Sodium in PDB 8s87: Kod-H4 Dna Polymerase Mutant - Apo Structure

All present enzymatic activity of Kod-H4 Dna Polymerase Mutant - Apo Structure:
2.7.7.7;

The structure of Kod-H4 Dna Polymerase Mutant - Apo Structure, PDB code: 8s87 was solved by C.Gutfreund, K.Betz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.40 / 1.82
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.424, 110.629, 111.363, 90, 90, 90
R / Rfree (%)	23 / 27.1

The structure of Kod-H4 Dna Polymerase Mutant - Apo Structure also contains other interesting chemical elements:

Magnesium

(Mg)

9 atoms

The binding sites of Sodium atom in the Kod-H4 Dna Polymerase Mutant - Apo Structure (pdb code 8s87). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Kod-H4 Dna Polymerase Mutant - Apo Structure, PDB code: 8s87:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Kod-H4 Dna Polymerase Mutant - Apo Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na807 b:60.5 occ:1.00 O A:GLY429 3.3 50.7 1.0 HB2 A:GLU430 4.0 57.7 1.0 C A:GLY429 4.1 55.2 1.0 HA3 A:GLY429 4.2 68.2 1.0 CA A:GLY429 4.7 56.7 1.0 HA2 A:GLY429 4.8 68.2 1.0 CB A:GLU430 4.9 48.5 1.0 HA A:GLU430 5.0 62.8 1.0

Sodium binding site 2 out of 2 in the Kod-H4 Dna Polymerase Mutant - Apo Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Kod-H4 Dna Polymerase Mutant - Apo Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na809 b:59.8 occ:1.00 HH11 A:ARG359 2.0 42.8 1.0 OE2 A:GLU363 2.5 49.1 1.0 HD3 A:ARG359 2.7 48.7 1.0 O A:HOH977 2.8 44.0 1.0 NH1 A:ARG359 2.8 36.0 1.0 HA2 A:GLY125 3.0 50.0 1.0 HG3 A:ARG359 3.1 43.0 1.0 O A:HOH946 3.1 55.0 1.0 HG2 A:ARG359 3.2 43.0 1.0 HH12 A:ARG359 3.2 42.8 1.0 CD A:ARG359 3.4 40.5 1.0 CG A:ARG359 3.4 36.2 1.0 HG2 A:GLU363 3.4 63.2 1.0 CD A:GLU363 3.5 60.3 1.0 HG3 A:GLU363 3.6 63.2 1.0 CG A:GLU363 3.7 52.6 1.0 CZ A:ARG359 3.8 44.5 1.0 CA A:GLY125 3.9 41.6 1.0 NE A:ARG359 4.0 45.3 1.0 HA3 A:GLY125 4.1 50.0 1.0 HD2 A:ARG359 4.2 48.7 1.0 C A:GLY125 4.5 47.1 1.0 O A:ILE122 4.6 44.5 1.0 O A:GLY125 4.6 43.3 1.0 OE1 A:GLU363 4.7 52.1 1.0 HG22 A:VAL127 4.7 56.1 1.0 H A:GLY125 4.7 53.6 1.0 HE A:ARG359 4.8 54.5 1.0 N A:GLY125 4.8 44.6 1.0 HA A:ILE122 4.9 49.3 1.0 CB A:ARG359 4.9 36.1 1.0

C.Gutfreund, K.Betz. Structural Insights Into A Dna Polymerase Reading the Xeno Nucleic Acid Hna Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962