Magnesium in PDB 5yus: Dna Polymerase IV - Dna Ternary Complex 2

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 2:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 2, PDB code: 5yus 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)	44.72 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.840, 57.120, 110.550, 90.00, 95.00, 90.00
R / Rfree (%)	19 / 22.8

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 2 (pdb code 5yus). 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 2, PDB code: 5yus:
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 2


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:24.4 occ:1.00 OD1 F:ASP8 2.1 41.8 1.0 O1A F:TTP900 2.2 31.0 1.0 O1G F:TTP900 2.3 29.2 1.0 O F:MET9 2.3 32.0 1.0 O2B F:TTP900 2.3 26.9 1.0 OD2 F:ASP103 2.4 32.8 1.0 CG F:ASP8 3.2 39.5 1.0 PA F:TTP900 3.4 30.8 1.0 PB F:TTP900 3.4 40.9 1.0 PG F:TTP900 3.5 33.9 1.0 CG F:ASP103 3.5 30.2 1.0 C F:MET9 3.5 30.6 1.0 MG F:MG902 3.6 58.2 1.0 O3A F:TTP900 3.7 36.2 1.0 OD2 F:ASP8 3.8 47.5 1.0 O3B F:TTP900 3.8 36.4 1.0 N F:MET9 3.9 27.6 1.0 OD1 F:ASP103 4.0 34.3 1.0 O F:HOH1028 4.0 37.6 1.0 O F:HOH1171 4.0 32.8 1.0 O F:HOH1140 4.0 35.5 1.0 O3G F:TTP900 4.1 37.5 1.0 C5' F:TTP900 4.2 28.4 1.0 CA F:MET9 4.2 28.6 1.0 O5' F:TTP900 4.2 31.9 1.0 C F:ASP8 4.3 26.6 1.0 CB F:ASP8 4.4 37.3 1.0 O2A F:TTP900 4.5 27.7 1.0 N F:ASP10 4.6 27.3 1.0 O2G F:TTP900 4.6 30.6 1.0 N F:CYS11 4.6 26.5 1.0 O1B F:TTP900 4.7 34.0 1.0 CA F:ASP8 4.7 32.9 1.0 CB F:ASP103 4.7 27.7 1.0 CB F:MET9 4.7 30.4 1.0 O F:ASP8 4.7 30.3 1.0 CA F:ASP10 4.8 23.8 1.0 N F:PHE12 4.8 29.9 1.0 CB F:PHE12 4.8 30.0 1.0 C F:ASP10 4.9 29.4 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:58.2 occ:1.00 OE1 F:GLU104 1.9 54.9 1.0 OD1 F:ASP103 2.4 34.3 1.0 O F:HOH1028 2.6 37.6 1.0 O1A F:TTP900 2.6 31.0 1.0 O3' H:DC873 2.9 43.3 1.0 CD F:GLU104 3.0 58.3 1.0 CG F:ASP103 3.3 30.2 1.0 OD2 F:ASP8 3.4 47.5 1.0 OD1 F:ASP8 3.4 41.8 1.0 OD2 F:ASP103 3.4 32.8 1.0 C3' H:DC873 3.4 37.6 1.0 CG F:GLU104 3.5 48.1 1.0 CB F:GLU104 3.6 30.4 1.0 CG F:ASP8 3.6 39.5 1.0 MG F:MG901 3.6 24.4 1.0 PA F:TTP900 3.7 30.8 1.0 OG F:SER101 3.9 38.8 1.0 C5' F:TTP900 4.0 28.4 1.0 O5' F:TTP900 4.0 31.9 1.0 OE2 F:GLU104 4.0 72.3 1.0 O2A F:TTP900 4.1 27.7 1.0 C4' H:DC873 4.5 36.5 1.0 C2' H:DC873 4.6 36.5 1.0 C F:ASP103 4.6 32.8 1.0 O F:ASP103 4.7 30.1 1.0 C5' H:DC873 4.7 36.9 1.0 O F:HOH1140 4.7 35.5 1.0 N F:GLU104 4.7 26.2 1.0 CB F:ASP103 4.7 27.7 1.0 CA F:GLU104 4.8 25.2 1.0 O5' H:DC873 4.8 44.1 1.0 O F:HOH1150 4.9 39.1 1.0 CB F:ASP8 4.9 37.3 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:32.6 occ:1.00 O1A A:TTP900 2.2 29.9 1.0 OD1 A:ASP8 2.2 58.0 1.0 O2B A:TTP900 2.3 35.5 1.0 O A:MET9 2.3 33.5 1.0 OD2 A:ASP103 2.3 35.2 1.0 O1G A:TTP900 2.4 43.8 1.0 CG A:ASP8 3.1 55.5 1.0 MG A:MG902 3.2 78.4 1.0 PB A:TTP900 3.3 31.6 1.0 PA A:TTP900 3.4 35.1 1.0 OD2 A:ASP8 3.4 65.9 1.0 CG A:ASP103 3.4 34.2 1.0 C A:MET9 3.5 31.4 1.0 PG A:TTP900 3.6 35.1 1.0 O3A A:TTP900 3.7 33.5 1.0 OD1 A:ASP103 3.8 37.2 1.0 O3B A:TTP900 3.9 31.0 1.0 N A:MET9 3.9 36.7 1.0 O A:HOH1035 3.9 39.5 1.0 NZ A:LYS157 4.1 36.8 1.0 O3G A:TTP900 4.1 32.3 1.0 C5' A:TTP900 4.1 29.4 1.0 CA A:MET9 4.2 37.1 1.0 O A:HOH1017 4.2 56.5 1.0 O5' A:TTP900 4.3 34.1 1.0 C A:ASP8 4.3 37.7 1.0 CB A:ASP8 4.4 45.9 1.0 N A:ASP10 4.5 36.6 1.0 O2A A:TTP900 4.5 35.6 1.0 O1B A:TTP900 4.6 30.2 1.0 N A:CYS11 4.7 37.4 1.0 CB A:MET9 4.7 37.7 1.0 CB A:ASP103 4.7 39.8 1.0 CA A:ASP10 4.7 31.7 1.0 CA A:ASP8 4.7 36.9 1.0 CB A:PHE12 4.8 33.5 1.0 O2G A:TTP900 4.8 34.7 1.0 N A:PHE12 4.8 38.4 1.0 O A:ASP8 4.9 33.3 1.0 CE A:LYS157 4.9 48.8 1.0 OE2 A:GLU104 4.9 69.1 1.0 C A:ASP10 4.9 30.4 1.0

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


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 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:78.4 occ:1.00 OE2 A:GLU104 1.9 69.1 1.0 OD1 A:ASP103 2.1 37.2 1.0 O1A A:TTP900 2.5 29.9 1.0 OD2 A:ASP8 2.6 65.9 1.0 O A:HOH1017 2.7 56.5 1.0 CD A:GLU104 2.9 61.0 1.0 CG A:ASP103 2.9 34.2 1.0 OD2 A:ASP103 3.0 35.2 1.0 O3' C:DC873 3.0 36.4 1.0 MG A:MG901 3.2 32.6 1.0 CG A:GLU104 3.3 55.0 1.0 CG A:ASP8 3.4 55.5 1.0 CB A:GLU104 3.6 46.8 1.0 PA A:TTP900 3.7 35.1 1.0 OD1 A:ASP8 3.7 58.0 1.0 C3' C:DC873 3.8 32.0 1.0 OE1 A:GLU104 4.0 60.1 1.0 OG A:SER101 4.0 38.8 1.0 C5' A:TTP900 4.1 29.4 1.0 O5' A:TTP900 4.1 34.1 1.0 O2A A:TTP900 4.2 35.6 1.0 O A:ASP103 4.3 40.1 1.0 C A:ASP103 4.3 39.0 1.0 CB A:ASP103 4.4 39.8 1.0 N A:GLU104 4.5 36.7 1.0 CB A:ASP8 4.5 45.9 1.0 O A:HOH1035 4.6 39.5 1.0 CA A:GLU104 4.6 37.8 1.0 C4' C:DC873 4.8 38.4 1.0 O2B A:TTP900 4.8 35.5 1.0 O1G A:TTP900 4.8 43.8 1.0 CA A:ASP103 4.9 41.5 1.0 CA A:ASP8 4.9 36.9 1.0 NZ A:LYS150 4.9 67.9 1.0 C2' C:DC873 4.9 27.2 1.0 O5' C:DC873 4.9 50.9 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