Magnesium in PDB 5zlv: Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2:
2.7.7.7;

The structure of Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2, PDB code: 5zlv 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)	50.78 / 2.35
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	86.310, 57.240, 110.390, 90.00, 94.74, 90.00
R / Rfree (%)	18.8 / 24.9

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2 (pdb code 5zlv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2, PDB code: 5zlv:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2


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 with 50MM MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg901 b:19.6 occ:1.00 OP1 H:DT874 2.1 24.1 1.0 OD1 F:ASP8 2.1 38.0 1.0 OD2 F:ASP103 2.3 31.5 1.0 O F:MET9 2.4 22.1 1.0 O1 F:PO4903 2.6 32.6 1.0 O2 F:PO4904 2.6 63.4 1.0 CG F:ASP8 3.2 41.7 1.0 CG F:ASP103 3.4 28.5 1.0 MG F:MG902 3.5 37.6 1.0 P H:DT874 3.5 26.5 1.0 C F:MET9 3.5 25.6 1.0 O4 F:PO4903 3.6 40.9 1.0 P F:PO4903 3.7 48.9 1.0 OD2 F:ASP8 3.7 51.3 1.0 P F:PO4904 3.8 61.9 1.0 OD1 F:ASP103 3.8 28.6 1.0 O4 F:PO4904 3.9 50.1 1.0 N F:MET9 3.9 27.2 1.0 O F:HOH1048 4.0 57.6 1.0 C5' H:DT874 4.0 17.7 1.0 O5' H:DT874 4.0 25.4 1.0 CA F:MET9 4.2 25.1 1.0 C F:ASP8 4.4 27.0 1.0 O3' H:DC873 4.5 27.1 1.0 CB F:ASP8 4.5 33.5 1.0 OP2 H:DT874 4.6 30.1 1.0 N F:ASP10 4.6 20.0 1.0 O2 F:PO4903 4.6 65.9 1.0 NZ F:LYS157 4.6 39.8 1.0 O F:HOH1003 4.7 42.7 1.0 CB F:MET9 4.7 18.4 1.0 N F:CYS11 4.7 20.8 1.0 CB F:ASP103 4.7 20.1 1.0 O3 F:PO4904 4.7 57.4 1.0 CA F:ASP8 4.7 30.4 1.0 O3 F:PO4903 4.8 50.5 1.0 N F:PHE12 4.8 20.1 1.0 CB F:PHE12 4.8 19.6 1.0 CA F:ASP10 4.9 24.3 1.0 O1 F:PO4904 4.9 76.9 1.0 O F:ASP8 5.0 32.5 1.0

Magnesium binding site 2 out of 5 in the Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2


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 with 50MM MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg902 b:37.6 occ:1.00 OE1 F:GLU104 2.1 42.7 1.0 O3' H:DC873 2.3 27.1 1.0 OD1 F:ASP103 2.4 28.6 1.0 OP1 H:DT874 2.4 24.1 1.0 P H:DT874 2.9 26.5 1.0 O F:HOH1003 2.9 42.7 1.0 CD F:GLU104 3.1 28.6 1.0 OD1 F:ASP8 3.3 38.0 1.0 CG F:ASP103 3.3 28.5 1.0 OD2 F:ASP103 3.4 31.5 1.0 CG F:GLU104 3.4 24.5 1.0 OD2 F:ASP8 3.5 51.3 1.0 MG F:MG901 3.5 19.6 1.0 C3' H:DC873 3.5 22.6 1.0 CG F:ASP8 3.6 41.7 1.0 CB F:GLU104 3.7 15.4 1.0 C4' H:DC873 3.8 17.1 1.0 OP2 H:DT874 4.0 30.1 1.0 C5' H:DC873 4.0 24.2 1.0 OG F:SER101 4.1 35.4 1.0 O5' H:DT874 4.1 25.4 1.0 C5' H:DT874 4.2 17.7 1.0 OE2 F:GLU104 4.2 30.0 1.0 O F:HOH1048 4.4 57.6 1.0 O F:HOH1049 4.5 33.8 1.0 C2' H:DC873 4.6 26.9 1.0 N F:GLU104 4.6 15.9 1.0 C F:ASP103 4.6 29.6 1.0 O F:ASP103 4.7 30.3 1.0 CB F:ASP103 4.7 20.1 1.0 CA F:GLU104 4.7 21.6 1.0 CB F:ASP8 4.9 33.5 1.0 O5' H:DC873 4.9 23.7 1.0

Magnesium binding site 3 out of 5 in the Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2


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 with 50MM MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:29.5 occ:1.00 O A:HOH1006 1.9 38.3 1.0 OP1 C:DT874 2.0 29.5 1.0 OD2 A:ASP103 2.3 33.1 1.0 O2 A:DPO903 2.4 38.4 1.0 OD1 A:ASP8 2.4 37.6 1.0 O A:MET9 2.5 27.4 1.0 O7 A:DPO903 2.9 68.8 1.0 MG A:MG902 3.2 49.1 1.0 CG A:ASP103 3.3 39.6 1.0 CG A:ASP8 3.3 43.4 1.0 P C:DT874 3.5 39.2 1.0 P1 A:DPO903 3.6 44.2 1.0 OD1 A:ASP103 3.6 39.2 1.0 C A:MET9 3.7 30.2 1.0 OD2 A:ASP8 3.8 53.7 1.0 P2 A:DPO903 3.9 65.2 1.0 O1 A:DPO903 3.9 41.5 1.0 C5' C:DT874 4.0 31.4 1.0 O5' C:DT874 4.0 33.7 1.0 O5 A:DPO903 4.0 60.7 1.0 N A:MET9 4.0 27.7 1.0 NZ A:LYS157 4.1 37.5 1.0 O4 A:DPO903 4.1 56.6 1.0 CA A:MET9 4.3 30.5 1.0 O3' C:DC873 4.3 41.6 1.0 C A:ASP8 4.4 35.2 1.0 OP2 C:DT874 4.5 33.1 1.0 CB A:ASP8 4.5 38.0 1.0 CB A:ASP103 4.7 35.9 1.0 CB A:MET9 4.7 32.7 1.0 N A:ASP10 4.7 25.8 1.0 CA A:ASP8 4.8 30.5 1.0 O3 A:DPO903 4.8 43.9 1.0 CB A:PHE12 4.9 27.6 1.0 CE A:LYS157 4.9 42.6 1.0 O A:ASP103 4.9 39.6 1.0 N A:CYS11 4.9 29.1 1.0 O A:ASP8 4.9 40.1 1.0 OE2 A:GLU104 5.0 49.8 1.0

Magnesium binding site 4 out of 5 in the Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2


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 with 50MM MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:49.1 occ:1.00 OE2 A:GLU104 2.0 49.8 1.0 OD1 A:ASP103 2.3 39.2 1.0 OP1 C:DT874 2.5 29.5 1.0 O3' C:DC873 2.7 41.6 1.0 OD1 A:ASP8 2.7 37.6 1.0 CD A:GLU104 2.9 47.1 1.0 P C:DT874 3.2 39.2 1.0 MG A:MG901 3.2 29.5 1.0 CG A:ASP103 3.2 39.6 1.0 CG A:GLU104 3.3 40.2 1.0 OD2 A:ASP103 3.4 33.1 1.0 CG A:ASP8 3.4 43.4 1.0 CB A:GLU104 3.5 31.9 1.0 OD2 A:ASP8 3.5 53.7 1.0 C3' C:DC873 3.9 34.4 1.0 C4' C:DC873 4.1 38.3 1.0 OE1 A:GLU104 4.1 41.1 1.0 OG A:SER101 4.1 46.8 1.0 C5' C:DC873 4.2 33.1 1.0 O A:HOH1006 4.2 38.3 1.0 OP2 C:DT874 4.2 33.1 1.0 O5' C:DT874 4.3 33.7 1.0 C5' C:DT874 4.3 31.4 1.0 O A:ASP103 4.4 39.6 1.0 C A:ASP103 4.4 40.3 1.0 N A:GLU104 4.5 30.4 1.0 CB A:ASP103 4.6 35.9 1.0 CA A:GLU104 4.6 31.8 1.0 CB A:ASP8 4.7 38.0 1.0 C2' C:DC873 4.9 33.0 1.0 O A:HOH1073 4.9 35.2 1.0 O2 A:DPO903 5.0 38.4 1.0

Magnesium binding site 5 out of 5 in the Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dna Polymerase IV - Dna Ternary Complex with 50MM MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ H:Mg901 b:54.6 occ:1.00 OP2 H:DT874 1.9 30.1 1.0 O4 F:PO4903 2.7 40.9 1.0 P H:DT874 3.2 26.5 1.0 C7 H:DT874 3.5 17.6 1.0 OP1 H:DT874 3.7 24.1 1.0 O F:HOH1048 3.7 57.6 1.0 O F:HOH1129 3.8 47.6 1.0 O5' H:DT874 3.9 25.4 1.0 O3 F:PO4904 4.0 57.4 1.0 P F:PO4903 4.2 48.9 1.0 O3' H:DC873 4.4 27.1 1.0 O2 F:PO4904 4.4 63.4 1.0 C5 H:DT874 4.7 17.3 1.0 C3' H:DC873 4.7 22.6 1.0 O2 F:PO4903 4.8 65.9 1.0 C6 H:DT874 4.8 24.3 1.0 O3 F:PO4903 4.9 50.5 1.0 OG F:SER55 4.9 24.9 1.0 P F:PO4904 4.9 61.9 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