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Manganese in PDB 6uok: Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp

Enzymatic activity of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp

All present enzymatic activity of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp:
2.7.7.7;

Protein crystallography data

The structure of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp, PDB code: 6uok was solved by M.R.Smith, B.D.Freudenthal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.14 / 2.55
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.687, 79.957, 100.832, 90.00, 97.64, 90.00
R / Rfree (%) 22.4 / 27.9

Other elements in 6uok:

The structure of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 6 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp (pdb code 6uok). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp, PDB code: 6uok:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6uok

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Manganese binding site 1 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn402

b:41.4
occ:1.00
 O F:HOH507 1.8 28.9 1.0
O1G F:8GT406 2.0 37.6 1.0
O2A F:8GT406 2.0 34.6 1.0
OD1 F:ASP190 2.1 28.8 1.0
O1B F:8GT406 2.2 36.0 1.0
OD2 F:ASP192 2.3 33.3 1.0
PB F:8GT406 3.1 30.8 1.0
CG F:ASP192 3.2 38.4 1.0
CG F:ASP190 3.2 35.2 1.0
PA F:8GT406 3.3 34.9 1.0
PG F:8GT406 3.3 34.6 1.0
OD1 F:ASP192 3.4 37.1 1.0
O3A F:8GT406 3.4 37.4 1.0
O3B F:8GT406 3.5 32.8 1.0
OD2 F:ASP190 3.7 38.4 1.0
OG F:SER180 4.0 38.5 1.0
N F:SER180 4.2 35.0 1.0
O1A F:8GT406 4.2 48.3 1.0
C5' F:8GT406 4.2 30.4 1.0
O2G F:8GT406 4.2 45.0 1.0
N F:ASP190 4.3 33.8 1.0
NA F:NA405 4.3 28.8 1.0
O F:ASP190 4.3 33.8 1.0
O3G F:8GT406 4.3 42.2 1.0
O5' F:8GT406 4.3 28.5 1.0
C F:ASP190 4.4 38.0 1.0
O F:HOH506 4.5 24.9 1.0
CB F:ASP190 4.5 30.1 1.0
O2B F:8GT406 4.5 35.8 1.0
CB F:SER180 4.5 29.7 1.0
CB F:ASP192 4.6 27.7 1.0
CA F:ASP190 4.6 34.4 1.0
CA F:GLY179 4.7 26.8 1.0
N F:MET191 4.8 38.7 1.0
N F:ASP192 4.8 28.3 1.0

Manganese binding site 2 out of 6 in 6uok

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Manganese binding site 2 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn403

b:68.2
occ:1.00
 OD2 F:ASP145 2.1 45.7 1.0
ND1 F:HIS252 2.4 37.3 1.0
CE1 F:HIS252 2.9 44.8 1.0
CG F:ASP145 3.3 42.3 1.0
CG F:HIS252 3.7 32.8 1.0
OD1 F:ASP145 3.8 46.1 1.0
N F:HIS252 4.1 34.2 1.0
NE2 F:HIS252 4.2 39.4 1.0
CB F:HIS252 4.4 37.2 1.0
CD1 F:TYR142 4.4 39.0 1.0
CB F:ASP145 4.4 34.2 1.0
CD2 F:HIS252 4.6 28.6 1.0
CE1 F:TYR142 4.6 38.3 1.0
CA F:PRO251 4.7 35.3 1.0
NE2 F:GLN240 4.9 46.1 1.0
CA F:HIS252 4.9 30.6 1.0
C F:PRO251 4.9 35.1 1.0
O F:TYR250 5.0 42.9 1.0

Manganese binding site 3 out of 6 in 6uok

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Manganese binding site 3 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn404

b:75.5
occ:1.00
 OD1 F:ASP124 2.4 60.7 1.0
O F:HOH501 2.4 47.1 1.0
OD2 F:ASP124 3.1 43.4 1.0
CG F:ASP124 3.1 46.8 1.0
NZ F:LYS127 3.9 45.8 1.0
OG1 F:THR121 4.3 41.8 1.0
CE F:LYS127 4.3 51.7 1.0
CB F:ASP124 4.6 39.9 1.0

Manganese binding site 4 out of 6 in 6uok

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Manganese binding site 4 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn407

b:76.0
occ:1.00
 OD1 F:ASP318 2.9 55.2 1.0
CB F:ASP314 3.1 54.9 1.0
OD2 F:ASP314 3.2 52.0 1.0
OD2 F:ASP318 3.2 55.8 1.0
CG F:ASP318 3.4 52.1 1.0
CG F:ASP314 3.6 59.3 1.0
CA F:ASP314 4.4 47.3 1.0
C F:ASP314 4.7 44.9 1.0
N F:ASP314 4.7 49.4 1.0
OD1 F:ASP314 4.8 63.7 1.0
N F:SER315 4.8 46.6 1.0
CB F:ASP318 4.9 49.6 1.0

Manganese binding site 5 out of 6 in 6uok

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Manganese binding site 5 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn408

b:94.7
occ:1.00
 O3G F:8GT406 3.1 42.2 1.0
O1A F:8GT406 3.9 48.3 1.0
PG F:8GT406 4.3 34.6 1.0
O1G F:8GT406 4.4 37.6 1.0
OD2 F:ASP190 4.4 38.4 1.0
OP2 C:DOC10 4.6 26.9 1.0
CA F:GLY189 4.6 35.2 1.0
OP1 C:DOC10 4.6 32.1 1.0
CG F:ASP190 4.7 35.2 1.0
C F:GLY189 4.8 32.0 1.0
PA F:8GT406 4.9 34.9 1.0

Manganese binding site 6 out of 6 in 6uok

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Manganese binding site 6 out of 6 in the Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Y271G Dna Polymerase Beta Substrate Complex with Templating Cytosine and Incoming R8-Oxo-Gtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:52.2
occ:0.56
 O A:HOH515 1.9 47.6 1.0
OD2 A:ASP192 2.2 65.4 1.0
OD2 A:ASP190 2.3 54.4 1.0
O3A A:8GT405 2.6 61.6 0.8
O3B A:8GT405 2.7 59.2 0.8
O1A A:8GT405 3.0 58.4 0.8
CG A:ASP192 3.1 58.8 1.0
PB A:8GT405 3.1 57.3 0.8
PA A:8GT405 3.4 67.6 0.8
OD1 A:ASP192 3.4 57.3 1.0
CG A:ASP190 3.5 51.5 1.0
O2B A:8GT405 3.6 62.7 0.8
O A:ASP190 3.9 44.1 1.0
PG A:8GT405 3.9 57.7 0.8
O1G A:8GT405 3.9 58.8 0.8
NA A:NA406 4.1 54.1 1.0
OD1 A:ASP190 4.1 53.5 1.0
C5' A:8GT405 4.2 61.1 0.8
CB A:ASP192 4.3 44.4 1.0
O5' A:8GT405 4.3 64.6 0.8
CA A:GLY179 4.3 48.4 1.0
C3' A:8GT405 4.4 62.7 0.8
C A:ASP190 4.4 40.9 1.0
O1B A:8GT405 4.5 56.8 0.8
N A:ASP190 4.5 36.5 1.0
O2A A:8GT405 4.6 62.7 0.8
CB A:ASP190 4.7 44.0 1.0
N A:SER180 4.7 46.7 1.0
N A:ASP192 4.7 48.2 1.0
O3G A:8GT405 4.7 52.5 0.8
CA A:ASP190 4.8 41.0 1.0
C4' A:8GT405 4.8 62.8 0.8
O3' A:8GT405 4.9 59.3 0.8

Reference:

M.R.Smith, K.S.Alnajjar, N.M.Hoitsma, J.B.Sweasy, B.D.Freudenthal. Molecular Characterization of Oxidized Ribonucleotide Insertion By Human Dna Polymerase Beta J.Biol.Chem. 2020.
ISSN: ESSN 1083-351X
Page generated: Sun Oct 6 07:15:33 2024

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