Magnesium in PDB 9emi: Kod-H4 Dna Polymerase Mutant in A Ternary Complex Containing Six Hna Nucleotides and A Non-Hydrolyzable Triphosphate

All present enzymatic activity of Kod-H4 Dna Polymerase Mutant in A Ternary Complex Containing Six Hna Nucleotides and A Non-Hydrolyzable Triphosphate:
2.7.7.7;

The structure of Kod-H4 Dna Polymerase Mutant in A Ternary Complex Containing Six Hna Nucleotides and A Non-Hydrolyzable Triphosphate, PDB code: 9emi 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)	41.04 / 2.27
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	111.454, 151.548, 70.406, 90, 90, 90
R / Rfree (%)	23.5 / 26.5

The binding sites of Magnesium atom in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex Containing Six Hna Nucleotides and A Non-Hydrolyzable Triphosphate (pdb code 9emi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex Containing Six Hna Nucleotides and A Non-Hydrolyzable Triphosphate, PDB code: 9emi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex Containing Six Hna Nucleotides and A Non-Hydrolyzable Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Kod-H4 Dna Polymerase Mutant in A Ternary Complex Containing Six Hna Nucleotides and A Non-Hydrolyzable Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:66.7 occ:1.00 O A:HOH904 2.4 71.5 1.0 OE2 A:GLU580 2.5 71.6 1.0 O A:HOH905 2.5 73.7 1.0 OD2 A:ASP404 2.7 73.2 1.0 O1G A:XG4803 2.8 82.1 1.0 O A:PHE405 3.0 61.6 1.0 O2B A:XG4803 3.1 68.1 1.0 CG A:ASP404 3.3 65.9 1.0 OD1 A:ASP404 3.3 74.8 1.0 CD A:GLU580 3.7 91.4 1.0 PG A:XG4803 3.9 61.9 1.0 C A:PHE405 4.0 59.9 1.0 PB A:XG4803 4.1 62.1 1.0 O3B A:XG4803 4.1 65.3 1.0 CA A:ARG406 4.3 55.9 1.0 OE2 A:GLU578 4.3 80.0 1.0 OE1 A:GLU580 4.4 95.6 1.0 O2G A:XG4803 4.4 74.6 1.0 O A:HOH914 4.5 71.4 1.0 N3A A:XG4803 4.5 86.1 1.0 N A:ARG406 4.5 57.2 1.0 CB A:ASP404 4.6 56.6 1.0 CG A:GLU580 4.7 85.2 1.0 O A:ASP404 4.8 54.4 1.0 C A:ASP404 4.8 55.8 1.0 N A:SER407 4.8 50.3 1.0 OD2 A:ASP542 5.0 63.2 1.0 N A:PHE405 5.0 51.8 1.0

Magnesium binding site 2 out of 2 in the Kod-H4 Dna Polymerase Mutant in A Ternary Complex Containing Six Hna Nucleotides and A Non-Hydrolyzable Triphosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Kod-H4 Dna Polymerase Mutant in A Ternary Complex Containing Six Hna Nucleotides and A Non-Hydrolyzable Triphosphate within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg102 b:69.5 occ:1.00 O2A A:XG4803 2.2 66.0 1.0 O A:HOH914 2.2 71.4 1.0 O A:HOH926 2.2 74.4 1.0 O3' P:DA13 2.3 58.7 1.0 C3' P:DA13 3.3 64.5 1.0 OD2 A:ASP542 3.3 63.2 1.0 PA A:XG4803 3.6 60.5 1.0 OD1 A:ASP542 3.9 57.2 1.0 C2' P:DA13 4.0 54.5 1.0 OD2 A:ASP404 4.0 73.2 1.0 N3A A:XG4803 4.1 86.1 1.0 CG A:ASP542 4.1 58.0 1.0 OH A:TYR402 4.2 69.3 1.0 O5' A:XG4803 4.4 64.3 1.0 O A:HOH904 4.5 71.5 1.0 O5' P:DA13 4.5 62.0 1.0 O1A A:XG4803 4.6 55.6 1.0 C4' P:DA13 4.6 62.4 1.0 O3B A:XG4803 4.6 65.3 1.0 C5' A:XG4803 4.8 66.2 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