Sodium in PDB 4klq: Observing A Dna Polymerase Choose Right From Wrong.

All present enzymatic activity of Observing A Dna Polymerase Choose Right From Wrong.:
2.7.7.7;

The structure of Observing A Dna Polymerase Choose Right From Wrong., PDB code: 4klq was solved by B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.04 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.822, 78.412, 54.962, 90.00, 113.24, 90.00
R / Rfree (%)	21.4 / 26.7

The structure of Observing A Dna Polymerase Choose Right From Wrong. also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Sodium atom in the Observing A Dna Polymerase Choose Right From Wrong. (pdb code 4klq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Observing A Dna Polymerase Choose Right From Wrong., PDB code: 4klq:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Observing A Dna Polymerase Choose Right From Wrong.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Observing A Dna Polymerase Choose Right From Wrong. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na406 b:51.7 occ:1.00 O A:HOH537 2.3 53.7 1.0 O A:HOH634 2.4 53.9 1.0 O21 A:PPV402 2.6 37.4 0.3 O2G A:DTP401 2.7 37.8 0.7 O3G A:DTP401 3.5 38.0 0.7 P1 A:PPV402 3.5 36.8 0.3 O11 A:PPV402 3.6 35.5 0.3 PG A:DTP401 3.6 34.6 0.7 O1A A:DTP401 3.9 32.1 0.7 OPP A:PPV402 3.9 40.8 0.3 O3A A:DTP401 4.0 33.4 0.7 O3B A:DTP401 4.2 44.6 0.7 O12 A:PPV402 4.3 32.5 0.3 O A:HOH553 4.5 39.4 1.0 PA A:DTP401 4.5 33.4 0.7 O A:HOH632 4.7 48.7 1.0 P2 A:PPV402 4.7 34.2 0.3 PB A:DTP401 4.8 39.0 0.7 O31 A:PPV402 4.9 36.1 0.3 O1G A:DTP401 4.9 35.9 0.7 O2A A:DTP401 4.9 14.7 0.7 CA A:GLY189 4.9 25.2 1.0

Sodium binding site 2 out of 3 in the Observing A Dna Polymerase Choose Right From Wrong.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Observing A Dna Polymerase Choose Right From Wrong. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na407 b:22.4 occ:1.00 O A:THR101 2.3 26.0 1.0 O A:ILE106 2.4 21.3 1.0 O P:HOH102 2.4 28.9 1.0 O A:VAL103 2.5 20.6 1.0 O A:HOH556 2.5 36.0 1.0 OP1 P:DG9 2.5 28.3 1.0 C A:THR101 3.3 23.7 1.0 C A:ILE106 3.4 17.3 1.0 C A:VAL103 3.4 26.1 1.0 P P:DG9 3.6 25.8 1.0 O A:HOH584 3.6 34.0 1.0 OP2 P:DG9 3.8 26.1 1.0 N A:ILE106 3.8 19.4 1.0 CA A:THR101 3.8 23.9 1.0 N A:GLY105 3.9 22.6 1.0 CA A:SER104 4.1 22.8 1.0 N A:VAL103 4.1 20.5 1.0 N A:SER104 4.1 20.0 1.0 CA A:ILE106 4.1 21.2 1.0 C A:ARG102 4.3 22.7 1.0 N A:ARG102 4.3 23.2 1.0 CB A:THR101 4.3 24.5 1.0 N A:GLY107 4.4 18.6 1.0 CA A:VAL103 4.4 26.3 1.0 C A:SER104 4.4 26.6 1.0 CB A:ILE106 4.5 20.1 1.0 O3' P:DC8 4.6 23.4 1.0 CA A:ARG102 4.6 23.6 1.0 CA A:GLY107 4.6 23.8 1.0 C A:GLY105 4.7 23.4 1.0 O5' P:DG9 4.7 25.6 1.0 O A:LEU100 4.8 23.0 1.0 O A:ARG102 4.9 24.1 1.0 CA A:GLY105 4.9 21.4 1.0 O A:HOH572 5.0 37.7 1.0

Sodium binding site 3 out of 3 in the Observing A Dna Polymerase Choose Right From Wrong.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Observing A Dna Polymerase Choose Right From Wrong. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na408 b:30.0 occ:1.00 O A:VAL65 2.3 28.3 1.0 O A:LEU62 2.4 27.2 1.0 O A:LYS60 2.5 32.3 1.0 O A:HOH524 2.5 31.8 1.0 O D:HOH102 2.6 27.0 1.0 OP1 D:DC3 2.6 23.2 1.0 C A:LEU62 3.2 32.5 1.0 C A:VAL65 3.5 30.5 1.0 C A:LYS60 3.5 29.5 1.0 P D:DC3 3.7 28.6 1.0 OP2 D:DC3 3.9 24.2 1.0 N A:VAL65 3.9 24.3 1.0 N A:LEU62 3.9 26.6 1.0 C A:LYS61 3.9 35.1 1.0 N A:PRO63 3.9 31.0 1.0 CA A:PRO63 4.0 29.9 1.0 CD A:LYS60 4.0 40.6 1.0 CA A:VAL65 4.1 22.5 1.0 O A:LYS61 4.1 30.3 1.0 CA A:LEU62 4.2 30.0 1.0 CB A:VAL65 4.3 34.2 1.0 CA A:LYS60 4.3 27.9 1.0 N A:GLY64 4.3 25.9 1.0 N A:LYS61 4.4 30.6 1.0 C A:PRO63 4.5 36.5 1.0 CA A:LYS61 4.5 29.1 1.0 N A:GLY66 4.6 25.1 1.0 CE A:LYS60 4.6 38.0 1.0 O A:ALA59 4.7 28.7 1.0 O3' D:DT2 4.7 25.1 1.0 CA A:GLY66 4.8 27.7 1.0 CG A:LYS60 4.8 39.3 1.0 O5' D:DC3 4.9 28.4 1.0 C A:GLY64 4.9 26.9 1.0

B.D.Freudenthal, W.A.Beard, D.D.Shock, S.H.Wilson. Observing A Dna Polymerase Choose Right From Wrong. Cell(Cambridge,Mass.) V. 154 157 2013.
ISSN: ISSN 0092-8674
PubMed: 23827680
DOI: 10.1016/J.CELL.2013.05.048