Magnesium in PDB 5yuv: Dna Polymerase IV - Dna Ternary Complex 5

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 5:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 5, PDB code: 5yuv 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)	44.48 / 2.06
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.660, 56.940, 109.780, 90.00, 95.00, 90.00
R / Rfree (%)	18.7 / 23.4

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 5 (pdb code 5yuv). 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 5, PDB code: 5yuv:
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 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:23.2 occ:1.00 O1A H:TTP901 1.8 22.0 0.3 O1B H:TTP901 2.1 24.6 0.7 OD1 F:ASP8 2.1 38.1 1.0 O1A H:TTP901 2.2 31.5 0.7 O F:MET9 2.2 21.5 1.0 O3G H:TTP901 2.3 36.1 0.7 O1B H:TTP901 2.3 30.2 0.3 OD2 F:ASP103 2.4 29.0 1.0 O3G H:TTP901 2.4 36.9 0.3 PB H:TTP901 3.1 30.9 0.7 PA H:TTP901 3.1 31.4 0.3 CG F:ASP8 3.2 40.4 1.0 PB H:TTP901 3.4 30.1 0.3 MG F:MG902 3.4 56.9 1.0 C F:MET9 3.4 25.1 1.0 PG H:TTP901 3.5 35.3 0.7 CG F:ASP103 3.5 30.7 1.0 O3A H:TTP901 3.5 34.3 0.7 O3A H:TTP901 3.6 26.9 0.3 PG H:TTP901 3.6 36.7 0.3 PA H:TTP901 3.6 28.8 0.7 OD2 F:ASP8 3.7 50.8 1.0 O3B H:TTP901 3.7 37.4 0.7 OD1 F:ASP103 3.9 32.0 1.0 N F:MET9 3.9 23.3 1.0 NZ F:LYS157 4.0 25.0 1.0 O3B H:TTP901 4.0 35.0 0.3 C5' H:TTP901 4.0 23.3 0.3 O F:HOH1093 4.0 40.9 1.0 O1G H:TTP901 4.1 38.8 0.3 O5' H:TTP901 4.1 27.0 0.3 O1G H:TTP901 4.1 38.5 0.7 C5' H:TTP901 4.2 23.6 0.7 CA F:MET9 4.2 24.7 1.0 O2A H:TTP901 4.2 27.7 0.3 C F:ASP8 4.3 24.6 1.0 O3' H:DC873 4.3 31.5 0.7 O2B H:TTP901 4.4 27.5 0.7 CB F:ASP8 4.4 35.2 1.0 N F:ASP10 4.5 24.6 1.0 O5' H:TTP901 4.5 25.9 0.7 N F:CYS11 4.6 20.8 1.0 O F:HOH1086 4.6 50.4 1.0 CB F:MET9 4.7 23.1 1.0 CE F:LYS157 4.7 47.6 1.0 O2G H:TTP901 4.7 43.2 0.7 CA F:ASP10 4.7 23.3 1.0 O2B H:TTP901 4.7 29.4 0.3 CB F:PHE12 4.7 22.9 1.0 O2A H:TTP901 4.7 26.7 0.7 CA F:ASP8 4.7 30.9 1.0 CB F:ASP103 4.7 22.4 1.0 N F:PHE12 4.8 28.7 1.0 O F:ASP8 4.8 28.2 1.0 O2G H:TTP901 4.9 42.1 0.3 C F:ASP10 4.9 26.2 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:56.9 occ:1.00 OE2 F:GLU104 1.9 61.1 1.0 O3' H:DC873 2.3 31.5 0.7 O1A H:TTP901 2.3 31.5 0.7 OD1 F:ASP103 2.4 32.0 1.0 O3' H:DC873 2.4 24.9 0.3 O1A H:TTP901 2.5 22.0 0.3 O F:HOH1086 3.0 50.4 1.0 CD F:GLU104 3.0 47.4 1.0 OD1 F:ASP8 3.2 38.1 1.0 PA H:TTP901 3.2 28.8 0.7 CG F:ASP103 3.2 30.7 1.0 OD2 F:ASP103 3.3 29.0 1.0 OD2 F:ASP8 3.4 50.8 1.0 MG F:MG901 3.4 23.2 1.0 PA H:TTP901 3.4 31.4 0.3 CG F:GLU104 3.5 37.0 1.0 CG F:ASP8 3.5 40.4 1.0 O2A H:TTP901 3.5 27.7 0.3 C3' H:DC873 3.5 27.2 0.7 C3' H:DC873 3.7 29.1 0.3 CB F:GLU104 3.7 29.8 1.0 O5' H:TTP901 3.9 27.0 0.3 C5' H:TTP901 3.9 23.3 0.3 C4' H:DC873 3.9 30.7 0.7 O5' H:TTP901 4.0 25.9 0.7 C5' H:TTP901 4.0 23.6 0.7 O2A H:TTP901 4.1 26.7 0.7 OE1 F:GLU104 4.1 50.7 1.0 C5' H:DC873 4.1 33.1 0.7 OG F:SER101 4.2 37.8 1.0 O H:HOH1022 4.4 91.3 1.0 C4' H:DC873 4.4 31.4 0.3 O F:HOH1093 4.4 40.9 1.0 O3A H:TTP901 4.5 34.3 0.7 C2' H:DC873 4.5 32.0 0.7 C5' H:DC873 4.6 32.8 0.3 O F:ASP103 4.6 26.6 1.0 C F:ASP103 4.6 29.8 1.0 CB F:ASP103 4.7 22.4 1.0 CB F:ASP8 4.7 35.2 1.0 N F:GLU104 4.8 25.7 1.0 C2' H:DC873 4.8 29.3 0.3 CA F:GLU104 4.8 26.2 1.0 O1B H:TTP901 4.8 24.6 0.7 O3A H:TTP901 4.9 26.9 0.3 O3G H:TTP901 4.9 36.1 0.7 O5' H:DC873 5.0 36.7 0.3 O3G H:TTP901 5.0 36.9 0.3

Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:27.2 occ:1.00 O2B C:TTP901 1.9 34.1 0.3 OD1 A:ASP8 2.0 40.1 1.0 O2A C:TTP901 2.1 34.7 0.7 O2B C:TTP901 2.2 34.2 0.7 O2G C:TTP901 2.3 44.3 0.3 OD2 A:ASP103 2.3 39.8 1.0 O A:MET9 2.3 25.8 1.0 O2A C:TTP901 2.4 35.9 0.3 O2G C:TTP901 2.4 46.8 0.7 PB C:TTP901 3.0 37.0 0.3 MG A:MG902 3.1 89.5 1.0 CG A:ASP8 3.2 46.1 1.0 PB C:TTP901 3.3 32.0 0.7 PA C:TTP901 3.3 40.2 0.7 CG A:ASP103 3.4 32.4 1.0 PG C:TTP901 3.4 42.3 0.3 C A:MET9 3.5 35.8 1.0 PG C:TTP901 3.6 43.1 0.7 O3A C:TTP901 3.6 38.9 0.3 O3B C:TTP901 3.6 37.1 0.3 O3A C:TTP901 3.6 36.9 0.7 PA C:TTP901 3.7 32.8 0.3 OD1 A:ASP103 3.7 34.8 1.0 OD2 A:ASP8 3.8 53.4 1.0 O3G C:TTP901 3.9 41.1 0.3 O3B C:TTP901 3.9 35.6 0.7 N A:MET9 3.9 26.8 1.0 NZ A:LYS157 4.0 36.2 1.0 O C:HOH1021 4.0 40.8 1.0 O3G C:TTP901 4.0 39.2 0.7 C5' C:TTP901 4.1 27.9 0.7 C5' C:TTP901 4.2 30.0 0.3 O5' C:TTP901 4.2 33.6 0.7 CA A:MET9 4.2 30.8 1.0 O1B C:TTP901 4.3 38.0 0.3 O3' C:DC873 4.4 32.1 0.3 C A:ASP8 4.4 32.0 1.0 O1A C:TTP901 4.4 38.5 0.7 CB A:ASP8 4.5 36.6 1.0 O5' C:TTP901 4.5 33.8 0.3 N A:ASP10 4.5 29.2 1.0 N A:CYS11 4.5 29.8 1.0 CE A:LYS157 4.6 47.8 1.0 O1B C:TTP901 4.6 25.3 0.7 CB A:ASP103 4.7 41.5 1.0 O1G C:TTP901 4.7 41.2 0.3 CB A:MET9 4.7 32.4 1.0 CA A:ASP10 4.7 26.3 1.0 N A:PHE12 4.7 27.7 1.0 CA A:ASP8 4.8 27.6 1.0 CB A:PHE12 4.8 28.6 1.0 O1A C:TTP901 4.8 40.2 0.3 O1G C:TTP901 4.8 38.7 0.7 C A:ASP10 4.8 27.7 1.0 O A:ASP8 4.9 30.4 1.0 OE2 A:GLU104 5.0 76.5 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 5


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 5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:89.5 occ:1.00 OE2 A:GLU104 2.0 76.5 1.0 OD1 A:ASP103 2.2 34.8 1.0 O2A C:TTP901 2.3 35.9 0.3 O2A C:TTP901 2.4 34.7 0.7 OD2 A:ASP8 2.7 53.4 1.0 OD1 A:ASP8 2.7 40.1 1.0 CG A:ASP8 2.8 46.1 1.0 CD A:GLU104 2.9 61.3 1.0 CG A:ASP103 3.0 32.4 1.0 O3' C:DC873 3.0 32.1 0.3 OD2 A:ASP103 3.0 39.8 1.0 MG A:MG901 3.1 27.2 1.0 CG A:GLU104 3.4 47.0 1.0 O3' C:DC873 3.4 37.1 0.7 PA C:TTP901 3.5 32.8 0.3 CB A:GLU104 3.5 32.2 1.0 O C:HOH1011 3.7 72.4 1.0 PA C:TTP901 3.7 40.2 0.7 OE1 A:GLU104 4.0 48.4 1.0 C3' C:DC873 4.1 34.1 0.7 O1A C:TTP901 4.1 38.5 0.7 CB A:ASP8 4.1 36.6 1.0 C3' C:DC873 4.2 33.6 0.3 O5' C:TTP901 4.2 33.6 0.7 O A:ASP103 4.2 32.6 1.0 O C:HOH1021 4.3 40.8 1.0 C5' C:TTP901 4.3 30.0 0.3 O1A C:TTP901 4.3 40.2 0.3 OG A:SER101 4.3 50.2 1.0 C A:ASP103 4.3 36.6 1.0 C5' C:DC873 4.3 43.8 0.3 C5' C:TTP901 4.4 27.9 0.7 O2B C:TTP901 4.4 34.1 0.3 C4' C:DC873 4.4 36.9 0.3 CB A:ASP103 4.4 41.5 1.0 CA A:ASP8 4.5 27.6 1.0 O5' C:TTP901 4.5 33.8 0.3 O2G C:TTP901 4.5 44.3 0.3 N A:GLU104 4.5 30.2 1.0 CA A:GLU104 4.6 28.2 1.0 O3A C:TTP901 4.6 38.9 0.3 O2G C:TTP901 4.7 46.8 0.7 N A:MET9 4.8 26.8 1.0 O2B C:TTP901 4.9 34.2 0.7 CA A:ASP103 4.9 38.7 1.0 O A:MET9 4.9 25.8 1.0 C4' C:DC873 5.0 38.3 0.7

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