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Manganese in PDB 4ub5: Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S

Enzymatic activity of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S, PDB code: 4ub5 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) 21.09 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.066, 77.713, 55.112, 90.00, 114.24, 90.00
R / Rfree (%) 22.6 / 29

Other elements in 4ub5:

The structure of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S (pdb code 4ub5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 5 binding sites of Manganese where determined in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S, PDB code: 4ub5:
Jump to Manganese binding site number: 1; 2; 3; 4; 5;

Manganese binding site 1 out of 5 in 4ub5

Go back to Manganese Binding Sites List in 4ub5
Manganese binding site 1 out of 5 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn101

b:65.4
occ:1.00
 O T:HOH215 2.2 39.2 1.0
O T:HOH202 2.2 45.2 1.0
O D:HOH101 2.2 47.2 1.0
N7 T:DG3 2.6 45.5 1.0
C8 T:DG3 3.5 44.6 1.0
C5 T:DG3 3.7 35.0 1.0
O6 T:DG3 3.9 38.8 1.0
C6 T:DG3 4.2 38.6 1.0
O4 D:DT2 4.4 25.7 1.0
N9 T:DG3 4.7 42.2 1.0
C4 T:DG3 4.8 33.6 1.0
C6 T:DC2 4.9 45.8 1.0
N6 T:DA4 5.0 36.9 1.0
C5 T:DC2 5.0 41.0 1.0

Manganese binding site 2 out of 5 in 4ub5

Go back to Manganese Binding Sites List in 4ub5
Manganese binding site 2 out of 5 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn101

b:77.0
occ:1.00
 O A:HOH571 2.2 49.1 1.0
O A:HOH573 2.2 63.0 1.0
O A:HOH572 2.2 56.3 1.0
O2A A:8DG403 2.2 50.0 1.0
O P:HOH208 2.2 44.7 1.0
O A:HOH541 2.2 46.9 1.0
PA A:8DG403 3.3 35.3 1.0
O3A A:8DG403 3.4 42.0 1.0
O5' A:8DG403 4.0 33.4 1.0
O8 A:8DG403 4.1 41.6 1.0
OP2 P:DC10 4.3 27.2 1.0
O A:HOH574 4.5 36.2 1.0
O A:HOH570 4.5 44.7 1.0
O2G A:8DG403 4.5 50.1 1.0
O1A A:8DG403 4.6 25.4 1.0
PB A:8DG403 4.8 50.5 1.0
O3B A:8DG403 4.9 38.9 1.0
O A:HOH527 4.9 56.4 1.0

Manganese binding site 3 out of 5 in 4ub5

Go back to Manganese Binding Sites List in 4ub5
Manganese binding site 3 out of 5 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn102

b:82.9
occ:1.00
 N7 P:DG4 2.6 59.2 1.0
O6 P:DG4 3.3 42.9 1.0
C5 P:DG4 3.4 49.6 1.0
O T:HOH214 3.5 40.0 1.0
C8 P:DG4 3.6 58.4 1.0
C6 P:DG4 3.7 38.6 1.0
C2' P:DT3 4.0 50.6 1.0
N6 P:DA5 4.1 43.0 1.0
C4 P:DG4 4.7 52.7 1.0
O4 T:DT12 4.7 38.9 1.0
N9 P:DG4 4.8 57.1 1.0
OP2 P:DG4 4.9 65.0 1.0
C1' P:DT3 4.9 43.3 1.0
C3' P:DT3 4.9 54.8 1.0

Manganese binding site 4 out of 5 in 4ub5

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Manganese binding site 4 out of 5 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:29.6
occ:1.00
 OD2 A:ASP190 2.1 28.2 1.0
OD1 A:ASP192 2.1 22.5 1.0
O1A A:8DG403 2.1 25.4 1.0
OD2 A:ASP256 2.2 32.8 1.0
O A:HOH574 2.2 36.2 1.0
O3' P:DC10 2.2 28.1 1.0
CG A:ASP190 3.1 35.4 1.0
CG A:ASP192 3.1 33.7 1.0
PA A:8DG403 3.3 35.3 1.0
OD1 A:ASP190 3.4 33.5 1.0
CG A:ASP256 3.4 30.8 1.0
C3' P:DC10 3.4 38.8 1.0
OD2 A:ASP192 3.5 31.5 1.0
MN A:MN402 3.5 34.1 1.0
O2A A:8DG403 3.5 50.0 1.0
H5'2 A:8DG403 3.7 46.6 1.0
O5' A:8DG403 3.8 33.4 1.0
H5'1 A:8DG403 4.0 46.6 1.0
C5' A:8DG403 4.1 38.8 1.0
CB A:ASP256 4.2 26.5 1.0
C4' P:DC10 4.2 39.9 1.0
OD1 A:ASP256 4.3 39.3 1.0
C5' P:DC10 4.4 35.7 1.0
CB A:ASP190 4.4 25.4 1.0
CB A:ASP192 4.5 25.8 1.0
O5' P:DC10 4.6 40.2 1.0
C2' P:DC10 4.6 34.8 1.0
OP1 P:DC10 4.7 33.7 1.0
O3A A:8DG403 4.7 42.0 1.0
O3G A:8DG403 4.8 35.1 1.0
O A:MET191 4.9 30.6 1.0
O1B A:8DG403 4.9 35.1 1.0
CA A:ASP192 5.0 21.9 1.0

Manganese binding site 5 out of 5 in 4ub5

Go back to Manganese Binding Sites List in 4ub5
Manganese binding site 5 out of 5 in the Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Dna Polymerase Beta Substrate Complex with A Templating Cytosine, Incoming 8-Oxodgtp, and MN2+, 5 S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:34.1
occ:1.00
 O1A A:8DG403 2.0 25.4 1.0
O1B A:8DG403 2.1 35.1 1.0
OD1 A:ASP190 2.1 33.5 1.0
OD2 A:ASP192 2.1 31.5 1.0
O A:HOH575 2.2 34.8 1.0
O3G A:8DG403 2.3 35.1 1.0
PB A:8DG403 3.1 50.5 1.0
CG A:ASP190 3.1 35.4 1.0
CG A:ASP192 3.2 33.7 1.0
PA A:8DG403 3.2 35.3 1.0
O3A A:8DG403 3.3 42.0 1.0
PG A:8DG403 3.5 41.7 1.0
OD1 A:ASP192 3.5 22.5 1.0
O3B A:8DG403 3.5 38.9 1.0
MN A:MN401 3.5 29.6 1.0
OD2 A:ASP190 3.5 28.2 1.0
H5'1 A:8DG403 3.6 46.6 1.0
O A:ASP190 4.1 29.2 1.0
O1G A:8DG403 4.2 45.0 1.0
O2A A:8DG403 4.2 50.0 1.0
OG A:SER180 4.2 43.9 1.0
O5' A:8DG403 4.3 33.4 1.0
O A:HOH528 4.3 37.1 1.0
N A:ASP190 4.3 28.9 1.0
C A:ASP190 4.3 28.6 1.0
C5' A:8DG403 4.4 38.8 1.0
CB A:ASP190 4.4 25.4 1.0
N A:SER180 4.4 40.6 1.0
O2B A:8DG403 4.4 38.9 1.0
CA A:GLY179 4.4 36.2 1.0
CB A:ASP192 4.5 25.8 1.0
CA A:ASP190 4.6 31.1 1.0
O A:HOH574 4.6 36.2 1.0
H5'2 A:8DG403 4.6 46.6 1.0
O2G A:8DG403 4.7 50.1 1.0
N A:ASP192 4.9 26.5 1.0
N A:MET191 4.9 29.0 1.0
C A:GLY179 5.0 36.0 1.0

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 Dec 15 04:29:25 2020

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