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

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate: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-Monochlororomethylene Triphosphate: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-Monochlororomethylene Triphosphate:Binding of S-Isomer, PDB code: 4doc 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) 21.22 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.688, 80.019, 55.716, 90.00, 107.68, 90.00
R / Rfree (%) 20 / 24.9

Other elements in 4doc:

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

Sodium binding site 1 out of 3 in 4doc

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

b:27.4
occ:1.00
 OD2 A:ASP256 2.3 29.6 1.0
OD1 A:ASP192 2.3 19.4 1.0
OD2 A:ASP190 2.3 23.3 1.0
O1A A:G1C410 3.1 17.7 1.0
CG A:ASP256 3.2 22.1 1.0
CG A:ASP190 3.2 18.9 1.0
CG A:ASP192 3.3 16.1 1.0
OD1 A:ASP190 3.5 16.7 1.0
OD2 A:ASP192 3.6 14.4 1.0
CB A:ASP256 3.8 21.8 1.0
C3' P:DOC10 3.8 27.2 1.0
C5' P:DOC10 3.9 32.5 1.0
MG A:MG401 4.0 17.6 1.0
C4' P:DOC10 4.0 32.3 1.0
OD1 A:ASP256 4.0 20.0 1.0
PA A:G1C410 4.1 17.5 1.0
O5' A:G1C410 4.2 17.9 1.0
O5' P:DOC10 4.2 33.2 1.0
C5' A:G1C410 4.3 18.4 1.0
CB A:ASP190 4.4 16.1 1.0
O P:HOH106 4.4 27.4 1.0
NH2 A:ARG254 4.5 18.8 1.0
CB A:ASP192 4.6 16.3 1.0
O A:MET191 4.6 15.4 1.0
N A:ASP256 4.7 16.5 1.0
OP1 P:DOC10 4.7 34.5 1.0
O2A A:G1C410 4.8 19.5 1.0
CA A:ASP256 4.9 17.1 1.0
C2' P:DOC10 4.9 27.2 1.0
O A:HOH620 5.0 32.2 1.0
CA A:ASP192 5.0 17.6 1.0
C A:MET191 5.0 14.9 1.0

Sodium binding site 2 out of 3 in 4doc

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

b:23.0
occ:1.00
 O A:ILE106 2.3 19.7 1.0
OP1 P:DG9 2.4 22.7 1.0
O A:THR101 2.4 23.3 1.0
O P:HOH115 2.5 26.5 1.0
O A:VAL103 2.5 18.1 1.0
O P:HOH101 2.5 30.3 1.0
C A:THR101 3.3 22.4 1.0
C A:ILE106 3.3 22.6 1.0
C A:VAL103 3.4 19.8 1.0
P P:DG9 3.5 23.8 1.0
OP2 P:DG9 3.7 23.0 1.0
N A:ILE106 3.8 19.1 1.0
CA A:THR101 3.9 21.1 1.0
O A:HOH756 3.9 33.6 1.0
N A:GLY105 4.0 19.2 1.0
CA A:SER104 4.0 19.7 1.0
CA A:ILE106 4.1 20.5 1.0
N A:SER104 4.1 19.7 1.0
N A:VAL103 4.2 18.7 1.0
N A:ARG102 4.3 21.2 1.0
N A:GLY107 4.3 18.8 1.0
C A:ARG102 4.3 21.0 1.0
C A:SER104 4.3 16.9 1.0
CA A:VAL103 4.4 21.2 1.0
O3' P:DC8 4.5 21.1 1.0
CB A:THR101 4.5 25.0 1.0
CB A:ILE106 4.5 21.1 1.0
CA A:GLY107 4.6 19.7 1.0
CA A:ARG102 4.6 25.6 1.0
C A:GLY105 4.6 24.1 1.0
O5' P:DG9 4.6 25.4 1.0
O A:LEU100 4.7 21.1 1.0
O A:ARG102 4.8 23.4 1.0
CA A:GLY105 4.9 22.8 1.0

Sodium binding site 3 out of 3 in 4doc

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

b:34.6
occ:1.00
 O A:LYS60 2.0 28.5 1.0
O A:VAL65 2.4 29.2 1.0
O A:LEU62 2.4 32.3 1.0
O A:HOH812 2.5 32.7 1.0
C A:LYS60 3.1 30.4 1.0
C A:LEU62 3.3 32.5 1.0
OP1 D:DC3 3.3 32.8 1.0
O A:HOH868 3.3 43.2 1.0
C A:VAL65 3.6 31.5 1.0
N A:LEU62 3.7 32.4 1.0
C A:LYS61 3.8 35.3 1.0
CA A:LYS60 3.9 28.1 1.0
N A:LYS61 4.0 31.6 1.0
N A:VAL65 4.1 29.7 1.0
N A:PRO63 4.1 33.1 1.0
O A:LYS61 4.1 36.9 1.0
CA A:LEU62 4.1 31.5 1.0
OP2 D:DC3 4.2 30.4 1.0
CG A:LYS60 4.2 31.3 1.0
CA A:VAL65 4.2 27.4 1.0
CA A:LYS61 4.2 33.3 1.0
CA A:PRO63 4.2 33.4 1.0
P D:DC3 4.2 36.8 1.0
CB A:VAL65 4.4 25.9 1.0
N A:GLY64 4.5 34.0 1.0
O A:ALA59 4.6 25.4 1.0
CB A:LYS60 4.6 28.8 1.0
N A:GLY66 4.6 29.2 1.0
C A:PRO63 4.7 33.7 1.0
CA A:GLY66 4.9 29.9 1.0
NZ A:LYS60 5.0 34.5 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 14:58:34 2024

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