Magnesium in PDB 6ig1: Dna Polymerase IV - Dna Ternary Complex 10

Enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 10

All present enzymatic activity of Dna Polymerase IV - Dna Ternary Complex 10:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase IV - Dna Ternary Complex 10, PDB code: 6ig1 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) 44.86 / 1.97
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 86.380, 57.160, 110.580, 90.00, 94.49, 90.00
R / Rfree (%) 20.1 / 24.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase IV - Dna Ternary Complex 10 (pdb code 6ig1). 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 10, PDB code: 6ig1:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6ig1

Go back to Magnesium Binding Sites List in 6ig1
Magnesium binding site 1 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 10


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 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg901

b:22.1
occ:1.00
O1A H:TTP901 2.1 30.4 0.3
OP1 H:DT874 2.1 30.9 0.7
O1B H:TTP901 2.2 32.5 0.3
OD1 F:ASP8 2.2 30.8 0.4
O1 F:DPO903 2.3 22.1 0.7
OD2 F:ASP103 2.3 31.1 1.0
O F:MET9 2.3 29.8 1.0
OD1 F:ASP8 2.4 26.4 0.6
O7 F:DPO903 2.4 43.7 0.7
O3G H:TTP901 2.5 43.6 0.3
PB H:TTP901 3.1 34.8 0.3
O3A H:TTP901 3.2 36.2 0.3
MG F:MG902 3.2 46.2 1.0
CG F:ASP8 3.3 32.4 0.4
CG F:ASP8 3.3 33.0 0.6
P1 F:DPO903 3.4 32.5 0.7
CG F:ASP103 3.4 29.3 1.0
C F:MET9 3.5 31.7 1.0
P H:DT874 3.6 31.4 0.7
PA H:TTP901 3.6 30.2 0.3
O2 F:DPO903 3.6 37.7 0.7
OD2 F:ASP8 3.6 35.3 0.4
PG H:TTP901 3.6 43.2 0.3
P2 F:DPO903 3.7 42.2 0.7
OD2 F:ASP8 3.7 39.0 0.6
OD1 F:ASP103 3.8 28.4 1.0
O3B H:TTP901 3.8 39.0 0.3
O4 F:DPO903 3.9 49.5 0.7
N F:MET9 4.0 27.0 1.0
O5' H:DT874 4.0 28.6 0.7
C5' H:TTP901 4.1 25.6 0.3
C5' H:DT874 4.1 24.1 0.7
O1G H:TTP901 4.3 35.8 0.3
O5' H:TTP901 4.3 28.3 0.3
CA F:MET9 4.3 31.6 1.0
O H:HOH1016 4.3 48.8 1.0
NZ F:LYS157 4.3 18.1 0.6
O5 F:DPO903 4.4 38.5 0.7
C F:ASP8 4.4 29.0 1.0
O3' H:DC873 4.4 27.1 0.3
OP2 H:DT874 4.4 22.6 0.7
O2B H:TTP901 4.5 37.9 0.3
O F:HOH1061 4.5 47.0 1.0
CB F:ASP8 4.6 32.0 0.4
N F:ASP10 4.6 28.8 1.0
CB F:ASP8 4.6 31.6 0.6
O3 F:DPO903 4.6 25.5 0.7
O3' H:DC873 4.6 29.8 0.7
N F:CYS11 4.7 26.5 1.0
CB F:ASP103 4.7 22.8 1.0
O2A H:TTP901 4.7 29.7 0.3
CB F:MET9 4.7 25.9 1.0
N F:PHE12 4.7 25.6 1.0
CB F:PHE12 4.8 29.2 1.0
CA F:ASP10 4.8 29.0 1.0
O6 F:DPO903 4.8 47.9 0.7
CA F:ASP8 4.8 27.8 1.0
O2G H:TTP901 4.9 46.8 0.3
O F:ASP8 4.9 27.5 1.0
C F:ASP10 5.0 25.0 1.0

Magnesium binding site 2 out of 4 in 6ig1

Go back to Magnesium Binding Sites List in 6ig1
Magnesium binding site 2 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 10


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 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg902

b:46.2
occ:1.00
OE1 F:GLU104 2.0 58.3 1.0
OP1 H:DT874 2.2 30.9 0.7
O1A H:TTP901 2.3 30.4 0.3
OD1 F:ASP103 2.3 28.4 1.0
OD1 F:ASP8 2.6 26.4 0.6
O3' H:DC873 2.7 29.8 0.7
OD2 F:ASP8 2.7 35.3 0.4
O3' H:DC873 2.8 27.1 0.3
P H:DT874 2.9 31.4 0.7
O F:HOH1061 3.0 47.0 1.0
CD F:GLU104 3.1 37.8 1.0
CG F:ASP103 3.1 29.3 1.0
CG F:ASP8 3.2 33.0 0.6
MG F:MG901 3.2 22.1 1.0
CG F:ASP8 3.3 32.4 0.4
OD2 F:ASP103 3.3 31.1 1.0
OD1 F:ASP8 3.4 30.8 0.4
OD2 F:ASP8 3.4 39.0 0.6
PA H:TTP901 3.5 30.2 0.3
CB F:GLU104 3.5 27.9 1.0
CG F:GLU104 3.6 34.6 1.0
OP2 H:DT874 3.9 22.6 0.7
C3' H:DC873 4.0 30.4 0.3
C3' H:DC873 4.0 29.0 0.7
OG F:SER101 4.0 43.7 1.0
O5' H:DT874 4.0 28.6 0.7
OE2 F:GLU104 4.1 37.5 1.0
C5' H:DT874 4.1 24.1 0.7
C4' H:DC873 4.2 29.1 0.3
C5' H:TTP901 4.2 25.6 0.3
O5' H:TTP901 4.3 28.3 0.3
O F:ASP103 4.4 32.6 1.0
C4' H:DC873 4.4 29.9 0.7
O3A H:TTP901 4.4 36.2 0.3
C F:ASP103 4.4 35.0 1.0
C5' H:DC873 4.5 34.2 0.3
CB F:ASP8 4.5 32.0 0.4
O2A H:TTP901 4.5 29.7 0.3
CB F:ASP8 4.5 31.6 0.6
CB F:ASP103 4.6 22.8 1.0
C5' H:DC873 4.6 32.5 0.7
N F:GLU104 4.6 26.5 1.0
CA F:GLU104 4.7 24.5 1.0
C2' H:DC873 4.7 33.4 0.3
O1B H:TTP901 4.8 32.5 0.3
O H:HOH1016 4.8 48.8 1.0
CA F:ASP8 4.9 27.8 1.0
O3G H:TTP901 4.9 43.6 0.3
O7 F:DPO903 5.0 43.7 0.7
CA F:ASP103 5.0 28.3 1.0

Magnesium binding site 3 out of 4 in 6ig1

Go back to Magnesium Binding Sites List in 6ig1
Magnesium binding site 3 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 10


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 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:28.8
occ:1.00
O2A C:TTP901 2.0 50.4 0.7
OP1 C:DT874 2.1 39.6 0.3
OD1 A:ASP8 2.2 45.8 0.5
O2B C:TTP901 2.3 44.5 0.7
O2G C:TTP901 2.3 59.0 0.7
O A:MET9 2.4 31.7 1.0
OD2 A:ASP103 2.4 33.5 1.0
OD1 A:ASP8 2.4 40.6 0.5
O2 A:DPO903 2.4 43.0 0.3
O7 A:DPO903 2.7 60.7 0.3
CG A:ASP8 3.0 46.2 0.5
PB C:TTP901 3.1 47.4 0.7
O3A C:TTP901 3.1 52.5 0.7
CG A:ASP8 3.2 45.9 0.5
MG A:MG902 3.2 55.9 1.0
OD2 A:ASP8 3.3 47.9 0.5
OD2 A:ASP8 3.4 51.8 0.5
CG A:ASP103 3.4 38.4 1.0
PA C:TTP901 3.5 46.3 0.7
P C:DT874 3.5 44.9 0.3
PG C:TTP901 3.5 61.7 0.7
P1 A:DPO903 3.5 42.6 0.3
C A:MET9 3.5 31.5 1.0
P2 A:DPO903 3.7 60.8 0.3
O3B C:TTP901 3.8 55.2 0.7
OD1 A:ASP103 3.8 36.2 1.0
O3 A:DPO903 3.8 44.5 0.3
O4 A:DPO903 3.9 55.2 0.3
N A:MET9 3.9 39.1 1.0
O3G C:TTP901 4.0 58.7 0.7
O5' C:DT874 4.0 42.3 0.3
C5' C:DT874 4.0 37.3 0.3
C5' C:TTP901 4.1 35.4 0.7
O6 A:DPO903 4.1 58.7 0.3
NZ A:LYS157 4.2 34.7 1.0
O A:HOH1061 4.2 53.9 1.0
CA A:MET9 4.3 34.2 1.0
O5' C:TTP901 4.3 43.1 0.7
O3' C:DC873 4.3 51.1 0.7
C A:ASP8 4.4 41.8 1.0
OP2 C:DT874 4.4 40.5 0.3
CB A:ASP8 4.4 42.5 0.5
CB A:ASP8 4.4 42.4 0.5
O1B C:TTP901 4.5 44.9 0.7
O3' C:DC873 4.5 44.7 0.3
CE A:LYS157 4.5 51.9 1.0
N A:ASP10 4.6 35.4 1.0
O1A C:TTP901 4.6 43.0 0.7
O A:HOH1079 4.6 65.8 1.0
N A:CYS11 4.7 33.4 1.0
CA A:ASP8 4.8 34.6 1.0
O1G C:TTP901 4.8 62.5 0.7
CB A:ASP103 4.8 36.8 1.0
CB A:MET9 4.8 37.5 1.0
N A:PHE12 4.8 34.2 1.0
O1 A:DPO903 4.8 29.9 0.3
CA A:ASP10 4.8 32.9 1.0
CB A:PHE12 4.8 39.0 1.0
O A:ASP8 4.9 38.3 1.0
OE2 A:GLU104 5.0 62.3 1.0

Magnesium binding site 4 out of 4 in 6ig1

Go back to Magnesium Binding Sites List in 6ig1
Magnesium binding site 4 out of 4 in the Dna Polymerase IV - Dna Ternary Complex 10


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 10 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg902

b:55.9
occ:1.00
OE2 A:GLU104 2.0 62.3 1.0
OD1 A:ASP103 2.1 36.2 1.0
OP1 C:DT874 2.3 39.6 0.3
O2A C:TTP901 2.3 50.4 0.7
OD2 A:ASP8 2.4 47.9 0.5
OD1 A:ASP8 2.4 40.6 0.5
O3' C:DC873 2.6 44.7 0.3
O3' C:DC873 2.8 51.1 0.7
CD A:GLU104 2.9 54.2 1.0
CG A:ASP103 2.9 38.4 1.0
P C:DT874 3.0 44.9 0.3
OD2 A:ASP103 3.1 33.5 1.0
CG A:ASP8 3.2 45.9 0.5
MG A:MG901 3.2 28.8 1.0
CG A:GLU104 3.2 48.5 1.0
CG A:ASP8 3.2 46.2 0.5
O A:HOH1079 3.3 65.8 1.0
OD2 A:ASP8 3.4 51.8 0.5
PA C:TTP901 3.5 46.3 0.7
CB A:GLU104 3.5 44.0 1.0
OD1 A:ASP8 3.7 45.8 0.5
OG A:SER101 3.9 41.6 1.0
C3' C:DC873 3.9 43.8 0.3
C3' C:DC873 3.9 43.5 0.7
O5' C:DT874 4.0 42.3 0.3
OE1 A:GLU104 4.1 44.5 1.0
C5' C:DT874 4.1 37.3 0.3
OP2 C:DT874 4.1 40.5 0.3
C4' C:DC873 4.2 43.9 0.7
O A:ASP103 4.2 38.0 1.0
C A:ASP103 4.2 40.4 1.0
C4' C:DC873 4.3 43.6 0.3
C5' C:TTP901 4.3 35.4 0.7
O5' C:TTP901 4.3 43.1 0.7
CB A:ASP103 4.4 36.8 1.0
N A:GLU104 4.4 40.5 1.0
C5' C:DC873 4.4 45.2 0.7
CB A:ASP8 4.4 42.5 0.5
CB A:ASP8 4.4 42.4 0.5
O3A C:TTP901 4.5 52.5 0.7
O1A C:TTP901 4.5 43.0 0.7
CA A:GLU104 4.6 36.1 1.0
C5' C:DC873 4.6 46.6 0.3
C2' C:DC873 4.7 45.1 0.7
CA A:ASP103 4.8 41.4 1.0
CA A:ASP8 4.8 34.6 1.0
C2' C:DC873 4.8 45.0 0.3
O2B C:TTP901 4.9 44.5 0.7
O2G C:TTP901 4.9 59.0 0.7
O2 A:DPO903 5.0 43.0 0.3
O A:HOH1061 5.0 53.9 1.0
N A:MET9 5.0 39.1 1.0

Reference:

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
Page generated: Mon Dec 14 22:57:11 2020

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