 1.0

Sodium binding site 4 out of 4 in the Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Da within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:24.7 occ:1.00 OG A:SER171 2.4 20.6 1.0 O A:HOH698 2.4 25.4 1.0 O A:HOH548 2.6 33.4 1.0 CB A:SER171 3.6 21.1 1.0 O A:HOH715 3.9 38.5 1.0 N A:SER171 4.0 19.3 1.0 O A:HOH608 4.3 25.5 1.0 CA A:SER171 4.4 18.9 1.0 OD1 A:ASP170 4.7 24.4 1.0 C A:SER171 5.0 22.0 1.0

B.J.Ryan, H.Yang, J.H.T.Bacurio, M.R.Smith, A.K.Basu, M.M.Greenberg, B.D.Freudenthal. Structural Dynamics of A Common Mutagenic Oxidative Dna Lesion in Duplex Dna and During Dna Replication. J.Am.Chem.Soc. V. 144 8054 2022.
ISSN: ESSN 1520-5126
PubMed: 35499923
DOI: 10.1021/JACS.2C00193