Magnesium in PDB 5yye: Dna Polymerase IV - Ternary Complex 16

All present enzymatic activity of Dna Polymerase IV - Ternary Complex 16:
2.7.7.7;

The structure of Dna Polymerase IV - Ternary Complex 16, PDB code: 5yye 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)	65.24 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.300, 56.950, 110.710, 90.00, 94.79, 90.00
R / Rfree (%)	20 / 25.5

The binding sites of Magnesium atom in the Dna Polymerase IV - Ternary Complex 16 (pdb code 5yye). 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 - Ternary Complex 16, PDB code: 5yye:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Dna Polymerase IV - Ternary Complex 16


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 - Ternary Complex 16 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:52.8 occ:1.00 O2B F:TTW900 2.1 47.8 1.0 O2A F:TTW900 2.1 43.3 1.0 O F:MET9 2.2 55.1 1.0 OD2 F:ASP103 2.2 55.1 1.0 OD1 F:ASP8 2.2 54.0 1.0 O2G F:TTW900 2.2 68.2 1.0 PB F:TTW900 3.2 48.5 1.0 PA F:TTW900 3.3 48.4 1.0 CG F:ASP103 3.3 49.8 1.0 C F:MET9 3.3 51.9 1.0 CG F:ASP8 3.4 54.2 1.0 O3A F:TTW900 3.4 47.0 1.0 PG F:TTW900 3.4 61.3 1.0 MG F:MG902 3.7 58.3 1.0 OD1 F:ASP103 3.8 49.3 1.0 N3B F:TTW900 3.8 55.7 1.0 C5' F:TTW900 3.8 43.0 1.0 N F:MET9 3.9 42.1 1.0 NZ F:LYS157 3.9 47.6 1.0 OD2 F:ASP8 4.0 53.1 1.0 O F:HOH1016 4.0 56.6 1.0 O1G F:TTW900 4.0 58.7 1.0 CA F:MET9 4.1 52.5 1.0 O5' F:TTW900 4.1 52.1 1.0 C F:ASP8 4.3 46.2 1.0 N F:ASP10 4.4 44.1 1.0 O1B F:TTW900 4.4 57.7 1.0 N F:CYS11 4.4 40.0 1.0 CB F:MET9 4.5 36.4 1.0 N F:PHE12 4.5 49.0 1.0 O1A F:TTW900 4.5 48.3 1.0 CB F:ASP103 4.5 44.1 1.0 O3G F:TTW900 4.6 60.3 1.0 CB F:PHE12 4.6 49.0 1.0 CB F:ASP8 4.6 47.7 1.0 CA F:ASP10 4.6 43.0 1.0 O F:HOH1024 4.7 53.7 1.0 C F:ASP10 4.7 41.1 1.0 CE F:LYS157 4.8 52.7 1.0 CA F:ASP8 4.8 47.8 1.0 O F:ASP8 4.9 46.8 1.0

Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Ternary Complex 16


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 - Ternary Complex 16 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:58.3 occ:1.00 OE1 F:GLU104 1.9 53.9 1.0 OD1 F:ASP103 2.3 49.3 1.0 O3' H:DC873 2.3 49.0 1.0 O2A F:TTW900 2.4 43.3 1.0 O F:HOH1024 2.7 53.7 1.0 OD2 F:ASP8 2.9 53.1 1.0 CD F:GLU104 3.0 49.5 1.0 CG F:ASP103 3.2 49.8 1.0 OD2 F:ASP103 3.4 55.1 1.0 PA F:TTW900 3.4 48.4 1.0 C3' H:DC873 3.4 41.6 1.0 OD1 F:ASP8 3.4 54.0 1.0 CG F:ASP8 3.4 54.2 1.0 CG F:GLU104 3.5 44.4 1.0 MG F:MG901 3.7 52.8 1.0 O1A F:TTW900 3.7 48.3 1.0 CB F:GLU104 3.7 39.1 1.0 O5' F:TTW900 3.8 52.1 1.0 C5' F:TTW900 4.0 43.0 1.0 OE2 F:GLU104 4.0 51.8 1.0 OG F:SER101 4.1 65.6 1.0 C4' H:DC873 4.1 55.9 1.0 C5' H:DC873 4.3 63.6 1.0 O F:HOH1016 4.5 56.6 1.0 CB F:ASP103 4.6 44.1 1.0 C2' H:DC873 4.6 47.8 1.0 C F:ASP103 4.7 54.3 1.0 O F:ASP103 4.7 47.7 1.0 CB F:ASP8 4.7 47.7 1.0 N F:GLU104 4.8 34.0 1.0 O3A F:TTW900 4.9 47.0 1.0 O5' H:DC873 4.9 60.4 1.0 CA F:GLU104 4.9 46.8 1.0 O2G F:TTW900 4.9 68.2 1.0 OP1 H:DC873 5.0 77.4 1.0

Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Ternary Complex 16


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 - Ternary Complex 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:57.0 occ:1.00 O2A A:TTW900 1.9 59.4 1.0 OD1 A:ASP8 2.0 71.4 1.0 O2G A:TTW900 2.2 78.3 1.0 O A:MET9 2.2 51.6 1.0 O2B A:TTW900 2.3 54.4 1.0 OD2 A:ASP103 2.3 67.0 1.0 MG A:MG902 2.9 1.0 1.0 CG A:ASP8 3.2 71.8 1.0 PA A:TTW900 3.2 60.8 1.0 PB A:TTW900 3.3 59.2 1.0 C A:MET9 3.4 56.9 1.0 PG A:TTW900 3.4 71.7 1.0 CG A:ASP103 3.4 67.7 1.0 O3A A:TTW900 3.6 56.3 1.0 OD2 A:ASP8 3.7 80.8 1.0 N A:MET9 3.8 59.5 1.0 N3B A:TTW900 3.8 58.9 1.0 O1G A:TTW900 3.9 68.1 1.0 OD1 A:ASP103 3.9 64.7 1.0 NZ A:LYS157 3.9 52.6 1.0 C5' A:TTW900 3.9 66.8 1.0 O5' A:TTW900 4.1 70.3 1.0 CA A:MET9 4.1 60.5 1.0 C A:ASP8 4.2 63.2 1.0 O1A A:TTW900 4.3 61.6 1.0 CB A:ASP8 4.4 63.1 1.0 N A:ASP10 4.4 60.6 1.0 CE A:LYS157 4.5 57.8 1.0 CB A:MET9 4.5 62.6 1.0 O3G A:TTW900 4.6 82.2 1.0 O1B A:TTW900 4.6 63.4 1.0 N A:CYS11 4.7 62.4 1.0 CA A:ASP8 4.7 63.5 1.0 CB A:ASP103 4.7 74.0 1.0 CA A:ASP10 4.7 56.1 1.0 OE2 A:GLU104 4.7 97.3 1.0 O A:ASP8 4.8 66.0 1.0 N A:PHE12 4.9 60.9 1.0 CB A:PHE12 4.9 64.5 1.0 C A:ASP10 4.9 59.1 1.0

Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Ternary Complex 16


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 - Ternary Complex 16 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:1.0 occ:1.00 OE2 A:GLU104 1.9 97.3 1.0 O2A A:TTW900 2.2 59.4 1.0 OD2 A:ASP8 2.4 80.8 1.0 CG A:GLU104 2.6 83.1 1.0 CD A:GLU104 2.6 91.6 1.0 OD1 A:ASP103 2.7 64.7 1.0 OD1 A:ASP8 2.7 71.4 1.0 CG A:ASP8 2.8 71.8 1.0 MG A:MG901 2.9 57.0 1.0 OD2 A:ASP103 3.0 67.0 1.0 CG A:ASP103 3.2 67.7 1.0 PA A:TTW900 3.4 60.8 1.0 O3' C:DC873 3.4 64.8 1.0 O1A A:TTW900 3.7 61.6 1.0 OE1 A:GLU104 3.8 88.4 1.0 O5' A:TTW900 4.0 70.3 1.0 CB A:GLU104 4.0 70.1 1.0 C3' C:DC873 4.1 60.7 1.0 O2G A:TTW900 4.1 78.3 1.0 CB A:ASP8 4.1 63.1 1.0 C5' A:TTW900 4.3 66.8 1.0 O A:ASP103 4.6 63.1 1.0 CA A:ASP8 4.6 63.5 1.0 C A:ASP103 4.7 66.4 1.0 O2B A:TTW900 4.7 54.4 1.0 CB A:ASP103 4.7 74.0 1.0 OG A:SER101 4.7 64.0 1.0 O3A A:TTW900 4.7 56.3 1.0 O A:MET9 4.7 51.6 1.0 N A:GLU104 4.8 67.5 1.0 CA A:GLU104 4.8 66.9 1.0 N A:MET9 4.8 59.5 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