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Manganese in PDB 3rh6: Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

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

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

Protein crystallography data

The structure of Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh6 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) 20.77 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.060, 79.810, 55.060, 90.00, 107.68, 90.00
R / Rfree (%) 19.5 / 26.6

Other elements in 3rh6:

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

Chlorine (Cl) 3 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 Ribonucleotide (Rctp) (pdb code 3rh6). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh6:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 3rh6

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Manganese binding site 1 out of 6 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn339

b:22.6
occ:1.00
 OD1 A:ASP190 2.1 19.5 1.0
O1G A:CTP338 2.2 23.5 1.0
O1A A:CTP338 2.2 22.9 1.0
O2B A:CTP338 2.2 16.9 1.0
OD2 A:ASP192 2.2 22.7 1.0
O A:HOH371 2.5 22.9 1.0
CG A:ASP192 3.1 22.8 1.0
CG A:ASP190 3.1 24.5 1.0
PB A:CTP338 3.2 26.9 1.0
OD1 A:ASP192 3.3 26.4 1.0
PG A:CTP338 3.4 24.7 1.0
MN A:MN340 3.4 37.8 1.0
PA A:CTP338 3.4 25.0 1.0
OD2 A:ASP190 3.6 23.7 1.0
O3B A:CTP338 3.6 26.9 1.0
O3A A:CTP338 3.7 27.8 1.0
O A:ASP190 4.0 26.0 1.0
C5' A:CTP338 4.0 23.3 1.0
OG A:SER180 4.1 25.9 1.0
C A:ASP190 4.2 25.5 1.0
O5' A:CTP338 4.2 28.4 1.0
O3G A:CTP338 4.3 17.9 1.0
N A:ASP190 4.4 22.3 1.0
N A:SER180 4.4 25.2 1.0
CB A:ASP190 4.4 22.9 1.0
O A:HOH579 4.4 20.2 1.0
O2G A:CTP338 4.5 23.7 1.0
CB A:ASP192 4.5 23.0 1.0
O2A A:CTP338 4.5 27.2 1.0
CA A:ASP190 4.6 18.0 1.0
O1B A:CTP338 4.6 24.4 1.0
CA A:GLY179 4.6 24.8 1.0
N A:ASP192 4.8 18.1 1.0
N A:MET191 4.8 17.9 1.0
O A:HOH592 4.8 38.9 1.0
C A:MET191 5.0 15.4 1.0

Manganese binding site 2 out of 6 in 3rh6

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Manganese binding site 2 out of 6 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn340

b:37.8
occ:1.00
 OD2 A:ASP190 2.2 23.7 1.0
OD1 A:ASP192 2.2 26.4 1.0
O A:HOH592 2.5 38.9 1.0
O1A A:CTP338 2.6 22.9 1.0
OD2 A:ASP256 2.7 31.9 1.0
CG A:ASP190 2.9 24.5 1.0
OD1 A:ASP190 3.0 19.5 1.0
CG A:ASP192 3.3 22.8 1.0
MN A:MN339 3.4 22.6 1.0
PA A:CTP338 3.7 25.0 1.0
OD2 A:ASP192 3.7 22.7 1.0
CG A:ASP256 3.8 28.6 1.0
O5' A:CTP338 3.9 28.4 1.0
C5' A:CTP338 4.0 23.3 1.0
C3' P:DDG10 4.1 35.0 1.0
O2A A:CTP338 4.2 27.2 1.0
CB A:ASP190 4.3 22.9 1.0
C5' P:DDG10 4.4 32.4 1.0
CB A:ASP256 4.5 28.2 1.0
CB A:ASP192 4.5 23.0 1.0
C4' P:DDG10 4.5 34.7 1.0
O A:HOH513 4.6 33.1 1.0
OD1 A:ASP256 4.6 26.4 1.0
O A:MET191 4.6 22.4 1.0
OP1 P:DDG10 4.7 39.9 1.0
O5' P:DDG10 4.8 32.5 1.0
O1G A:CTP338 4.8 23.5 1.0
C A:MET191 4.9 15.4 1.0
NH2 A:ARG254 5.0 22.4 1.0
CA A:ASP192 5.0 19.2 1.0

Manganese binding site 3 out of 6 in 3rh6

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Manganese binding site 3 out of 6 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn341

b:47.0
occ:1.00
 OD2 A:ASP145 2.5 29.3 1.0
O A:HOH397 2.5 34.8 1.0
ND1 A:HIS252 2.6 32.0 1.0
O A:HOH374 2.7 32.2 1.0
CG A:ASP145 3.3 33.8 1.0
CE1 A:HIS252 3.3 34.8 1.0
OD1 A:ASP145 3.5 31.2 1.0
CG A:HIS252 3.7 34.0 1.0
O A:HOH480 3.8 43.1 1.0
N A:HIS252 4.1 24.1 1.0
CB A:HIS252 4.1 24.3 1.0
CD1 A:TYR142 4.2 25.6 1.0
CE1 A:TYR142 4.4 27.8 1.0
NE2 A:HIS252 4.5 33.2 1.0
CB A:ASP145 4.6 20.9 1.0
O A:HOH510 4.6 38.9 1.0
CD2 A:HIS252 4.7 22.4 1.0
CA A:HIS252 4.7 25.0 1.0
O A:TYR250 5.0 23.8 1.0
C A:PRO251 5.0 27.0 1.0

Manganese binding site 4 out of 6 in 3rh6

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Manganese binding site 4 out of 6 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn342

b:68.4
occ:0.92
 O A:HOH426 2.4 38.2 1.0
O2G A:CTP338 3.1 23.7 1.0
O A:HOH513 3.7 33.1 1.0
O1G A:CTP338 4.0 23.5 1.0
OD2 A:ASP190 4.1 23.7 1.0
PG A:CTP338 4.2 24.7 1.0
CA A:GLY189 4.3 18.4 1.0
O2A A:CTP338 4.3 27.2 1.0
C A:GLY189 4.4 27.8 1.0
CG A:ASP190 4.5 24.5 1.0
O A:HOH592 4.5 38.9 1.0
O A:GLY189 4.6 24.9 1.0
O1A A:CTP338 4.7 22.9 1.0
O3B A:CTP338 4.8 26.9 1.0
N A:ASP190 4.9 22.3 1.0
CB A:ASP190 4.9 22.9 1.0

Manganese binding site 5 out of 6 in 3rh6

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Manganese binding site 5 out of 6 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
T:Mn344

b:57.6
occ:0.72
 O T:HOH259 2.2 37.7 1.0
O T:HOH186 3.9 42.9 1.0
O A:HOH479 4.1 35.5 1.0
O4' T:DC5 4.2 32.9 1.0
C4' T:DC5 4.3 36.8 1.0
C5' T:DC5 4.4 38.9 1.0
N3 T:DA4 4.4 29.9 1.0
C2 T:DA4 4.9 29.0 1.0

Manganese binding site 6 out of 6 in 3rh6

Go back to Manganese Binding Sites List in 3rh6
Manganese binding site 6 out of 6 in the Dna Polymerase Beta Mutant (Y271) with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)


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 Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn343

b:81.3
occ:0.90
 N7 D:DG4 2.6 36.0 1.0
C8 D:DG4 3.4 35.6 1.0
C2' D:DC3 3.6 42.7 1.0
C5 D:DG4 3.7 34.9 1.0
O6 D:DG4 3.9 37.6 1.0
O6 D:DG5 4.0 42.1 1.0
OP2 D:DG4 4.0 39.6 1.0
C6 D:DG4 4.2 31.8 1.0
C6 D:DC3 4.2 33.8 1.0
N1 D:DC3 4.6 40.6 1.0
C1' D:DC3 4.7 45.2 1.0
N9 D:DG4 4.7 35.1 1.0
C3' D:DC3 4.7 45.8 1.0
C5 D:DC3 4.8 35.4 1.0
C6 D:DG5 4.8 36.9 1.0
N7 D:DG5 4.8 44.1 1.0
C4 D:DG4 4.8 38.6 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: Tue Dec 15 04:14:46 2020

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