Sodium in PDB 4pgy: Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Gt at N-1 Position and Gc at N Position

All present enzymatic activity of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Gt at N-1 Position and Gc at N Position:
2.7.7.7;

The structure of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Gt at N-1 Position and Gc at N Position, PDB code: 4pgy was solved by M.C.Koag, S.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.12 / 2.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.440, 78.928, 54.348, 90.00, 106.90, 90.00
R / Rfree (%)	21 / 26.5

The binding sites of Sodium atom in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Gt at N-1 Position and Gc at N Position (pdb code 4pgy). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Gt at N-1 Position and Gc at N Position, PDB code: 4pgy:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Gt at N-1 Position and Gc at N Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Gt at N-1 Position and Gc at N Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:24.3 occ:1.00 O A:THR101 2.3 27.5 1.0 OP1 P:DG9 2.3 28.6 1.0 O A:ILE106 2.4 26.5 1.0 O A:HOH522 2.5 23.9 1.0 O A:VAL103 2.6 25.9 1.0 C A:THR101 3.2 28.3 1.0 C A:ILE106 3.4 25.5 1.0 O A:HOH520 3.4 26.9 1.0 C A:VAL103 3.4 29.1 1.0 P P:DG9 3.5 29.4 1.0 OP2 P:DG9 3.7 30.8 1.0 CA A:THR101 3.8 22.7 1.0 N A:ILE106 3.8 24.3 1.0 CA A:SER104 4.0 25.6 1.0 N A:SER104 4.0 25.6 1.0 N A:GLY105 4.1 24.1 1.0 N A:VAL103 4.1 26.1 1.0 CA A:ILE106 4.1 26.7 1.0 N A:ARG102 4.2 25.5 1.0 C A:ARG102 4.2 28.3 1.0 N A:GLY107 4.3 25.2 1.0 CB A:THR101 4.4 27.4 1.0 CA A:VAL103 4.4 24.2 1.0 C A:SER104 4.4 25.1 1.0 CA A:ARG102 4.5 26.3 1.0 O3' P:DC8 4.5 27.8 1.0 CB A:ILE106 4.5 25.4 1.0 O5' P:DG9 4.6 31.3 1.0 CA A:GLY107 4.6 24.8 1.0 C A:GLY105 4.7 25.4 1.0 O A:ARG102 4.7 30.5 1.0 O A:LEU100 4.7 27.4 1.0

Sodium binding site 2 out of 2 in the Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Gt at N-1 Position and Gc at N Position


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Dna Polymerase Beta Complexed with A Nicked Dna Containing A Gt at N-1 Position and Gc at N Position within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:40.8 occ:1.00 O D:HOH106 2.5 32.6 1.0 O A:LYS60 2.5 40.8 1.0 O A:LEU62 2.5 30.6 1.0 OP1 D:DC3 2.6 36.3 1.0 O A:VAL65 2.9 35.7 1.0 C A:LEU62 3.4 31.5 1.0 C A:LYS60 3.5 37.8 1.0 P D:DC3 3.8 31.9 1.0 C A:VAL65 3.9 30.8 1.0 O D:HOH109 3.9 44.4 1.0 C A:LYS61 4.0 36.7 1.0 OP2 D:DC3 4.0 35.0 1.0 N A:LEU62 4.1 31.9 1.0 N A:PRO63 4.1 29.0 1.0 CA A:PRO63 4.1 35.7 1.0 O A:LYS61 4.2 37.5 1.0 N A:VAL65 4.2 33.9 1.0 N A:GLY64 4.4 34.4 1.0 CA A:LEU62 4.4 31.9 1.0 CA A:LYS60 4.4 33.8 1.0 N A:LYS61 4.4 35.2 1.0 CA A:LYS61 4.5 32.2 1.0 CA A:VAL65 4.5 31.3 1.0 CG A:LYS60 4.6 34.3 1.0 C A:PRO63 4.7 34.1 1.0 CB A:VAL65 4.8 32.1 1.0 O3' D:DT2 4.8 33.5 1.0 O5' D:DC3 4.9 32.2 1.0 N A:GLY66 5.0 29.8 1.0

M.C.Koag, S.Lee. The Spontaneous Base Substitution Mechanisms of Human Dna Polymerase Beta To Be Published.