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Sodium in PDB 4do9: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene 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-Monofluoromethylene 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-Monofluoromethylene 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-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4do9 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) 20.28 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.693, 79.914, 55.607, 90.00, 107.66, 90.00
R / Rfree (%) 18.8 / 24.3

Other elements in 4do9:

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

Fluorine (F) 1 atom
Magnesium (Mg) 1 atom
Chlorine (Cl) 5 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer (pdb code 4do9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4do9:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4do9

Go back to Sodium Binding Sites List in 4do9
Sodium binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:27.4
occ:1.00
 OD1 A:ASP192 2.5 18.7 1.0
OD2 A:ASP190 2.8 23.4 1.0
OD2 A:ASP256 2.8 24.9 1.0
O1A A:GFH410 3.0 13.5 1.0
CG A:ASP190 3.4 17.8 1.0
C3' P:DOC10 3.4 19.8 1.0
CG A:ASP192 3.5 15.9 1.0
C5' P:DOC10 3.5 27.6 1.0
OD1 A:ASP190 3.5 14.3 1.0
CG A:ASP256 3.6 19.9 1.0
C4' P:DOC10 3.7 31.5 1.0
OD2 A:ASP192 3.7 14.2 1.0
PA A:GFH410 3.9 17.4 1.0
O5' A:GFH410 3.9 15.3 1.0
MG A:MG401 4.0 15.8 1.0
CB A:ASP256 4.1 19.0 1.0
O5' P:DOC10 4.2 28.4 1.0
C5' A:GFH410 4.2 14.7 1.0
O2A A:GFH410 4.3 17.0 1.0
OD1 A:ASP256 4.4 19.0 1.0
OP1 P:DOC10 4.4 28.2 1.0
O A:HOH630 4.5 30.0 1.0
NH2 A:ARG254 4.5 16.3 1.0
C2' P:DOC10 4.7 25.6 1.0
CB A:ASP190 4.7 13.3 1.0
O A:MET191 4.8 15.8 0.4
CB A:ASP192 4.9 16.0 1.0
O A:MET191 4.9 15.8 0.6
P P:DOC10 5.0 22.3 1.0

Sodium binding site 2 out of 3 in 4do9

Go back to Sodium Binding Sites List in 4do9
Sodium binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:26.5
occ:1.00
 OP1 P:DG9 2.5 18.9 1.0
O P:HOH101 2.6 23.6 1.0
O A:THR101 2.6 20.4 1.0
O A:VAL103 2.7 17.3 1.0
O A:ILE106 2.7 20.6 1.0
O A:HOH548 3.0 37.8 1.0
C A:THR101 3.4 19.5 1.0
C A:VAL103 3.5 18.2 1.0
P P:DG9 3.6 19.7 1.0
C A:ILE106 3.6 20.2 1.0
N A:ILE106 3.7 14.7 1.0
O A:HOH685 3.8 30.7 1.0
OP2 P:DG9 3.8 24.5 1.0
N A:GLY105 3.9 16.9 1.0
CA A:SER104 3.9 18.2 1.0
N A:SER104 4.0 16.6 1.0
CA A:THR101 4.0 18.8 1.0
CA A:ILE106 4.2 20.1 1.0
C A:SER104 4.2 18.7 1.0
N A:VAL103 4.2 19.6 1.0
C A:ARG102 4.3 19.2 1.0
N A:ARG102 4.4 22.3 1.0
CA A:VAL103 4.5 21.0 1.0
N A:GLY107 4.5 18.0 1.0
O3' P:DC8 4.5 17.6 1.0
CB A:THR101 4.6 20.3 1.0
CB A:ILE106 4.6 20.0 1.0
C A:GLY105 4.6 19.3 1.0
CA A:ARG102 4.6 23.3 1.0
O A:ARG102 4.7 16.4 1.0
O5' P:DG9 4.8 26.4 1.0
CA A:GLY105 4.8 20.6 1.0
CA A:GLY107 4.8 22.4 1.0
O A:LEU100 4.9 17.9 1.0

Sodium binding site 3 out of 3 in 4do9

Go back to Sodium Binding Sites List in 4do9
Sodium binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:37.0
occ:1.00
 O A:VAL65 2.7 31.7 1.0
O A:HOH727 2.7 38.3 1.0
O A:LYS60 2.7 40.1 1.0
O A:LEU62 2.8 29.8 1.0
OP1 D:DC3 2.9 31.4 1.0
O D:HOH102 2.9 35.4 1.0
C A:LYS60 3.5 34.5 1.0
C A:LEU62 3.6 29.9 1.0
C A:VAL65 3.7 29.1 1.0
P D:DC3 3.9 35.9 1.0
OP2 D:DC3 4.0 31.9 1.0
C A:LYS61 4.1 38.6 1.0
N A:VAL65 4.1 26.5 1.0
N A:LEU62 4.2 32.7 1.0
CA A:LYS60 4.2 30.1 1.0
O A:LYS61 4.2 36.0 1.0
CG A:LYS60 4.2 28.9 1.0
N A:PRO63 4.3 31.4 1.0
CA A:PRO63 4.3 30.1 1.0
N A:GLY64 4.3 29.8 1.0
CA A:VAL65 4.4 24.7 1.0
N A:LYS61 4.4 31.1 1.0
CA A:LYS61 4.5 35.3 1.0
CA A:LEU62 4.5 32.5 1.0
CB A:VAL65 4.6 26.6 1.0
O3' D:DT2 4.7 36.2 1.0
C A:PRO63 4.7 30.2 1.0
N A:GLY66 4.8 29.4 1.0
NZ A:LYS60 4.8 44.4 1.0
CB A:LYS60 4.8 28.2 1.0
O A:ALA59 4.9 27.0 1.0
CA A:GLY66 5.0 28.2 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: Mon Oct 7 14:58:03 2024

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