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Manganese in PDB 3rh4: Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp)

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

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

Protein crystallography data

The structure of Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh4 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) 22.59 / 1.92
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 51.170, 79.790, 55.000, 90.00, 107.95, 90.00
R / Rfree (%) 17.5 / 24

Other elements in 3rh4:

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

Chlorine (Cl) 6 atoms
Sodium (Na) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) (pdb code 3rh4). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp), PDB code: 3rh4:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 3rh4

Go back to Manganese Binding Sites List in 3rh4
Manganese binding site 1 out of 8 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Mn345

b:33.7
occ:0.50
 N7 P:DG9 2.4 20.3 1.0
O P:HOH213 2.5 40.0 1.0
O P:HOH128 2.7 33.1 1.0
O A:HOH602 3.0 36.8 1.0
C8 P:DG9 3.1 22.4 1.0
C5 P:DG9 3.5 25.9 1.0
O P:HOH318 3.8 31.0 1.0
O P:HOH290 3.9 31.4 1.0
O6 P:DG9 3.9 26.8 1.0
C6 P:DG9 4.1 22.6 1.0
NZ A:LYS27 4.3 36.7 0.7
N9 P:DG9 4.3 20.9 1.0
C6 P:DC8 4.4 19.1 1.0
C5 P:DC8 4.4 25.9 1.0
O P:HOH250 4.5 34.0 1.0
C4 P:DG9 4.5 21.8 1.0
O P:HOH178 4.6 33.8 1.0
C2' P:DC8 4.8 21.9 1.0
N1 P:DC8 4.9 22.8 1.0
CE A:LYS27 4.9 23.4 0.7
O6 P:DDG10 4.9 20.2 1.0

Manganese binding site 2 out of 8 in 3rh4

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Manganese binding site 2 out of 8 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn344

b:66.7
occ:0.77
 N7 D:DG4 2.6 29.3 1.0
C8 D:DG4 3.5 29.0 1.0
C5 D:DG4 3.6 26.2 1.0
O6 D:DG5 3.7 34.8 1.0
O6 D:DG4 3.8 31.6 1.0
C6 D:DG4 4.1 23.5 1.0
C2' D:DC3 4.1 33.5 1.0
O D:HOH346 4.3 42.2 1.0
C6 D:DC3 4.4 28.9 1.0
OP2 D:DG4 4.4 40.0 1.0
C6 D:DG5 4.5 31.1 1.0
N7 D:DG5 4.6 34.4 1.0
N9 D:DG4 4.7 33.4 1.0
C4 D:DG4 4.8 29.4 1.0
N4 T:DC1 4.8 34.8 1.0
C5 D:DC3 4.8 28.2 1.0
N1 D:DC3 4.8 35.8 1.0
C5 D:DG5 4.9 30.3 1.0
C1' D:DC3 5.0 36.9 1.0

Manganese binding site 3 out of 8 in 3rh4

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Manganese binding site 3 out of 8 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn339

b:17.2
occ:1.00
 O2B A:CTP338 2.1 13.8 1.0
OD1 A:ASP190 2.1 18.6 1.0
OD2 A:ASP192 2.1 18.5 1.0
O1G A:CTP338 2.2 16.9 1.0
O A:HOH403 2.3 16.5 1.0
O1A A:CTP338 2.3 11.7 1.0
CG A:ASP192 3.1 13.2 1.0
PB A:CTP338 3.1 16.1 1.0
CG A:ASP190 3.2 17.5 1.0
PG A:CTP338 3.4 19.6 1.0
PA A:CTP338 3.4 13.3 1.0
OD1 A:ASP192 3.4 15.5 1.0
MN A:MN340 3.5 19.4 1.0
O3A A:CTP338 3.6 21.2 1.0
O3B A:CTP338 3.6 21.0 1.0
OD2 A:ASP190 3.8 20.8 1.0
O A:ASP190 3.9 19.9 1.0
O A:HOH644 4.1 24.9 1.0
C5' A:CTP338 4.1 16.2 1.0
O3G A:CTP338 4.1 19.6 1.0
C A:ASP190 4.1 17.1 1.0
OG A:SER180 4.2 19.9 1.0
N A:ASP190 4.3 15.2 1.0
O5' A:CTP338 4.3 15.1 1.0
N A:SER180 4.4 18.8 1.0
CB A:ASP190 4.4 17.9 1.0
CB A:ASP192 4.4 14.6 1.0
O1B A:CTP338 4.5 18.5 1.0
O2G A:CTP338 4.5 15.4 1.0
CA A:ASP190 4.5 14.8 1.0
O A:HOH365 4.5 15.6 1.0
O2A A:CTP338 4.6 16.8 1.0
CA A:GLY179 4.6 15.3 1.0
N A:MET191 4.7 15.9 1.0
N A:ASP192 4.8 15.7 1.0
O P:HOH11 4.9 18.6 1.0
C A:MET191 4.9 17.4 1.0
CB A:SER180 5.0 21.2 1.0

Manganese binding site 4 out of 8 in 3rh4

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Manganese binding site 4 out of 8 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn340

b:19.4
occ:1.00
 OD1 A:ASP192 2.2 15.5 1.0
OD2 A:ASP190 2.2 20.8 1.0
OD2 A:ASP256 2.2 13.4 1.0
O1A A:CTP338 2.3 11.7 1.0
O P:HOH11 2.4 18.6 1.0
CG A:ASP190 2.9 17.5 1.0
OD1 A:ASP190 3.0 18.6 1.0
CG A:ASP192 3.2 13.2 1.0
CG A:ASP256 3.3 17.8 1.0
PA A:CTP338 3.5 13.3 1.0
MN A:MN339 3.5 17.2 1.0
OD2 A:ASP192 3.5 18.5 1.0
O5' A:CTP338 3.7 15.1 1.0
C5' A:CTP338 3.9 16.2 1.0
CB A:ASP256 4.0 19.4 1.0
O2A A:CTP338 4.0 16.8 1.0
C3' P:DDG10 4.2 17.9 1.0
OD1 A:ASP256 4.3 17.2 1.0
O A:HOH644 4.3 24.9 1.0
CB A:ASP190 4.4 17.9 1.0
OP1 P:DDG10 4.5 14.8 1.0
CB A:ASP192 4.5 14.6 1.0
O A:HOH638 4.5 29.0 1.0
O A:MET191 4.6 13.9 1.0
O1G A:CTP338 4.7 16.9 1.0
C5' P:DDG10 4.7 13.4 1.0
C4' P:DDG10 4.8 19.1 1.0
NH2 A:ARG254 4.8 22.5 1.0
O3A A:CTP338 4.8 21.2 1.0
C A:MET191 5.0 17.4 1.0
CA A:ASP192 5.0 13.8 1.0
O2B A:CTP338 5.0 13.8 1.0

Manganese binding site 5 out of 8 in 3rh4

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Manganese binding site 5 out of 8 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn341

b:32.1
occ:1.00
 OD2 A:ASP145 2.3 24.9 1.0
O A:HOH555 2.3 27.3 1.0
O A:HOH552 2.4 23.6 1.0
ND1 A:HIS252 2.5 23.4 1.0
O A:HOH553 2.6 32.1 1.0
CE1 A:HIS252 3.2 19.7 1.0
CG A:ASP145 3.2 27.1 1.0
OD1 A:ASP145 3.5 26.2 1.0
CG A:HIS252 3.6 23.3 1.0
O A:HOH369 3.8 39.5 1.0
O A:HOH682 4.0 35.1 1.0
N A:HIS252 4.0 19.6 1.0
CB A:HIS252 4.1 16.6 1.0
CD1 A:TYR142 4.3 19.6 1.0
CE1 A:TYR142 4.4 17.2 1.0
NE2 A:HIS252 4.4 27.9 1.0
CB A:ASP145 4.5 16.1 1.0
O A:HOH570 4.5 32.2 1.0
CD2 A:HIS252 4.6 22.8 1.0
CA A:HIS252 4.7 17.3 1.0
C A:PRO251 4.9 21.5 1.0
CA A:PRO251 5.0 16.5 1.0
O A:TYR250 5.0 18.9 1.0
O A:HOH510 5.0 39.0 1.0
NE2 A:GLN240 5.0 23.4 1.0
O A:HOH397 5.0 40.6 1.0

Manganese binding site 6 out of 8 in 3rh4

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Manganese binding site 6 out of 8 in the Dna Polymerase Beta 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 with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn342

b:66.2
occ:0.74
 O A:HOH413 2.4 52.0 1.0
ND1 A:HIS285 2.5 38.8 1.0
OE1 A:GLU288 2.8 40.0 1.0
CE1 A:HIS285 3.3 33.7 1.0
CG A:HIS285 3.6 31.8 1.0
CB A:HIS285 4.0 30.0 1.0
CD A:GLU288 4.0 45.1 1.0
CA A:HIS285 4.4 33.1 1.0
NE2 A:HIS285 4.5 38.9 1.0
OE2 A:GLU288 4.6 55.5 1.0
CD2 A:HIS285 4.7 26.2 1.0
NE1 A:TRP325 4.9 29.8 1.0

Manganese binding site 7 out of 8 in 3rh4

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Manganese binding site 7 out of 8 in the Dna Polymerase Beta 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 7 of Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn343

b:62.8
occ:0.62
 O3G A:CTP350 2.3 55.4 1.0
O1B A:CTP350 2.4 67.2 1.0
O1A A:CTP350 2.4 56.9 1.0
PB A:CTP350 3.6 64.8 1.0
PG A:CTP350 3.6 81.0 1.0
PA A:CTP350 3.7 61.2 1.0
O A:HOH409 3.9 52.0 1.0
O3B A:CTP350 4.0 69.3 1.0
O3A A:CTP350 4.1 64.3 1.0
O5' A:CTP350 4.4 57.8 1.0
O2G A:CTP350 4.4 77.7 1.0
C5' A:CTP350 4.6 60.8 1.0
O1G A:CTP350 4.7 59.9 1.0
O2B A:CTP350 4.8 40.6 1.0
O2A A:CTP350 4.9 64.0 1.0

Manganese binding site 8 out of 8 in 3rh4

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Manganese binding site 8 out of 8 in the Dna Polymerase Beta 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 8 of Dna Polymerase Beta with A Dideoxy-Terminated Primer with An Incoming Ribonucleotide (Rctp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn346

b:39.9
occ:0.49
 O A:HOH644 2.2 24.9 1.0
O2G A:CTP338 2.4 15.4 1.0
O A:HOH442 2.9 39.4 1.0
PG A:CTP338 3.7 19.6 1.0
O1G A:CTP338 3.9 16.9 1.0
CA A:GLY189 3.9 13.9 1.0
O A:HOH638 4.5 29.0 1.0
C A:GLY189 4.5 21.3 1.0
O3B A:CTP338 4.5 21.0 1.0
O A:HOH431 4.6 38.9 1.0
O3G A:CTP338 4.7 19.6 1.0
O A:GLY189 4.8 16.0 1.0
N A:GLY189 4.8 18.9 1.0
O2A A:CTP338 4.9 16.8 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 17:45:08 2024

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