Magnesium in PDB 5yuu: Dna Polymerase IV - Dna Ternary Complex 4

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 4:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex 4, PDB code: 5yuu 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)	70.55 / 1.89
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.309, 57.022, 110.198, 90.00, 94.63, 90.00
R / Rfree (%)	19.5 / 23.9

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 4 (pdb code 5yuu). 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 4, PDB code: 5yuu:
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 4


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:29.6 occ:1.00 O1B F:TTP900 1.8 38.5 0.3 O1A F:TTP900 2.0 31.6 0.7 OD1 F:ASP8 2.2 39.1 0.5 O3G F:TTP900 2.2 43.1 0.3 OD2 F:ASP103 2.2 36.7 1.0 O F:MET9 2.3 39.8 1.0 O1A F:TTP900 2.3 37.8 0.3 O3G F:TTP900 2.4 40.7 0.7 OD1 F:ASP8 2.4 29.8 0.5 O1B F:TTP900 2.4 31.6 0.7 PB F:TTP900 3.0 36.4 0.3 CG F:ASP8 3.1 38.2 0.5 PA F:TTP900 3.2 39.8 0.7 MG F:MG902 3.2 45.4 1.0 CG F:ASP8 3.3 38.7 0.5 PB F:TTP900 3.3 35.0 0.7 OD2 F:ASP8 3.3 38.7 0.5 CG F:ASP103 3.4 37.3 1.0 PG F:TTP900 3.4 39.1 0.3 C F:MET9 3.5 30.9 1.0 PA F:TTP900 3.5 33.7 0.3 O3A F:TTP900 3.5 35.0 0.7 PG F:TTP900 3.6 40.7 0.7 O3A F:TTP900 3.6 37.6 0.3 O3B F:TTP900 3.6 36.4 0.3 OD2 F:ASP8 3.7 35.2 0.5 OD1 F:ASP103 3.8 37.0 1.0 N F:MET9 3.9 33.7 1.0 O3B F:TTP900 3.9 38.5 0.7 O F:HOH1039 3.9 50.4 1.0 O1G F:TTP900 4.1 36.4 0.3 C5' F:TTP900 4.1 31.9 0.7 NZ F:LYS157 4.1 33.7 1.0 O5' F:TTP900 4.2 33.3 0.7 CA F:MET9 4.2 37.7 1.0 C5' F:TTP900 4.2 32.5 0.3 O1G F:TTP900 4.2 42.8 0.7 O2B F:TTP900 4.2 35.0 0.3 C F:ASP8 4.3 31.3 1.0 O3' H:DC873 4.3 35.2 0.3 O5' F:TTP900 4.3 34.9 0.3 O2A F:TTP900 4.4 32.1 0.7 CB F:ASP8 4.4 36.2 0.5 CB F:ASP8 4.5 34.4 0.5 N F:ASP10 4.5 34.5 1.0 O2G F:TTP900 4.6 43.8 0.3 CB F:ASP103 4.6 29.8 1.0 O2A F:TTP900 4.6 35.5 0.3 O2B F:TTP900 4.6 35.0 0.7 O F:HOH1086 4.6 48.2 1.0 CB F:MET9 4.7 33.7 1.0 N F:CYS11 4.7 31.0 1.0 O F:ASP8 4.7 33.5 1.0 CA F:ASP8 4.7 34.2 1.0 O2G F:TTP900 4.7 46.7 0.7 CA F:ASP10 4.8 33.4 1.0 CB F:PHE12 4.8 35.1 1.0 N F:PHE12 4.8 34.3 1.0 O F:ASP103 4.9 31.3 1.0 C F:ASP10 5.0 37.0 1.0

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:45.4 occ:1.00 OE1 F:GLU104 2.0 50.9 1.0 O1A F:TTP900 2.1 37.8 0.3 OD1 F:ASP103 2.2 37.0 1.0 OD2 F:ASP8 2.3 38.7 0.5 O1A F:TTP900 2.3 31.6 0.7 O3' H:DC873 2.6 43.0 0.7 OD1 F:ASP8 2.7 29.8 0.5 O3' H:DC873 2.7 35.2 0.3 CG F:ASP103 3.0 37.3 1.0 CD F:GLU104 3.1 45.1 1.0 O F:HOH1086 3.1 48.2 1.0 OD2 F:ASP103 3.1 36.7 1.0 CG F:ASP8 3.2 38.2 0.5 MG F:MG901 3.2 29.6 1.0 CG F:ASP8 3.3 38.7 0.5 PA F:TTP900 3.3 33.7 0.3 PA F:TTP900 3.5 39.8 0.7 OD2 F:ASP8 3.5 35.2 0.5 CG F:GLU104 3.5 40.9 1.0 CB F:GLU104 3.6 35.4 1.0 OD1 F:ASP8 3.6 39.1 0.5 C4' H:DC873 3.8 42.0 0.3 C3' H:DC873 3.8 39.5 0.3 C3' H:DC873 3.9 38.7 0.7 O2A F:TTP900 3.9 32.1 0.7 O2A F:TTP900 3.9 35.5 0.3 OG F:SER101 4.0 49.4 1.0 O5' F:TTP900 4.0 33.3 0.7 C5' F:TTP900 4.0 31.9 0.7 O5' F:TTP900 4.1 34.9 0.3 C5' H:DC873 4.1 41.3 0.3 OE2 F:GLU104 4.1 49.3 1.0 C5' F:TTP900 4.2 32.5 0.3 O1B F:TTP900 4.4 38.5 0.3 O F:ASP103 4.4 31.3 1.0 C F:ASP103 4.5 41.1 1.0 CB F:ASP8 4.5 36.2 0.5 O F:HOH1039 4.5 50.4 1.0 CB F:ASP103 4.5 29.8 1.0 CB F:ASP8 4.6 34.4 0.5 N F:GLU104 4.6 33.8 1.0 C4' H:DC873 4.6 41.4 0.7 O3A F:TTP900 4.7 37.6 0.3 CA F:GLU104 4.7 30.6 1.0 O3G F:TTP900 4.7 43.1 0.3 C2' H:DC873 4.8 41.8 0.3 C5' H:DC873 4.8 36.7 0.7 O3G F:TTP900 4.9 40.7 0.7 O3A F:TTP900 4.9 35.0 0.7 CA F:ASP8 4.9 34.2 1.0 CA F:ASP103 5.0 37.2 1.0

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:34.8 occ:1.00 OD1 A:ASP8 2.1 56.2 0.4 O2A A:TTP900 2.1 62.5 1.0 O2B A:TTP900 2.2 42.3 1.0 OD2 A:ASP103 2.3 43.7 1.0 O2G A:TTP900 2.3 52.5 1.0 O A:MET9 2.3 39.9 1.0 OD2 A:ASP8 2.3 60.2 0.6 OD1 A:ASP8 2.4 63.4 0.6 CG A:ASP8 2.7 58.4 0.6 CG A:ASP8 2.9 58.5 0.4 OD2 A:ASP8 3.0 63.2 0.4 O A:HOH1001 3.3 64.9 1.0 MG A:MG902 3.3 95.8 1.0 PB A:TTP900 3.3 41.4 1.0 PA A:TTP900 3.3 50.6 1.0 CG A:ASP103 3.4 44.9 1.0 PG A:TTP900 3.5 48.1 1.0 C A:MET9 3.5 38.5 1.0 O3A A:TTP900 3.6 46.7 1.0 OD1 A:ASP103 3.8 43.1 1.0 O A:HOH1060 3.8 60.5 1.0 O3B A:TTP900 3.8 38.3 1.0 O3G A:TTP900 3.9 46.0 1.0 N A:MET9 3.9 44.1 1.0 NZ A:LYS157 4.1 42.4 1.0 CB A:ASP8 4.1 53.9 0.6 C5' A:TTP900 4.2 40.1 1.0 CA A:MET9 4.2 45.5 1.0 C A:ASP8 4.2 43.7 1.0 CB A:ASP8 4.2 53.7 0.4 O5' A:TTP900 4.3 46.8 1.0 O1A A:TTP900 4.5 46.9 1.0 N A:ASP10 4.5 42.3 1.0 CA A:ASP8 4.6 46.1 1.0 O1B A:TTP900 4.7 44.5 1.0 CB A:ASP103 4.7 47.5 1.0 CB A:MET9 4.7 47.2 1.0 O A:ASP8 4.7 45.0 1.0 O1G A:TTP900 4.7 49.6 1.0 CA A:ASP10 4.8 38.5 1.0 N A:CYS11 4.8 44.3 1.0 OE2 A:GLU104 4.8 81.8 1.0 CE A:LYS157 4.8 57.4 1.0 CB A:PHE12 4.8 46.0 1.0 N A:PHE12 4.9 43.5 1.0

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


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 4 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:95.8 occ:1.00 O A:HOH1001 1.3 64.9 1.0 OD1 A:ASP8 2.0 63.4 0.6 OE2 A:GLU104 2.0 81.8 1.0 CG A:GLU104 2.0 69.3 1.0 OD1 A:ASP103 2.2 43.1 1.0 CD A:GLU104 2.3 71.0 1.0 OD1 A:ASP8 2.3 56.2 0.4 O2A A:TTP900 2.6 62.5 1.0 CG A:ASP103 3.0 44.9 1.0 O3' C:DC873 3.1 56.1 1.0 OD2 A:ASP103 3.1 43.7 1.0 CG A:ASP8 3.2 58.4 0.6 CG A:ASP8 3.3 58.5 0.4 MG A:MG901 3.3 34.8 1.0 CB A:GLU104 3.4 48.8 1.0 OE1 A:GLU104 3.5 63.6 1.0 PA A:TTP900 3.9 50.6 1.0 OG A:SER101 3.9 53.4 1.0 C3' C:DC873 4.0 50.5 1.0 CB A:ASP8 4.0 53.9 0.6 OD2 A:ASP8 4.1 63.2 0.4 OD2 A:ASP8 4.1 60.2 0.6 CB A:ASP8 4.1 53.7 0.4 O A:ASP103 4.1 43.0 1.0 C A:ASP103 4.2 46.6 1.0 CA A:GLU104 4.2 41.4 1.0 N A:GLU104 4.3 40.8 1.0 O1A A:TTP900 4.4 46.9 1.0 CB A:ASP103 4.4 47.5 1.0 C5' A:TTP900 4.4 40.1 1.0 O5' A:TTP900 4.5 46.8 1.0 CA A:ASP8 4.5 46.1 1.0 O A:HOH1060 4.5 60.5 1.0 C4' C:DC873 4.8 48.6 1.0 CA A:ASP103 4.8 49.3 1.0 O2G A:TTP900 4.9 52.5 1.0 N A:MET9 5.0 44.1 1.0 C5' C:DC873 5.0 52.4 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