Manganese in PDB 6uol: Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp

Enzymatic activity of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp

All present enzymatic activity of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp:
2.7.7.7;

Protein crystallography data

The structure of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp, PDB code: 6uol 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) 25.09 / 1.94
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.800, 80.400, 55.500, 90.00, 107.90, 90.00
R / Rfree (%) 18.7 / 25

Other elements in 6uol:

The structure of Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Manganese Binding Sites:

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

Manganese binding site 1 out of 5 in 6uol

Go back to Manganese Binding Sites List in 6uol
Manganese binding site 1 out of 5 in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp


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 A Templating Cytosine and Incoming Rgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:78.0
occ:1.00
 ND1 A:HIS285 2.3 46.0 1.0
O A:HOH643 2.6 50.7 1.0
OE1 A:GLU288 2.7 62.3 1.0
CE1 A:HIS285 3.1 45.9 1.0
CG A:HIS285 3.2 40.5 1.0
CB A:HIS285 3.6 34.6 1.0
CD A:GLU288 3.8 59.0 1.0
NE2 A:HIS285 4.2 41.5 1.0
CA A:HIS285 4.2 33.9 1.0
CD2 A:HIS285 4.2 40.9 1.0
OE2 A:GLU288 4.2 62.5 1.0

Manganese binding site 2 out of 5 in 6uol

Go back to Manganese Binding Sites List in 6uol
Manganese binding site 2 out of 5 in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp


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 A Templating Cytosine and Incoming Rgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:94.4
occ:1.00
 NE2 A:HIS222 2.3 49.7 1.0
CE1 A:HIS222 2.6 37.0 1.0
CD2 A:HIS222 3.6 29.7 1.0
ND1 A:HIS222 3.9 39.4 1.0
CG A:HIS222 4.4 35.4 1.0
O A:LYS220 4.7 31.0 1.0

Manganese binding site 3 out of 5 in 6uol

Go back to Manganese Binding Sites List in 6uol
Manganese binding site 3 out of 5 in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp


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 A Templating Cytosine and Incoming Rgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn404

b:31.9
occ:1.00
 OD2 A:ASP145 2.1 23.4 1.0
ND1 A:HIS252 2.4 17.1 1.0
O A:HOH577 2.5 22.8 1.0
O A:HOH634 2.5 24.6 1.0
CE1 A:HIS252 3.0 18.1 1.0
CG A:ASP145 3.2 23.2 1.0
CG A:HIS252 3.6 22.1 1.0
OD1 A:ASP145 3.6 23.6 1.0
N A:HIS252 4.0 13.4 1.0
CB A:HIS252 4.1 16.3 1.0
NE2 A:HIS252 4.2 21.3 1.0
CD1 A:TYR142 4.4 15.4 1.0
CB A:ASP145 4.4 18.6 1.0
CE1 A:TYR142 4.5 19.3 1.0
CD2 A:HIS252 4.5 20.7 1.0
OE1 A:GLU249 4.7 55.2 0.5
CA A:HIS252 4.7 18.3 1.0
CD A:GLU249 4.8 48.2 0.5
O A:HOH504 4.9 31.6 1.0
C A:PRO251 4.9 17.6 1.0
CA A:PRO251 5.0 15.2 1.0

Manganese binding site 4 out of 5 in 6uol

Go back to Manganese Binding Sites List in 6uol
Manganese binding site 4 out of 5 in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp


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 A Templating Cytosine and Incoming Rgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn410

b:14.1
occ:1.00
 O1B A:GTP409 2.1 11.4 1.0
O1G A:GTP409 2.1 13.8 1.0
OD2 A:ASP192 2.1 10.4 1.0
OD1 A:ASP190 2.2 9.8 1.0
O A:HOH555 2.2 13.0 1.0
O1A A:GTP409 2.2 8.7 1.0
CG A:ASP192 3.1 9.3 1.0
PB A:GTP409 3.1 12.2 1.0
CG A:ASP190 3.1 11.2 1.0
PA A:GTP409 3.3 14.3 1.0
PG A:GTP409 3.4 14.8 1.0
MN A:MN411 3.4 16.9 0.6
OD1 A:ASP192 3.4 11.9 1.0
O3A A:GTP409 3.5 15.8 1.0
OD2 A:ASP190 3.5 15.4 1.0
O3B A:GTP409 3.6 12.1 1.0
O A:ASP190 3.9 14.8 1.0
C5' A:GTP409 3.9 14.8 1.0
O5' A:GTP409 4.2 13.9 1.0
C A:ASP190 4.2 11.5 1.0
O2G A:GTP409 4.2 14.1 1.0
OG A:SER180 4.3 15.6 1.0
N A:ASP190 4.4 13.8 1.0
O A:HOH599 4.4 12.1 1.0
CB A:ASP190 4.4 11.5 1.0
N A:SER180 4.4 17.2 1.0
CB A:ASP192 4.5 11.8 1.0
CA A:GLY179 4.5 12.9 1.0
O3G A:GTP409 4.5 19.4 1.0
CA A:ASP190 4.6 9.5 1.0
O2A A:GTP409 4.6 18.9 1.0
O2B A:GTP409 4.6 13.4 1.0
O A:HOH605 4.7 25.8 1.0
N A:ASP192 4.7 12.1 1.0
N A:MET191 4.7 10.9 0.4
N A:MET191 4.8 10.7 0.6
C A:MET191 4.9 13.9 0.6

Manganese binding site 5 out of 5 in 6uol

Go back to Manganese Binding Sites List in 6uol
Manganese binding site 5 out of 5 in the Y271G Dna Polymerase Beta Substrate Complex with A Templating Cytosine and Incoming Rgtp


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 A Templating Cytosine and Incoming Rgtp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn411

b:16.9
occ:0.55
 O A:HOH511 2.0 18.4 1.0
OD1 A:ASP192 2.1 11.9 1.0
OD2 A:ASP190 2.4 15.4 1.0
O1A A:GTP409 2.4 8.7 1.0
O A:HOH614 2.6 15.7 1.0
CG A:ASP190 2.9 11.2 1.0
OD1 A:ASP190 2.9 9.8 1.0
CG A:ASP192 3.2 9.3 1.0
MN A:MN410 3.4 14.1 1.0
OD2 A:ASP192 3.5 10.4 1.0
PA A:GTP409 3.6 14.3 1.0
OD2 A:ASP256 3.9 19.3 1.0
O5' A:GTP409 4.0 13.9 1.0
C5' A:GTP409 4.1 14.8 1.0
O A:HOH622 4.2 33.9 1.0
CB A:ASP190 4.2 11.5 1.0
CG A:ASP256 4.2 22.6 1.0
O2A A:GTP409 4.2 18.9 1.0
OP1 P:DOC10 4.3 15.1 1.0
C5' P:DOC10 4.4 22.4 1.0
O A:MET191 4.5 11.1 0.4
CB A:ASP192 4.5 11.8 1.0
O A:MET191 4.5 11.1 0.6
O P:HOH107 4.5 21.1 1.0
OD1 A:ASP256 4.6 13.9 1.0
C3' P:DOC10 4.7 21.5 1.0
O1G A:GTP409 4.7 13.8 1.0
CB A:ASP256 4.7 17.1 1.0
O A:HOH605 4.7 25.8 1.0
C A:MET191 4.8 13.9 0.6
C4' P:DOC10 4.8 19.0 1.0
C A:MET191 4.9 13.9 0.4
O3A A:GTP409 4.9 15.8 1.0
CA A:ASP192 5.0 13.5 1.0

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: Tue Dec 15 05:02:49 2020

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