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Magnesium in PDB 4ubb: Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S

Enzymatic activity of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S

All present enzymatic activity of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S, PDB code: 4ubb was solved by B.D.Freudenthal, S.H.Wilson, W.A.Beard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.90 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.798, 79.849, 55.625, 90.00, 107.58, 90.00
R / Rfree (%) 18.1 / 22.8

Other elements in 4ubb:

The structure of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S (pdb code 4ubb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S, PDB code: 4ubb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 4ubb

Go back to Magnesium Binding Sites List in 4ubb
Magnesium binding site 1 out of 3 in the Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mg101

b:28.3
occ:0.40
 O1A A:8DG401 1.6 16.0 0.6
O A:HOH681 1.7 40.5 0.6
O A:HOH717 2.0 47.7 0.4
CA P:CA102 2.0 51.4 0.6
O P:HOH214 2.1 45.1 0.4
O A:HOH588 2.1 30.2 1.0
OP2 P:8OG11 2.3 23.9 0.4
O12 A:PPV404 2.3 19.5 0.4
PA A:8DG401 2.3 16.2 0.6
O A:HOH708 2.4 36.8 0.5
O3A A:8DG401 2.4 23.1 0.6
O3B A:8DG401 2.9 21.2 0.6
O A:HOH716 3.1 50.5 1.0
P P:8OG11 3.2 24.7 0.4
O2G A:8DG401 3.2 21.5 0.6
O2A A:8DG401 3.2 18.5 0.6
PG A:8DG401 3.3 19.7 0.6
PB A:8DG401 3.3 18.8 0.6
O3G A:8DG401 3.4 16.4 0.6
OP1 P:8OG11 3.4 17.4 0.4
O11 A:PPV404 3.6 20.6 0.4
P2 A:PPV404 3.6 18.8 0.4
O5' P:8OG11 3.7 18.3 0.4
O5' A:8DG401 3.7 19.9 0.6
O P:HOH208 3.7 38.2 0.6
O21 A:PPV404 3.8 17.9 0.4
OPP A:PPV404 3.9 16.7 0.4
P1 A:PPV404 4.0 21.6 0.4
O P:HOH202 4.1 31.4 1.0
O A:HOH667 4.3 38.0 1.0
O8 P:8OG11 4.3 18.9 0.4
O A:HOH573 4.3 19.2 1.0
O2B A:8DG401 4.3 16.5 0.6
MG A:MG403 4.4 13.5 1.0
O22 A:PPV404 4.4 19.8 0.4
O1B A:8DG401 4.4 19.8 0.6
O8 A:8DG401 4.6 23.2 0.6
O3' P:DC10 4.6 26.0 0.5
O32 A:PPV404 4.6 15.1 0.4
O1G A:8DG401 4.9 19.0 0.6
C5' A:8DG401 4.9 17.6 0.6
C5' P:8OG11 4.9 17.6 0.4

Magnesium binding site 2 out of 3 in 4ubb

Go back to Magnesium Binding Sites List in 4ubb
Magnesium binding site 2 out of 3 in the Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:17.4
occ:1.00
 OD2 A:ASP256 2.1 21.2 1.0
OD1 A:ASP192 2.2 19.5 1.0
O P:HOH202 2.2 31.4 1.0
OD2 A:ASP190 2.2 30.1 1.0
OP1 P:8OG11 2.3 17.4 0.4
O3' P:DC10 2.4 26.0 0.5
O2A A:8DG401 2.5 18.5 0.6
O3' P:DC10 2.5 25.3 0.5
P P:8OG11 2.8 24.7 0.4
CG A:ASP190 3.1 21.9 1.0
OD1 A:ASP190 3.2 22.9 1.0
CG A:ASP192 3.3 16.5 1.0
CG A:ASP256 3.3 22.9 1.0
C3' P:DC10 3.5 22.9 0.5
PA A:8DG401 3.6 16.2 0.6
C3' P:DC10 3.7 22.7 0.5
OP2 P:8OG11 3.7 23.9 0.4
OD2 A:ASP192 3.7 15.3 1.0
MG A:MG403 3.7 13.5 1.0
O5' A:8DG401 3.9 19.9 0.6
CB A:ASP256 3.9 18.3 1.0
C4' P:DC10 3.9 25.8 0.5
O1A A:8DG401 4.0 16.0 0.6
C5' P:DC10 4.0 25.4 0.5
O5' P:8OG11 4.1 18.3 0.4
C4' P:DC10 4.1 25.9 0.5
C5' P:DC10 4.1 25.4 0.5
C5' A:8DG401 4.1 17.6 0.6
C5' P:8OG11 4.3 17.6 0.4
OD1 A:ASP256 4.3 20.4 1.0
CB A:ASP190 4.5 17.2 1.0
CB A:ASP192 4.5 17.8 1.0
O A:HOH708 4.6 36.8 0.5
O3G A:8DG401 4.6 16.4 0.6
C2' P:DC10 4.8 24.4 0.5
NH2 A:ARG254 4.8 24.2 1.0
C2' P:DC10 4.8 24.6 0.5
O5' P:DC10 4.8 23.7 0.5
OP1 P:DC10 4.8 23.9 0.5
O A:MET191 4.8 18.5 1.0
O5' P:DC10 4.8 24.3 0.5
OP1 P:DC10 4.9 23.8 0.5
O12 A:PPV404 4.9 19.5 0.4

Magnesium binding site 3 out of 3 in 4ubb

Go back to Magnesium Binding Sites List in 4ubb
Magnesium binding site 3 out of 3 in the Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dna Polymerase Beta Reactant Complex with A Templating Cytosine and Incoming 8-Oxodgtp, 40 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:13.5
occ:1.00
 O3G A:8DG401 2.1 16.4 0.6
O2A A:8DG401 2.1 18.5 0.6
O A:HOH566 2.1 18.9 1.0
OD2 A:ASP192 2.1 15.3 1.0
OD1 A:ASP190 2.2 22.9 1.0
O32 A:PPV404 2.3 15.1 0.4
O2B A:8DG401 2.3 16.5 0.6
OP1 P:8OG11 2.3 17.4 0.4
O11 A:PPV404 2.6 20.6 0.4
O12 A:PPV404 3.0 19.5 0.4
P2 A:PPV404 3.1 18.8 0.4
CG A:ASP192 3.1 16.5 1.0
PB A:8DG401 3.2 18.8 0.6
PG A:8DG401 3.3 19.7 0.6
CG A:ASP190 3.3 21.9 1.0
PA A:8DG401 3.3 16.2 0.6
OD1 A:ASP192 3.4 19.5 1.0
O3B A:8DG401 3.5 21.2 0.6
O3A A:8DG401 3.6 23.1 0.6
MG A:MG402 3.7 17.4 1.0
P P:8OG11 3.8 24.7 0.4
OPP A:PPV404 3.8 16.7 0.4
P1 A:PPV404 3.8 21.6 0.4
OD2 A:ASP190 3.9 30.1 1.0
O1G A:8DG401 3.9 19.0 0.6
O A:HOH708 4.0 36.8 0.5
O A:ASP190 4.0 21.3 1.0
C A:ASP190 4.3 17.1 1.0
O1A A:8DG401 4.3 16.0 0.6
O5' P:8OG11 4.3 18.3 0.4
O5' A:8DG401 4.3 19.9 0.6
C5' A:8DG401 4.3 17.6 0.6
N A:ASP190 4.3 14.3 1.0
C5' P:8OG11 4.4 17.6 0.4
O A:HOH576 4.4 20.8 1.0
O22 A:PPV404 4.4 19.8 0.4
MG P:MG101 4.4 28.3 0.4
O31 A:PPV404 4.5 16.9 0.4
CB A:ASP192 4.5 17.8 1.0
OG A:SER180 4.5 22.6 1.0
N A:SER180 4.5 16.3 1.0
CB A:ASP190 4.5 17.2 1.0
OP2 P:8OG11 4.5 23.9 0.4
CA A:GLY179 4.5 16.0 1.0
O2G A:8DG401 4.5 21.5 0.6
O P:HOH202 4.6 31.4 1.0
CA A:ASP190 4.6 13.6 1.0
O1B A:8DG401 4.6 19.8 0.6
O3' P:DC10 4.8 26.0 0.5
N A:ASP192 4.9 16.4 1.0
N A:MET191 4.9 15.8 1.0
O21 A:PPV404 5.0 17.9 0.4

Reference:

B.D.Freudenthal, W.A.Beard, L.Perera, D.D.Shock, T.Kim, T.Schlick, S.H.Wilson. Uncovering the Polymerase-Induced Cytotoxicty of An Oxidized Nucleotide Nature 2014.
ISSN: ESSN 1476-4687
DOI: 10.1038/NATURE13886
Page generated: Tue Aug 20 04:35:12 2024

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