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Sodium 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:

Magnesium (Mg) 1 atom
Chlorine (Cl) 6 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer (pdb code 4dob). 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer, PDB code: 4dob:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4dob

Go back to Sodium Binding Sites List in 4dob
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-Monochlororomethylene 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:24.9
occ:1.00
 OD2 A:ASP256 2.3 30.9 1.0
OD1 A:ASP192 2.3 20.2 1.0
OD2 A:ASP190 2.3 26.0 1.0
O1A A:GRC410 2.9 18.5 1.0
CG A:ASP190 3.1 23.1 1.0
OD1 A:ASP190 3.3 18.6 1.0
CG A:ASP192 3.3 16.7 1.0
CG A:ASP256 3.4 26.6 1.0
OD2 A:ASP192 3.6 19.5 1.0
C3' P:DOC10 3.7 30.5 1.0
MG A:MG401 3.7 16.1 1.0
PA A:GRC410 3.8 19.2 1.0
C4' P:DOC10 3.9 38.2 1.0
C5' P:DOC10 4.0 28.9 1.0
O5' A:GRC410 4.0 17.9 1.0
CB A:ASP256 4.1 20.1 1.0
C5' A:GRC410 4.2 20.2 1.0
O2A A:GRC410 4.3 17.5 1.0
OD1 A:ASP256 4.3 22.3 1.0
CB A:ASP190 4.4 21.4 1.0
O5' P:DOC10 4.5 36.6 1.0
OP2 P:DOC10 4.5 26.2 1.0
O P:HOH108 4.6 31.5 1.0
NH2 A:ARG254 4.6 20.6 1.0
CB A:ASP192 4.6 17.3 1.0
O A:HOH669 4.7 33.7 1.0
O A:MET191 4.7 17.3 1.0
C2' P:DOC10 4.7 31.7 1.0
O1G A:GRC410 4.8 21.8 1.0

Sodium binding site 2 out of 3 in 4dob

Go back to Sodium Binding Sites List in 4dob
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-Monochlororomethylene 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:24.6
occ:1.00
 O A:ILE106 2.3 19.2 1.0
O A:THR101 2.4 25.2 1.0
O P:HOH101 2.4 27.6 1.0
OP1 P:DG9 2.5 23.1 1.0
O A:VAL103 2.6 21.0 1.0
C A:THR101 3.3 27.1 1.0
C A:ILE106 3.4 22.6 1.0
C A:VAL103 3.5 22.9 1.0
P P:DG9 3.5 24.7 1.0
OP2 P:DG9 3.6 23.1 1.0
N A:ILE106 3.8 21.3 1.0
CA A:THR101 3.9 26.4 1.0
O A:HOH585 3.9 29.9 1.0
N A:GLY105 4.0 19.5 1.0
CA A:SER104 4.1 21.6 1.0
CA A:ILE106 4.1 21.2 1.0
N A:SER104 4.1 19.4 1.0
N A:VAL103 4.2 23.4 1.0
N A:GLY107 4.3 20.1 1.0
N A:ARG102 4.3 24.0 1.0
C A:SER104 4.3 21.4 1.0
C A:ARG102 4.4 21.3 1.0
CB A:THR101 4.4 26.1 1.0
CB A:ILE106 4.5 25.0 1.0
CA A:VAL103 4.5 22.5 1.0
CA A:GLY107 4.5 20.2 1.0
O3' P:DC8 4.6 22.1 1.0
CA A:ARG102 4.6 30.7 1.0
O5' P:DG9 4.6 28.8 1.0
C A:GLY105 4.7 25.6 1.0
O A:ARG102 4.8 23.2 1.0
O A:LEU100 4.8 19.5 1.0
CA A:GLY105 4.9 28.7 1.0

Sodium binding site 3 out of 3 in 4dob

Go back to Sodium Binding Sites List in 4dob
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-Monochlororomethylene 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-Monochlororomethylene Triphosphate: Stereoselective Binding of R-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:41.8
occ:1.00
 O A:LYS60 2.2 39.4 1.0
O A:VAL65 2.3 33.0 1.0
O A:HOH514 2.4 39.4 1.0
O A:LEU62 2.4 38.9 1.0
OP1 D:DC3 2.9 37.6 1.0
C A:LYS60 3.2 36.9 1.0
C A:LEU62 3.4 35.4 1.0
C A:VAL65 3.5 34.0 1.0
N A:LEU62 3.9 37.4 1.0
C A:LYS61 3.9 40.7 1.0
P D:DC3 3.9 39.6 1.0
N A:VAL65 4.0 28.4 1.0
CA A:LYS60 4.0 32.4 1.0
OP2 D:DC3 4.0 31.8 1.0
O A:LYS61 4.1 39.3 1.0
CG A:LYS60 4.1 38.0 1.0
N A:PRO63 4.1 30.8 1.0
CA A:PRO63 4.1 32.6 1.0
CA A:VAL65 4.1 28.3 1.0
N A:LYS61 4.2 33.6 1.0
CA A:LEU62 4.3 35.7 1.0
N A:GLY64 4.3 35.0 1.0
CA A:LYS61 4.4 37.6 1.0
CB A:VAL65 4.4 33.4 1.0
N A:GLY66 4.6 35.2 1.0
C A:PRO63 4.6 35.7 1.0
NZ A:LYS60 4.7 43.2 1.0
CB A:LYS60 4.7 32.8 1.0
O A:ALA59 4.7 32.0 1.0
CA A:GLY66 4.8 29.3 1.0
O3' D:DT2 4.9 39.0 1.0
C A:GLY64 5.0 30.9 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 14:58:26 2024

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