Sodium in PDB 7s9j: Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Dc

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

The structure of Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Dc, PDB code: 7s9j 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)	24.86 / 1.91
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.383, 79.494, 54.885, 90, 105.72, 90
R / Rfree (%)	18.8 / 23.8

The binding sites of Sodium atom in the Crystal Structure of Dna Polymerase Beta with Fapy-Dg Base-Paired with A Dc (pdb code 7s9j). 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 Dc, PDB code: 7s9j:
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 Dc


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 Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:14.2 occ:1.00 O A:THR101 2.3 13.6 1.0 OP1 P:DG9 2.3 10.9 1.0 O A:VAL103 2.4 10.8 1.0 O A:ILE106 2.4 11.7 1.0 O P:HOH115 2.6 12.3 1.0 O A:HOH769 2.7 15.1 1.0 C A:VAL103 3.3 15.5 1.0 C A:THR101 3.3 14.3 1.0 NA A:NA403 3.3 27.8 1.0 C A:ILE106 3.4 9.5 1.0 P P:DG9 3.5 13.8 1.0 N A:ILE106 3.7 12.0 1.0 OP2 P:DG9 3.7 12.9 1.0 CA A:SER104 3.8 13.1 1.0 CA A:THR101 3.9 11.7 1.0 N A:SER104 3.9 13.2 1.0 N A:GLY105 4.0 11.7 1.0 CA A:ILE106 4.0 11.3 1.0 N A:VAL103 4.2 11.9 1.0 C A:SER104 4.3 9.4 1.0 C A:ARG102 4.3 17.9 1.0 N A:GLY107 4.3 9.1 1.0 N A:ARG102 4.4 14.5 1.0 CA A:VAL103 4.4 13.9 1.0 CB A:THR101 4.4 14.7 1.0 CB A:ILE106 4.4 14.2 1.0 O3' P:DC8 4.5 12.9 1.0 C A:GLY105 4.6 10.9 1.0 CA A:ARG102 4.6 15.3 1.0 O5' P:DG9 4.6 13.3 1.0 CA A:GLY107 4.7 12.0 1.0 O A:ARG102 4.7 14.1 1.0 CA A:GLY105 4.8 12.7 1.0 O A:HOH790 4.9 29.8 1.0 O A:LEU100 4.9 15.2 1.0

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


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 Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:20.3 occ:1.00 O A:VAL65 2.3 21.6 1.0 O D:HOH114 2.4 20.5 1.0 O A:LEU62 2.4 22.6 1.0 O A:LYS60 2.4 20.0 1.0 O A:HOH725 2.5 23.5 1.0 OP1 D:DC3 2.7 18.4 1.0 C A:VAL65 3.4 19.8 1.0 C A:LEU62 3.4 24.5 1.0 C A:LYS60 3.5 24.1 1.0 P D:DC3 3.7 17.5 1.0 N A:VAL65 3.8 23.4 1.0 OP2 D:DC3 3.9 18.0 1.0 CA A:PRO63 4.1 25.9 1.0 N A:LEU62 4.1 21.4 1.0 C A:LYS61 4.1 23.7 1.0 CA A:VAL65 4.1 19.7 1.0 N A:GLY64 4.1 21.4 1.0 N A:PRO63 4.2 22.7 1.0 CA A:LYS60 4.2 19.5 1.0 O A:LYS61 4.4 21.8 1.0 CA A:LEU62 4.4 22.9 1.0 N A:LYS61 4.4 23.8 1.0 CB A:VAL65 4.5 21.6 1.0 C A:PRO63 4.5 23.1 1.0 CG A:LYS60 4.5 27.0 1.0 N A:GLY66 4.5 15.4 1.0 CA A:LYS61 4.5 22.7 1.0 O3' D:DT2 4.6 18.5 1.0 CA A:GLY66 4.7 17.2 1.0 C A:GLY64 4.8 21.9 1.0 O A:ALA59 4.9 19.3 1.0 CB A:LYS60 5.0 20.0 1.0 O5' D:DC3 5.0 15.5 1.0

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


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 Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:27.8 occ:1.00 O A:HOH809 2.4 18.9 1.0 O A:HOH545 2.4 17.9 1.0 O A:THR101 2.5 13.6 1.0 O A:HOH790 2.5 29.8 1.0 O P:HOH115 2.6 12.3 1.0 O A:HOH769 2.8 15.1 1.0 O A:HOH568 3.2 36.5 1.0 NA A:NA401 3.3 14.2 1.0 C A:THR101 3.4 14.3 1.0 CA A:ARG102 3.9 15.3 1.0 N A:ARG102 4.1 14.5 1.0 OG1 A:THR101 4.3 12.8 1.0 CB A:THR101 4.3 14.7 1.0 O A:HOH813 4.5 26.9 1.0 CA A:THR101 4.5 11.7 1.0 C A:ARG102 4.5 17.9 1.0 NZ A:LYS27 4.6 19.5 0.5 O A:ARG102 4.7 14.1 1.0 O A:HOH580 4.8 21.6 1.0 O A:HOH635 4.8 26.4 1.0 O P:HOH121 4.9 27.9 1.0 OP1 P:DG9 4.9 10.9 1.0 OP2 P:DG9 5.0 12.9 1.0 O A:ILE106 5.0 11.7 1.0

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


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 Dc within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:39.0 occ:1.00 OD1 A:ASP170 2.8 18.6 1.0 O A:HOH785 3.0 28.2 1.0 O A:HOH726 3.2 17.8 1.0 OG A:SER171 3.4 16.0 1.0 O A:HOH534 3.6 16.4 1.0 CG A:ASP170 3.7 17.2 1.0 N A:SER171 3.9 13.7 1.0 CG A:GLU172 4.0 21.1 1.0 OE1 A:GLU172 4.1 37.5 1.0 N A:GLU172 4.1 13.6 1.0 OD2 A:ASP170 4.2 18.9 1.0 CD A:GLU172 4.4 36.9 1.0 CB A:GLU172 4.5 20.4 1.0 CB A:SER171 4.5 14.5 1.0 O A:HOH812 4.6 23.1 1.0 C A:ASP170 4.6 16.3 1.0 CA A:SER171 4.6 15.9 1.0 CA A:ASP170 4.6 13.3 1.0 C A:SER171 4.7 19.8 1.0 CB A:ASP170 4.8 14.2 1.0 CA A:GLU172 4.9 22.6 1.0 O A:HOH566 5.0 19.7 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