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Magnesium in PDB 4dob: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4dob was solved by V.K.Batra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.36 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.601, 80.403, 55.634, 90.00, 107.72, 90.00
R / Rfree (%) 20.5 / 26.3

Other elements in 4dob:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms
Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer (pdb code 4dob). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4dob:

Magnesium binding site 1 out of 1 in 4dob

Go back to Magnesium Binding Sites List in 4dob
Magnesium binding site 1 out of 1 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:16.1
occ:1.00
 O1G A:GRC410 2.0 21.8 1.0
OD1 A:ASP190 2.0 18.6 1.0
O1A A:GRC410 2.1 18.5 1.0
OD2 A:ASP192 2.1 19.5 1.0
O A:HOH653 2.1 15.2 1.0
O2B A:GRC410 2.2 15.1 1.0
CG A:ASP190 3.1 23.1 1.0
CG A:ASP192 3.1 16.7 1.0
PB A:GRC410 3.2 16.1 1.0
PG A:GRC410 3.3 25.3 1.0
PA A:GRC410 3.4 19.2 1.0
OD1 A:ASP192 3.5 20.2 1.0
OD2 A:ASP190 3.5 26.0 1.0
O3A A:GRC410 3.6 16.7 1.0
NA A:NA402 3.7 24.9 1.0
O3G A:GRC410 3.7 22.4 1.0
C3B A:GRC410 3.8 21.8 1.0
O A:ASP190 3.9 20.4 1.0
C5' A:GRC410 4.1 20.2 1.0
C A:ASP190 4.2 18.2 1.0
O5' A:GRC410 4.2 17.9 1.0
O A:HOH507 4.3 16.6 1.0
O A:HOH669 4.3 33.7 1.0
CB A:ASP190 4.3 21.4 1.0
N A:ASP190 4.4 20.0 1.0
CB A:ASP192 4.4 17.3 1.0
CA A:GLY179 4.5 11.8 1.0
O2A A:GRC410 4.5 17.5 1.0
CA A:ASP190 4.5 16.7 1.0
O1B A:GRC410 4.5 17.9 1.0
O2G A:GRC410 4.6 27.8 1.0
N A:SER180 4.6 17.4 1.0
N A:MET191 4.8 12.7 1.0
OG A:SER180 4.8 21.9 1.0
N A:ASP192 4.8 18.1 1.0
C A:MET191 5.0 18.3 1.0

Reference:

Y.Wu, V.M.Zakharova, B.A.Kashemirov, M.F.Goodman, V.K.Batra, S.H.Wilson, C.E.Mckenna. Beta,Gamma-Chf- and Beta,Gamma-Chcl-Dgtp Diastereomers: Synthesis, Discrete (31)P uc(Nmr) Signatures, and Absolute Configurations of New Stereochemical Probes For Dna Polymerases J.Am.Chem.Soc. V. 134 8734 2012.
ISSN: ISSN 0002-7863
PubMed: 22397499
DOI: 10.1021/JA300218X
Page generated: Thu Aug 15 17:19:14 2024

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