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Sodium in PDB 4doa: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Non-Interactive Binding of S-Isomer

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Non-Interactive Binding of S-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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer, PDB code: 4doa 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) 20.27 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.638, 79.933, 55.519, 90.00, 107.70, 90.00
R / Rfree (%) 19.1 / 24.3

Other elements in 4doa:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monofluoromethylene Triphosphate: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer (pdb code 4doa). 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: Non-Interactive Binding of S-Isomer, PDB code: 4doa:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4doa

Go back to Sodium Binding Sites List in 4doa
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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:30.1
occ:1.00
 OD2 A:ASP190 2.3 25.6 1.0
OD1 A:ASP192 2.3 18.4 1.0
OD2 A:ASP256 2.4 32.3 1.0
O1A A:FHG410 2.7 18.0 1.0
CG A:ASP190 3.0 19.8 1.0
OD1 A:ASP190 3.1 15.9 1.0
CG A:ASP192 3.3 19.4 1.0
C3' P:DOC10 3.4 42.1 1.0
CG A:ASP256 3.5 27.2 1.0
MG A:MG401 3.5 14.3 1.0
OD2 A:ASP192 3.6 17.9 1.0
P1 A:FHG410 3.7 20.5 1.0
O5' A:FHG410 4.0 18.9 1.0
O2A A:FHG410 4.1 18.1 1.0
C5' A:FHG410 4.2 17.1 1.0
CB A:ASP256 4.2 26.9 1.0
C5' P:DOC10 4.2 33.8 1.0
C4' P:DOC10 4.2 46.9 1.0
CB A:ASP190 4.4 14.8 1.0
OD1 A:ASP256 4.4 18.6 1.0
O5' P:DOC10 4.4 33.5 1.0
O A:HOH651 4.4 29.1 1.0
C2' P:DOC10 4.5 35.1 1.0
OP2 P:DOC10 4.6 28.7 1.0
CB A:ASP192 4.7 20.9 1.0
O1G A:FHG410 4.8 20.3 1.0
O A:MET191 4.8 15.9 1.0
O A:HOH653 4.8 23.0 1.0
NH2 A:ARG254 4.8 24.7 1.0

Sodium binding site 2 out of 3 in 4doa

Go back to Sodium Binding Sites List in 4doa
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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:22.8
occ:1.00
 O A:ILE106 2.3 16.4 1.0
OP1 P:DG9 2.4 21.6 1.0
O A:THR101 2.5 24.6 1.0
O A:VAL103 2.5 17.9 1.0
O P:HOH101 2.6 28.3 1.0
C A:ILE106 3.3 21.2 1.0
C A:THR101 3.3 21.3 1.0
C A:VAL103 3.4 22.6 1.0
P P:DG9 3.5 23.8 1.0
OP2 P:DG9 3.7 23.1 1.0
N A:ILE106 3.7 18.5 1.0
N A:GLY105 3.8 20.8 1.0
CA A:THR101 3.9 24.5 1.0
CA A:SER104 3.9 18.8 1.0
CA A:ILE106 4.0 21.7 1.0
N A:SER104 4.0 17.9 1.0
O A:HOH617 4.1 29.8 1.0
C A:SER104 4.2 19.8 1.0
N A:VAL103 4.2 21.6 1.0
N A:GLY107 4.3 19.0 1.0
N A:ARG102 4.3 20.8 1.0
C A:ARG102 4.4 22.2 1.0
CB A:ILE106 4.4 17.6 1.0
CA A:VAL103 4.4 20.9 1.0
O3' P:DC8 4.5 16.9 1.0
CB A:THR101 4.5 26.5 1.0
C A:GLY105 4.5 23.2 1.0
CA A:GLY107 4.6 24.1 1.0
CA A:ARG102 4.6 26.6 1.0
O5' P:DG9 4.6 25.3 1.0
O A:LEU100 4.7 19.3 1.0
CA A:GLY105 4.7 24.6 1.0
O A:ARG102 4.8 27.6 1.0

Sodium binding site 3 out of 3 in 4doa

Go back to Sodium Binding Sites List in 4doa
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: Non-Interactive Binding of S-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: Non-Interactive Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:39.6
occ:1.00
 O A:LYS60 2.2 39.2 1.0
O A:VAL65 2.3 36.3 1.0
O A:LEU62 2.3 39.4 1.0
O D:HOH102 2.9 34.5 1.0
OP1 D:DC3 3.0 36.4 1.0
C A:LYS60 3.3 38.2 1.0
C A:LEU62 3.3 37.6 1.0
C A:VAL65 3.5 33.4 1.0
N A:LEU62 3.8 34.8 1.0
C A:LYS61 3.9 43.1 1.0
P D:DC3 3.9 35.8 1.0
OP2 D:DC3 4.0 29.1 1.0
N A:VAL65 4.0 27.6 1.0
CA A:PRO63 4.0 37.1 1.0
N A:PRO63 4.0 34.4 1.0
CA A:LYS60 4.1 31.1 1.0
CA A:LEU62 4.2 35.5 1.0
CA A:VAL65 4.2 28.0 1.0
O D:HOH105 4.2 48.0 1.0
N A:LYS61 4.2 32.6 1.0
O A:LYS61 4.2 37.6 1.0
N A:GLY64 4.3 35.1 1.0
CG A:LYS60 4.3 35.6 1.0
CA A:LYS61 4.4 38.0 1.0
CB A:VAL65 4.4 29.8 1.0
N A:GLY66 4.5 29.7 1.0
C A:PRO63 4.6 41.6 1.0
O A:ALA59 4.7 29.8 1.0
CB A:LYS60 4.8 27.2 1.0
CA A:GLY66 4.8 28.9 1.0
O3' D:DT2 4.9 40.2 1.0
NZ A:LYS60 4.9 49.6 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 14:58:20 2024

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