Sodium in PDB 4m9l: Dna Polymerase Beta E295K Soaked with Dctp

All present enzymatic activity of Dna Polymerase Beta E295K Soaked with Dctp:
2.7.7.7;

The structure of Dna Polymerase Beta E295K Soaked with Dctp, PDB code: 4m9l 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)	13.84 / 2.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.362, 80.198, 54.599, 90.00, 108.59, 90.00
R / Rfree (%)	18.9 / 23.1

The structure of Dna Polymerase Beta E295K Soaked with Dctp also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Dna Polymerase Beta E295K Soaked with Dctp (pdb code 4m9l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dna Polymerase Beta E295K Soaked with Dctp, PDB code: 4m9l:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dna Polymerase Beta E295K Soaked with Dctp


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 E295K Soaked with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:18.1 occ:1.00 OP1 P:DG9 2.3 18.1 1.0 O A:THR101 2.4 18.3 1.0 O A:HOH501 2.4 19.5 1.0 O A:ILE106 2.4 18.9 1.0 O A:VAL103 2.5 20.2 1.0 O P:HOH102 2.5 17.4 1.0 O A:HOH502 3.3 25.4 1.0 C A:THR101 3.3 19.2 1.0 C A:ILE106 3.4 18.2 1.0 P P:DG9 3.4 20.1 1.0 C A:VAL103 3.5 20.5 1.0 OP2 P:DG9 3.6 24.0 1.0 N A:ILE106 3.8 18.4 1.0 CA A:THR101 3.9 18.5 1.0 CA A:SER104 4.0 22.8 1.0 CA A:ILE106 4.1 19.3 1.0 N A:GLY105 4.1 21.8 1.0 N A:SER104 4.1 20.8 1.0 N A:VAL103 4.2 15.7 1.0 N A:GLY107 4.3 18.4 1.0 N A:ARG102 4.4 20.9 1.0 C A:SER104 4.4 22.0 1.0 CB A:THR101 4.4 21.2 1.0 C A:ARG102 4.4 19.7 1.0 O3' P:DC8 4.5 23.5 1.0 CA A:VAL103 4.5 21.2 1.0 O5' P:DG9 4.5 17.8 1.0 CB A:ILE106 4.5 19.6 1.0 CA A:GLY107 4.6 16.6 1.0 O P:HOH122 4.6 38.7 1.0 CA A:ARG102 4.7 20.6 1.0 O A:HOH522 4.7 49.0 1.0 C A:GLY105 4.7 22.5 1.0 O A:LEU100 4.9 25.0 1.0 O A:HOH514 4.9 23.6 1.0 O A:HOH591 5.0 45.3 1.0 O A:ARG102 5.0 20.4 1.0

Sodium binding site 2 out of 3 in the Dna Polymerase Beta E295K Soaked with Dctp


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 E295K Soaked with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:41.9 occ:1.00 O A:LYS60 2.4 42.6 1.0 O A:VAL65 2.5 40.4 1.0 O D:HOH101 2.5 32.8 1.0 O A:HOH503 2.5 45.8 1.0 O A:LEU62 2.7 38.1 1.0 OP1 D:DC3 2.8 55.9 1.0 C A:VAL65 3.6 29.7 1.0 C A:LYS60 3.6 40.6 1.0 C A:LEU62 3.6 38.2 1.0 OP2 D:DC3 3.7 42.6 1.0 P D:DC3 3.7 42.1 1.0 N A:VAL65 4.0 34.5 1.0 CA A:VAL65 4.2 32.3 1.0 N A:LEU62 4.2 35.4 1.0 C A:LYS61 4.2 39.7 1.0 O D:HOH105 4.3 42.3 1.0 CA A:PRO63 4.3 41.4 1.0 N A:GLY64 4.3 33.6 1.0 N A:PRO63 4.4 41.3 1.0 CA A:LYS60 4.4 37.7 1.0 O A:LYS61 4.5 40.5 1.0 CB A:VAL65 4.5 33.8 1.0 N A:LYS61 4.5 42.8 1.0 CA A:LEU62 4.6 35.8 1.0 N A:GLY66 4.6 29.5 1.0 CA A:LYS61 4.7 43.0 1.0 O3' D:DT2 4.7 37.9 1.0 CD A:LYS60 4.7 47.9 1.0 C A:PRO63 4.8 37.6 1.0 CG A:LYS60 4.8 48.6 1.0 CA A:GLY66 4.8 32.1 1.0 C A:GLY64 5.0 31.8 1.0

Sodium binding site 3 out of 3 in the Dna Polymerase Beta E295K Soaked with Dctp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dna Polymerase Beta E295K Soaked with Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:31.6 occ:1.00 OD1 A:ASP192 2.3 28.9 1.0 O A:HOH588 2.4 27.7 1.0 OD2 A:ASP190 2.4 31.9 1.0 O2A A:DCP405 2.5 24.6 1.0 OD1 A:ASP190 2.7 25.0 1.0 CG A:ASP190 2.8 28.1 1.0 O A:HOH561 2.9 31.1 1.0 CG A:ASP192 3.2 28.9 1.0 MG A:MG404 3.3 26.7 1.0 OD2 A:ASP192 3.3 30.3 1.0 PA A:DCP405 3.5 28.0 1.0 O1A A:DCP405 3.8 28.6 1.0 O5' A:DCP405 4.0 30.2 1.0 CB A:ASP190 4.1 24.6 1.0 O A:HOH587 4.1 31.3 1.0 OD2 A:ASP256 4.3 32.6 1.0 OP1 P:DC10 4.4 31.8 1.0 O A:HOH642 4.4 51.5 1.0 C5' A:DCP405 4.4 31.9 1.0 O2G A:DCP405 4.4 26.7 1.0 O A:HOH592 4.5 32.1 1.0 CG A:ASP256 4.5 31.0 1.0 CB A:ASP192 4.5 31.9 1.0 C3' P:DC10 4.6 42.4 1.0 C5' P:DC10 4.6 38.3 1.0 O A:MET191 4.7 28.1 1.0 OD1 A:ASP256 4.8 32.5 1.0 O2B A:DCP405 4.8 20.6 1.0 C4' P:DC10 4.9 36.8 1.0 O3' P:DC10 4.9 42.8 1.0 CB A:ASP256 4.9 25.7 1.0 O3A A:DCP405 4.9 44.0 1.0 C A:MET191 4.9 28.1 1.0

B.E.Eckenroth, J.B.Towle-Weicksel, J.B.Sweasy, S.Doublie. The E295K Cancer Variant of Human Polymerase Beta Favors the Mismatch Conformational Pathway During Nucleotide Selection. J.Biol.Chem. V. 288 34850 2013.
ISSN: ISSN 0021-9258
PubMed: 24133209
DOI: 10.1074/JBC.M113.510891