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Manganese in PDB 3rh5: Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)

Enzymatic activity of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)

All present enzymatic activity of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp):
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp), PDB code: 3rh5 was solved by N.A.Cavanaugh, W.A.Beard, V.K.Batra, L.Perera, L.G.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.70 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.220, 79.920, 55.090, 90.00, 107.93, 90.00
R / Rfree (%) 20.8 / 28.1

Other elements in 3rh5:

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) (pdb code 3rh5). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 7 binding sites of Manganese where determined in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp), PDB code: 3rh5:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7;

Manganese binding site 1 out of 7 in 3rh5

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Manganese binding site 1 out of 7 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


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 Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn339

b:22.4
occ:1.00
 O1G A:DCP338 2.0 25.1 1.0
O2B A:DCP338 2.1 19.6 1.0
O1A A:DCP338 2.1 19.8 1.0
OD1 A:ASP190 2.2 22.0 1.0
OD2 A:ASP192 2.2 21.1 1.0
O A:HOH374 2.5 23.3 1.0
PB A:DCP338 3.1 28.1 1.0
CG A:ASP192 3.1 20.9 1.0
CG A:ASP190 3.2 21.3 1.0
PG A:DCP338 3.3 24.4 1.0
OD1 A:ASP192 3.4 23.0 1.0
PA A:DCP338 3.4 21.3 1.0
MN A:MN340 3.5 30.9 1.0
OD2 A:ASP190 3.6 19.1 1.0
O3B A:DCP338 3.6 24.0 1.0
O3A A:DCP338 3.6 25.8 1.0
O A:ASP190 3.9 25.5 1.0
C5' A:DCP338 4.1 25.5 1.0
O3G A:DCP338 4.1 16.1 1.0
C A:ASP190 4.2 20.3 1.0
O5' A:DCP338 4.3 24.6 1.0
OG A:SER180 4.4 26.6 1.0
CB A:ASP190 4.4 20.2 1.0
N A:SER180 4.5 23.3 1.0
N A:ASP190 4.5 23.7 1.0
O2A A:DCP338 4.5 19.5 1.0
CB A:ASP192 4.5 23.8 1.0
CA A:GLY179 4.5 23.8 1.0
O1B A:DCP338 4.5 24.4 1.0
O2G A:DCP338 4.5 25.6 1.0
O A:HOH336 4.5 15.7 1.0
CA A:ASP190 4.6 18.5 1.0
N A:ASP192 4.8 21.8 1.0
N A:MET191 4.8 17.9 1.0
C A:MET191 4.9 19.2 1.0

Manganese binding site 2 out of 7 in 3rh5

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Manganese binding site 2 out of 7 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


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 Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn340

b:30.9
occ:1.00
 OD2 A:ASP190 2.2 19.1 1.0
OD1 A:ASP192 2.2 23.0 1.0
OD2 A:ASP256 2.3 25.4 1.0
O1A A:DCP338 2.5 19.8 1.0
CG A:ASP190 2.9 21.3 1.0
OD1 A:ASP190 3.1 22.0 1.0
CG A:ASP192 3.2 20.9 1.0
CG A:ASP256 3.4 25.6 1.0
MN A:MN339 3.5 22.4 1.0
OD2 A:ASP192 3.6 21.1 1.0
PA A:DCP338 3.6 21.3 1.0
O5' A:DCP338 3.9 24.6 1.0
C3' P:DDG10 4.0 28.2 1.0
C5' A:DCP338 4.0 25.5 1.0
O2A A:DCP338 4.1 19.5 1.0
CB A:ASP256 4.2 22.3 1.0
OD1 A:ASP256 4.3 20.6 1.0
CB A:ASP190 4.3 20.2 1.0
C5' P:DDG10 4.4 27.9 1.0
CB A:ASP192 4.6 23.8 1.0
C4' P:DDG10 4.6 29.5 1.0
OP1 P:DDG10 4.6 26.5 1.0
O A:MET191 4.6 18.9 1.0
O1G A:DCP338 4.7 25.1 1.0
O5' P:DDG10 4.8 31.1 1.0
NH2 A:ARG254 4.8 21.2 1.0
C A:MET191 5.0 19.2 1.0
O2B A:DCP338 5.0 19.6 1.0
O3A A:DCP338 5.0 25.8 1.0

Manganese binding site 3 out of 7 in 3rh5

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Manganese binding site 3 out of 7 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


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 Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn341

b:45.1
occ:1.00
 OD2 A:ASP145 2.3 23.5 1.0
O A:HOH397 2.5 36.5 1.0
O A:HOH400 2.6 28.1 1.0
ND1 A:HIS252 2.6 25.8 1.0
CG A:ASP145 3.2 32.6 1.0
CE1 A:HIS252 3.3 28.0 1.0
OD1 A:ASP145 3.4 31.1 1.0
CG A:HIS252 3.8 25.0 1.0
CB A:HIS252 4.2 21.7 1.0
N A:HIS252 4.2 22.5 1.0
CD1 A:TYR142 4.3 28.2 1.0
O A:HOH514 4.4 33.6 1.0
CE1 A:TYR142 4.4 27.2 1.0
CB A:ASP145 4.5 25.5 1.0
NE2 A:HIS252 4.6 27.7 1.0
O A:HOH546 4.6 37.6 1.0
CD2 A:HIS252 4.8 27.3 1.0
CA A:HIS252 4.8 24.1 1.0
CA A:PRO251 5.0 26.3 1.0
C A:PRO251 5.0 25.7 1.0

Manganese binding site 4 out of 7 in 3rh5

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Manganese binding site 4 out of 7 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


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 Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn343

b:92.6
occ:1.00
 O3B A:DCP350 2.4 78.5 1.0
O1A A:DCP350 2.7 69.3 1.0
O2G A:DCP350 3.1 81.2 1.0
O A:HOH529 3.1 58.6 1.0
PG A:DCP350 3.3 83.8 1.0
PB A:DCP350 3.4 71.7 1.0
O1B A:DCP350 3.4 69.1 1.0
PA A:DCP350 3.8 78.4 1.0
O3G A:DCP350 3.9 76.3 1.0
O3A A:DCP350 4.0 68.4 1.0
O5' A:DCP350 4.4 68.6 1.0
O1G A:DCP350 4.6 66.3 1.0
C5' A:DCP350 4.7 62.3 1.0
O2B A:DCP350 4.7 64.5 1.0

Manganese binding site 5 out of 7 in 3rh5

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Manganese binding site 5 out of 7 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


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 Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn345

b:65.4
occ:1.00
 O2G A:DCP338 3.1 25.6 1.0
O2A A:DCP338 4.0 19.5 1.0
O1G A:DCP338 4.0 25.1 1.0
PG A:DCP338 4.2 24.4 1.0
OD2 A:ASP190 4.5 19.1 1.0
O1A A:DCP338 4.7 19.8 1.0
CA A:GLY189 4.7 21.9 1.0
C A:GLY189 4.8 21.6 1.0
CG A:ASP190 4.8 21.3 1.0
O A:GLY189 4.8 23.8 1.0
PA A:DCP338 4.8 21.3 1.0
O3B A:DCP338 4.9 24.0 1.0

Manganese binding site 6 out of 7 in 3rh5

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Manganese binding site 6 out of 7 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn344

b:58.6
occ:1.00
 N3 T:DA4 2.9 36.4 1.0
C2 T:DA4 3.4 35.2 1.0
O4' T:DC5 3.5 32.5 1.0
O D:HOH182 3.5 33.4 1.0
C4' T:DC5 3.9 36.7 1.0
C4 T:DA4 4.1 37.1 1.0
O T:HOH281 4.1 41.3 1.0
C5' T:DC5 4.2 38.9 1.0
O D:HOH157 4.2 36.4 1.0
C1' T:DA4 4.3 40.0 1.0
O T:HOH259 4.4 39.7 1.0
C1' T:DC5 4.5 30.4 1.0
N9 T:DA4 4.6 37.6 1.0
O2 T:DC5 4.6 29.3 1.0
N2 T:DG3 4.6 36.7 1.0
O4' T:DA4 4.6 49.0 1.0
N1 T:DA4 4.8 33.9 1.0

Manganese binding site 7 out of 7 in 3rh5

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Manganese binding site 7 out of 7 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Deoxynucleotide (Dctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn342

b:63.5
occ:1.00
 N7 D:DG4 2.7 36.8 1.0
O6 D:DG4 3.2 41.6 1.0
C5 D:DG4 3.5 36.5 1.0
C8 D:DG4 3.7 40.2 1.0
C6 D:DG4 3.7 37.8 1.0
O6 D:DG5 3.8 43.0 1.0
C2' D:DC3 4.3 39.6 1.0
C6 D:DC3 4.4 35.9 1.0
N4 T:DC1 4.5 48.2 1.0
C6 D:DG5 4.6 38.3 1.0
N7 D:DG5 4.7 42.0 1.0
OP2 D:DG4 4.7 36.7 1.0
C4 D:DG4 4.8 35.7 1.0
C5 D:DC3 4.8 33.6 1.0
N1 D:DC3 4.8 36.5 1.0
N9 D:DG4 4.8 37.6 1.0

Reference:

N.A.Cavanaugh, W.A.Beard, V.K.Batra, L.Perera, L.G.Pedersen, S.H.Wilson. Molecular Insights Into Dna Polymerase Deterrents For Ribonucleotide Insertion. J.Biol.Chem. V. 286 31650 2011.
ISSN: ISSN 0021-9258
PubMed: 21733843
DOI: 10.1074/JBC.M111.253401
Page generated: Sat Oct 5 17:45:29 2024

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