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

Enzymatic activity of 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;

Protein crystallography data

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

Magnesium Binding Sites:

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 5zlv

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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 5zlv

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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 5zlv

Go back to Magnesium Binding Sites List in 5zlv
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 5zlv

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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 5zlv

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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

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 Sep 30 18:40:30 2024

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