Atomistry » Manganese » PDB 3q7c-3rl4 » 3rh6
Atomistry »
  Manganese »
    PDB 3q7c-3rl4 »
      3rh6 »

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

Go back to Manganese Binding Sites List in 3rh6
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

Go back to Manganese Binding Sites List in 3rh6
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

Go back to Manganese Binding Sites List in 3rh6
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

Go back to Manganese Binding Sites List in 3rh6
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

Go back to Manganese Binding Sites List in 3rh6
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: Sat Oct 5 17:45:36 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy