Magnesium in PDB 5yuw: Dna Polymerase IV - Dna Ternary Complex 6

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 6:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 6, PDB code: 5yuw was solved by J.Kottur, D.T.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 2.12
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.190, 57.010, 110.040, 90.00, 94.59, 90.00
R / Rfree (%)	18.9 / 23.2

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 6 (pdb code 5yuw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Dna Polymerase IV - Dna Ternary Complex 6, PDB code: 5yuw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase IV - Dna Ternary Complex 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:34.6 occ:1.00 O2A C:TTP901 2.0 50.4 0.7 O2B A:TTP900 2.2 33.2 0.3 OD1 A:ASP8 2.2 45.0 1.0 O2B C:TTP901 2.2 44.5 0.7 O2A A:TTP900 2.2 39.8 0.3 O A:MET9 2.3 29.5 1.0 O2G C:TTP901 2.3 59.0 0.7 OD2 A:ASP103 2.4 33.3 1.0 O2G A:TTP900 2.6 45.6 0.3 PB C:TTP901 3.1 47.4 0.7 O3A C:TTP901 3.1 52.5 0.7 CG A:ASP8 3.3 51.4 1.0 MG A:MG902 3.3 68.9 1.0 PB A:TTP900 3.4 32.7 0.3 CG A:ASP103 3.5 32.9 1.0 PA A:TTP900 3.5 41.7 0.3 PA C:TTP901 3.5 46.3 0.7 PG C:TTP901 3.5 61.7 0.7 C A:MET9 3.5 33.1 1.0 PG A:TTP900 3.7 45.0 0.3 O3A A:TTP900 3.7 37.3 0.3 O3B C:TTP901 3.7 55.2 0.7 OD1 A:ASP103 3.8 33.6 1.0 O C:HOH1011 3.8 48.8 1.0 N A:MET9 3.9 34.0 1.0 OD2 A:ASP8 3.9 69.1 1.0 O3G C:TTP901 4.0 58.7 0.7 NZ A:LYS157 4.0 35.4 1.0 O3G A:TTP900 4.1 44.3 0.3 C5' C:TTP901 4.1 35.4 0.7 O3B A:TTP900 4.1 37.8 0.3 CA A:MET9 4.2 39.8 1.0 O5' C:TTP901 4.3 43.1 0.7 C5' A:TTP900 4.3 39.1 0.3 O3' C:DC873 4.3 51.1 0.7 C A:ASP8 4.3 35.1 1.0 O5' A:TTP900 4.4 40.3 0.3 CE A:LYS157 4.4 41.4 1.0 CB A:ASP8 4.4 43.1 1.0 O1B C:TTP901 4.4 44.9 0.7 O3' C:DC873 4.5 44.7 0.3 N A:ASP10 4.5 34.3 1.0 O1B A:TTP900 4.6 31.8 0.3 O1A A:TTP900 4.6 33.6 0.3 O1A C:TTP901 4.6 43.0 0.7 N A:CYS11 4.6 32.4 1.0 CA A:ASP8 4.7 34.6 1.0 CA A:ASP10 4.7 33.6 1.0 CB A:MET9 4.8 39.5 1.0 O1G C:TTP901 4.8 62.5 0.7 CB A:ASP103 4.8 35.1 1.0 N A:PHE12 4.8 31.7 1.0 O A:ASP8 4.9 38.4 1.0 CB A:PHE12 4.9 37.6 1.0 C A:ASP10 5.0 31.4 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase IV - Dna Ternary Complex 6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:68.9 occ:1.00 OE2 A:GLU104 1.8 60.2 1.0 O2A C:TTP901 2.2 50.4 0.7 OD1 A:ASP103 2.3 33.6 1.0 O3' C:DC873 2.3 44.7 0.3 O3' C:DC873 2.4 51.1 0.7 O2A A:TTP900 2.6 39.8 0.3 OD1 A:ASP8 2.8 45.0 1.0 CD A:GLU104 2.9 53.6 1.0 CG A:ASP103 3.2 32.9 1.0 PA C:TTP901 3.2 46.3 0.7 OD2 A:ASP8 3.3 69.1 1.0 CG A:ASP8 3.3 51.4 1.0 MG A:MG901 3.3 34.6 1.0 OD2 A:ASP103 3.4 33.3 1.0 CG A:GLU104 3.5 47.4 1.0 C3' C:DC873 3.6 43.8 0.3 C3' C:DC873 3.6 43.5 0.7 CB A:GLU104 3.7 36.6 1.0 PA A:TTP900 3.8 41.7 0.3 C4' C:DC873 3.9 43.9 0.7 OE1 A:GLU104 3.9 44.2 1.0 C4' C:DC873 3.9 43.6 0.3 OG A:SER101 4.1 42.3 1.0 C5' C:DC873 4.1 45.2 0.7 O5' C:TTP901 4.2 43.1 0.7 O1A C:TTP901 4.2 43.0 0.7 O1A A:TTP900 4.2 33.6 0.3 C5' C:DC873 4.2 46.6 0.3 C5' C:TTP901 4.3 35.4 0.7 C5' A:TTP900 4.3 39.1 0.3 O3A C:TTP901 4.3 52.5 0.7 O C:HOH1011 4.4 48.8 1.0 O5' A:TTP900 4.4 40.3 0.3 C2' C:DC873 4.5 45.1 0.7 O A:ASP103 4.5 30.0 1.0 C A:ASP103 4.6 35.6 1.0 C2' C:DC873 4.6 45.0 0.3 CB A:ASP103 4.6 35.1 1.0 CB A:ASP8 4.7 43.1 1.0 N A:GLU104 4.8 30.3 1.0 O5' C:DC873 4.8 52.6 0.7 O2G C:TTP901 4.9 59.0 0.7 CA A:GLU104 4.9 36.8 1.0 O5' C:DC873 4.9 51.4 0.3 O2B C:TTP901 4.9 44.5 0.7

Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna Polymerase IV - Dna Ternary Complex 6 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:26.4 occ:1.00 O1A F:TTP903 1.8 42.3 1.0 O1B F:TTP903 2.0 33.1 1.0 OD1 F:ASP8 2.2 28.1 0.5 O F:MET9 2.3 26.1 1.0 OD2 F:ASP103 2.3 33.4 1.0 OD1 F:ASP8 2.3 25.1 0.5 O3G F:TTP903 2.4 29.9 1.0 O3A F:TTP903 3.0 46.7 1.0 CG F:ASP8 3.1 29.3 0.5 PB F:TTP903 3.1 29.8 1.0 CG F:ASP8 3.2 29.5 0.5 OD2 F:ASP8 3.3 31.1 0.5 MG F:MG902 3.3 55.7 1.0 CG F:ASP103 3.4 33.1 1.0 C F:MET9 3.4 27.7 1.0 PA F:TTP903 3.5 37.1 1.0 OD2 F:ASP8 3.5 33.0 0.5 PG F:TTP903 3.5 35.9 1.0 O3B F:TTP903 3.7 42.9 1.0 OD1 F:ASP103 3.8 31.4 1.0 N F:MET9 3.8 27.6 1.0 NZ F:LYS157 4.0 21.1 0.3 C5' F:TTP903 4.1 24.3 1.0 CA F:MET9 4.2 31.6 1.0 O1G F:TTP903 4.2 34.1 1.0 C F:ASP8 4.3 29.8 1.0 O5' F:TTP903 4.4 34.4 1.0 CB F:ASP8 4.4 30.6 0.5 CE F:LYS157 4.4 20.8 0.3 O2A F:TTP903 4.4 28.2 1.0 CB F:ASP8 4.5 30.5 0.5 N F:ASP10 4.5 27.0 1.0 O3' H:DC873 4.5 39.4 1.0 O2B F:TTP903 4.5 32.2 1.0 N F:CYS11 4.7 21.6 1.0 CB F:ASP103 4.7 23.3 1.0 CB F:MET9 4.7 26.2 1.0 CA F:ASP10 4.7 26.6 1.0 O F:HOH1073 4.7 46.9 1.0 N F:PHE12 4.7 28.5 1.0 CA F:ASP8 4.7 32.9 1.0 O F:ASP8 4.8 31.4 1.0 CB F:PHE12 4.8 20.4 1.0 O2G F:TTP903 4.8 44.5 1.0 C F:ASP10 4.9 24.1 1.0 O F:ASP103 5.0 29.4 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 6


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dna Polymerase IV - Dna Ternary Complex 6 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:55.7 occ:1.00 OE1 F:GLU104 2.0 39.7 1.0 OD1 F:ASP103 2.4 31.4 1.0 OD2 F:ASP8 2.4 31.1 0.5 O1A F:TTP903 2.4 42.3 1.0 O3' H:DC873 2.5 39.4 1.0 OD1 F:ASP8 2.8 25.1 0.5 PA F:TTP903 2.8 37.1 1.0 O F:HOH1073 2.9 46.9 1.0 CD F:GLU104 3.1 37.5 1.0 CG F:ASP103 3.2 33.1 1.0 OD2 F:ASP103 3.3 33.4 1.0 MG F:MG901 3.3 26.4 1.0 CG F:ASP8 3.4 29.3 0.5 CG F:ASP8 3.4 29.5 0.5 OD2 F:ASP8 3.5 33.0 0.5 CG F:GLU104 3.7 31.4 1.0 C3' H:DC873 3.7 25.9 1.0 O5' F:TTP903 3.8 34.4 1.0 OD1 F:ASP8 3.8 28.1 0.5 CB F:GLU104 3.8 28.0 1.0 O2A F:TTP903 3.8 28.2 1.0 O3A F:TTP903 4.0 46.7 1.0 OG F:SER101 4.1 39.9 1.0 C5' F:TTP903 4.1 24.3 1.0 OE2 F:GLU104 4.2 50.0 1.0 C4' H:DC873 4.2 36.7 1.0 C5' H:DC873 4.3 34.1 1.0 O F:ASP103 4.6 29.4 1.0 CB F:ASP8 4.6 30.6 0.5 C F:ASP103 4.7 28.9 1.0 CB F:ASP103 4.7 23.3 1.0 CB F:ASP8 4.7 30.5 0.5 C2' H:DC873 4.7 30.0 1.0 O1B F:TTP903 4.8 33.1 1.0 N F:GLU104 4.8 23.5 1.0 O3G F:TTP903 4.9 29.9 1.0 CA F:GLU104 4.9 24.8 1.0 O5' H:DC873 4.9 37.4 1.0

J.Kottur, D.T.Nair. Pyrophosphate Hydrolysis Is An Intrinsic and Critical Step of the Dna Synthesis Reaction Nucleic Acids Res. V. 46 5875 2018.
ISSN: ESSN 1362-4962
PubMed: 29850882
DOI: 10.1093/NAR/GKY402