Sodium in PDB 3v7k: Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex

All present enzymatic activity of Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex:
2.7.7.7;

The structure of Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex, PDB code: 3v7k was solved by S.Rangarajan, J.Jaeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.30 / 2.27
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.464, 75.508, 117.359, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 27.7

The binding sites of Sodium atom in the Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex (pdb code 3v7k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex, PDB code: 3v7k:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:88.2 occ:1.00 OD2 A:ASP190 3.5 85.9 1.0 CG A:ASP190 4.0 77.8 1.0 C3' P:DT7 4.1 39.4 1.0 OD1 A:ASP190 4.5 90.0 1.0 O A:HOH588 4.6 44.0 1.0 CB A:ASP190 4.6 57.7 1.0 OD2 A:ASP192 4.9 57.1 1.0 NA A:NA402 4.9 52.2 1.0

Sodium binding site 2 out of 4 in the Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:52.2 occ:1.00 O A:ASP190 3.3 63.6 1.0 OD2 A:ASP190 3.9 85.9 1.0 C A:ASP190 4.0 53.0 1.0 CA A:GLY179 4.0 43.5 1.0 CB A:ASP192 4.2 42.1 1.0 O A:CYS178 4.2 43.4 1.0 N A:ASP192 4.2 35.4 1.0 CB A:SER188 4.3 50.5 1.0 CB A:ASP190 4.5 57.7 1.0 CA A:MET191 4.5 36.9 1.0 N A:SER180 4.5 50.9 1.0 C A:GLY179 4.6 46.5 1.0 N A:MET191 4.7 42.2 1.0 C A:MET191 4.7 43.5 1.0 CG A:ASP190 4.7 77.8 1.0 O A:HOH588 4.8 44.0 1.0 N A:GLY179 4.8 43.8 1.0 C A:CYS178 4.8 43.4 1.0 CA A:ASP190 4.8 46.6 1.0 OG A:SER188 4.8 45.0 1.0 OG A:SER180 4.9 57.1 1.0 CA A:ASP192 4.9 35.8 1.0 NA A:NA401 4.9 88.2 1.0 CE A:MET155 5.0 37.4 1.0

Sodium binding site 3 out of 4 in the Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na403 b:94.8 occ:1.00 O A:HOH536 4.1 49.2 1.0 OD1 A:ASP130 4.1 38.1 1.0 O A:LYS127 4.3 44.8 1.0 CG A:ASP130 4.5 42.0 1.0 OD2 A:ASP130 4.7 43.5 1.0

Sodium binding site 4 out of 4 in the Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Co-Crystal Structure of K72E Variant of Rat Polymerase Beta: Enzyme- Dna Binary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na404 b:48.5 occ:1.00 OP2 P:DG6 3.3 52.9 1.0 O A:THR101 3.4 27.6 1.0 O A:ILE106 3.6 31.7 1.0 O3' P:DA5 3.7 63.9 1.0 P P:DG6 4.1 37.1 1.0 CG2 A:THR101 4.1 45.5 1.0 OG1 A:THR101 4.2 46.0 1.0 C A:THR101 4.3 26.9 1.0 CB A:THR101 4.5 45.1 1.0 CA A:GLY107 4.6 34.4 1.0 CA A:THR101 4.6 32.8 1.0 O5' P:DG6 4.7 34.4 1.0 C A:ILE106 4.7 44.2 1.0

S.Rangarajan, C.L.Gridley, S.Firbank, S.Dalal, J.B.Sweasy, J.Jaeger. Crystallographic Studies of K72E Mutant Dna Polymerase Explain Loss of Lyase Function and Reveal Changes in the Overall Conformational State of the Polymerase Domain To Be Published.