Magnesium in PDB 5yut: Dna Polymerase IV - Dna Ternary Complex 3

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 3:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 3, PDB code: 5yut 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)	54.89 / 2.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.750, 56.930, 110.210, 90.00, 95.12, 90.00
R / Rfree (%)	18.8 / 23.8

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 3 (pdb code 5yut). 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 3, PDB code: 5yut:
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 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:20.5 occ:1.00 O1A F:TTP900 2.0 29.6 1.0 OD1 F:ASP8 2.0 31.9 1.0 O F:MET9 2.2 22.9 1.0 O2B F:TTP900 2.2 24.1 1.0 O1G F:TTP900 2.3 24.8 1.0 OD2 F:ASP103 2.3 30.1 1.0 CG F:ASP8 3.2 34.4 1.0 PB F:TTP900 3.3 29.9 1.0 PA F:TTP900 3.3 33.9 1.0 CG F:ASP103 3.4 28.6 1.0 MG F:MG902 3.4 51.3 1.0 C F:MET9 3.4 26.5 1.0 PG F:TTP900 3.5 29.5 1.0 O3A F:TTP900 3.6 32.3 1.0 OD2 F:ASP8 3.7 45.3 1.0 O3B F:TTP900 3.8 33.9 1.0 OD1 F:ASP103 3.8 24.9 1.0 N F:MET9 3.9 27.0 1.0 O F:HOH1075 3.9 33.6 1.0 NZ F:LYS157 4.0 27.9 1.0 C5' F:TTP900 4.1 26.6 1.0 O3G F:TTP900 4.1 27.1 1.0 CA F:MET9 4.2 27.7 1.0 O5' F:TTP900 4.2 30.8 1.0 C F:ASP8 4.2 30.2 1.0 O F:HOH1026 4.3 37.6 1.0 CB F:ASP8 4.4 32.3 1.0 O2A F:TTP900 4.5 28.2 1.0 N F:ASP10 4.5 24.2 1.0 O1B F:TTP900 4.6 25.2 1.0 CE F:LYS157 4.6 43.2 1.0 CB F:ASP103 4.6 21.2 1.0 CA F:ASP8 4.6 29.5 1.0 CB F:MET9 4.7 26.4 1.0 N F:CYS11 4.7 19.1 1.0 O2G F:TTP900 4.7 32.7 1.0 O F:ASP8 4.7 31.0 1.0 CA F:ASP10 4.7 24.9 1.0 CB F:PHE12 4.8 18.4 1.0 N F:PHE12 4.8 26.8 1.0 C F:ASP10 5.0 24.3 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 3


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:51.3 occ:1.00 OE1 F:GLU104 1.9 45.3 1.0 OD1 F:ASP103 2.3 24.9 1.0 O3' H:DC873 2.4 38.2 1.0 O1A F:TTP900 2.4 29.6 1.0 O F:HOH1026 2.7 37.6 1.0 CD F:GLU104 3.0 41.4 1.0 CG F:ASP103 3.2 28.6 1.0 OD2 F:ASP8 3.2 45.3 1.0 OD2 F:ASP103 3.3 30.1 1.0 OD1 F:ASP8 3.3 31.9 1.0 PA F:TTP900 3.4 33.9 1.0 MG F:MG901 3.4 20.5 1.0 CG F:ASP8 3.5 34.4 1.0 C3' H:DC873 3.5 32.6 1.0 CG F:GLU104 3.5 38.3 1.0 CB F:GLU104 3.7 27.6 1.0 O5' F:TTP900 3.8 30.8 1.0 O2A F:TTP900 3.8 28.2 1.0 C5' F:TTP900 4.0 26.6 1.0 OE2 F:GLU104 4.1 50.2 1.0 OG F:SER101 4.1 42.2 1.0 C4' H:DC873 4.3 36.1 1.0 O F:HOH1075 4.4 33.6 1.0 C5' H:DC873 4.6 37.2 1.0 CB F:ASP103 4.6 21.2 1.0 C2' H:DC873 4.7 31.9 1.0 C F:ASP103 4.7 32.8 1.0 O F:ASP103 4.7 29.3 1.0 CB F:ASP8 4.8 32.3 1.0 N F:GLU104 4.8 24.8 1.0 O3A F:TTP900 4.8 32.3 1.0 CA F:GLU104 4.9 26.8 1.0 O1G F:TTP900 4.9 24.8 1.0 O2B F:TTP900 4.9 24.1 1.0 O5' H:DC873 5.0 46.7 1.0

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


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:25.6 occ:1.00 O1A A:TTP900 2.1 37.4 1.0 OD1 A:ASP8 2.1 43.6 1.0 O1G A:TTP900 2.2 43.5 1.0 O2B A:TTP900 2.2 34.2 1.0 OD2 A:ASP103 2.3 35.5 1.0 O A:MET9 2.4 27.2 1.0 MG A:MG902 3.1 76.1 1.0 CG A:ASP8 3.1 45.6 1.0 PB A:TTP900 3.2 32.2 1.0 PA A:TTP900 3.3 42.3 1.0 CG A:ASP103 3.4 31.9 1.0 PG A:TTP900 3.4 40.9 1.0 O3A A:TTP900 3.5 37.3 1.0 C A:MET9 3.5 32.8 1.0 OD2 A:ASP8 3.6 51.9 1.0 O A:HOH1062 3.7 42.3 1.0 O3B A:TTP900 3.7 34.7 1.0 OD1 A:ASP103 3.8 29.8 1.0 NZ A:LYS157 4.0 34.8 1.0 N A:MET9 4.0 27.0 1.0 O3G A:TTP900 4.0 38.2 1.0 C5' A:TTP900 4.1 33.2 1.0 O5' A:TTP900 4.2 41.6 1.0 CA A:MET9 4.3 31.0 1.0 O2A A:TTP900 4.4 32.7 1.0 C A:ASP8 4.4 30.6 1.0 CB A:ASP8 4.4 36.5 1.0 O1B A:TTP900 4.5 36.8 1.0 N A:ASP10 4.6 30.5 1.0 O2G A:TTP900 4.6 36.2 1.0 N A:CYS11 4.7 29.3 1.0 CB A:ASP103 4.7 37.8 1.0 CE A:LYS157 4.7 45.3 1.0 CB A:MET9 4.7 35.6 1.0 CA A:ASP10 4.8 26.9 1.0 CA A:ASP8 4.8 26.6 1.0 CB A:PHE12 4.8 31.2 1.0 N A:PHE12 4.9 28.1 1.0 O A:ASP8 5.0 31.3 1.0 O A:HOH1064 5.0 53.5 1.0

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


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 3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:76.1 occ:1.00 OE2 A:GLU104 2.0 53.7 1.0 O1A A:TTP900 2.1 37.4 1.0 OD2 A:ASP8 2.4 51.9 1.0 OD1 A:ASP103 2.4 29.8 1.0 O A:HOH1064 2.9 53.5 1.0 CG A:ASP8 3.1 45.6 1.0 CD A:GLU104 3.1 48.5 1.0 O3' C:DC873 3.1 39.8 1.0 MG A:MG901 3.1 25.6 1.0 CG A:ASP103 3.2 31.9 1.0 OD1 A:ASP8 3.3 43.6 1.0 OD2 A:ASP103 3.3 35.5 1.0 PA A:TTP900 3.4 42.3 1.0 CG A:GLU104 3.7 39.2 1.0 C3' C:DC873 3.7 36.4 1.0 O2A A:TTP900 3.7 32.7 1.0 O A:HOH1062 3.8 42.3 1.0 CB A:GLU104 3.8 35.7 1.0 O5' A:TTP900 4.1 41.6 1.0 OE1 A:GLU104 4.1 50.0 1.0 C5' A:TTP900 4.2 33.2 1.0 OG A:SER101 4.3 41.3 1.0 CB A:ASP8 4.4 36.5 1.0 O1G A:TTP900 4.5 43.5 1.0 O A:ASP103 4.7 41.3 1.0 CB A:ASP103 4.7 37.8 1.0 C A:ASP103 4.7 38.8 1.0 C4' C:DC873 4.7 39.2 1.0 O3A A:TTP900 4.7 37.3 1.0 O2B A:TTP900 4.8 34.2 1.0 O5' C:DC873 4.8 55.4 1.0 N A:GLU104 4.8 36.2 1.0 C2' C:DC873 4.9 32.8 1.0 CA A:ASP8 4.9 26.6 1.0 CA A:GLU104 4.9 36.1 1.0 C5' C:DC873 4.9 42.2 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