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Sodium in PDB 3jpt: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate:
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-Fluoro Chloro Methylene Triphosphate, PDB code: 3jpt was solved by V.K.Batra, J.Upton, B.Kashmerov, W.A.Beard, S.H.Wilson, M.F.Goodman, C.E.Mckenna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.89 / 2.15
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.660, 80.120, 55.450, 90.00, 108.05, 90.00
R / Rfree (%) 19.4 / 25.4

Other elements in 3jpt:

The structure of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Chloro Methylene Triphosphate also contains other interesting chemical elements:

Fluorine (F) 1 atom
Magnesium (Mg) 1 atom
Chlorine (Cl) 4 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-Fluoro Chloro Methylene Triphosphate (pdb code 3jpt). 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-Fluoro Chloro Methylene Triphosphate, PDB code: 3jpt:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3jpt

Go back to Sodium Binding Sites List in 3jpt
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-Fluoro Chloro Methylene Triphosphate


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-Fluoro Chloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:23.7
occ:1.00
 OD1 A:ASP192 2.2 18.3 1.0
OD2 A:ASP190 2.2 17.7 1.0
O1A A:GFC338 2.6 13.7 1.0
OD2 A:ASP256 2.6 30.4 1.0
CG A:ASP190 2.9 15.6 1.0
OD1 A:ASP190 3.0 11.0 1.0
CG A:ASP192 3.1 15.5 1.0
MG A:MG339 3.2 12.9 1.0
OD2 A:ASP192 3.4 15.1 1.0
PA A:GFC338 3.6 14.9 1.0
C3' P:DOC10 3.6 32.9 1.0
CG A:ASP256 3.7 22.7 1.0
O5' A:GFC338 3.8 14.4 1.0
C5' A:GFC338 4.1 14.1 1.0
O2A A:GFC338 4.2 14.5 1.0
CB A:ASP190 4.2 13.0 1.0
CB A:ASP256 4.3 21.4 1.0
C5' P:DOC10 4.4 29.6 1.0
O A:HOH495 4.4 26.1 1.0
O A:MET191 4.4 13.4 1.0
O1G A:GFC338 4.5 15.2 1.0
CB A:ASP192 4.5 17.9 1.0
C4' P:DOC10 4.5 31.7 1.0
O P:HOH167 4.6 27.1 1.0
O5' P:DOC10 4.7 31.1 1.0
OD1 A:ASP256 4.7 25.1 1.0
OP1 P:DOC10 4.7 27.8 1.0
O2B A:GFC338 4.7 12.4 1.0
C2' P:DOC10 4.7 31.0 1.0
NH2 A:ARG254 4.8 14.9 1.0
C A:MET191 4.9 16.7 1.0
O3A A:GFC338 4.9 15.7 1.0
CA A:ASP192 4.9 16.9 1.0

Sodium binding site 2 out of 3 in 3jpt

Go back to Sodium Binding Sites List in 3jpt
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-Fluoro Chloro Methylene Triphosphate


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-Fluoro Chloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:22.2
occ:1.00
 OP1 P:DG9 2.3 19.0 1.0
O A:THR101 2.3 19.4 1.0
O A:HOH446 2.4 24.0 1.0
O A:HOH452 2.5 22.2 1.0
O A:ILE106 2.6 15.0 1.0
O A:VAL103 2.7 15.4 1.0
C A:THR101 3.3 18.9 1.0
P P:DG9 3.4 19.1 1.0
C A:ILE106 3.5 16.4 1.0
OP2 P:DG9 3.6 20.7 1.0
C A:VAL103 3.6 17.2 1.0
O A:HOH464 3.7 32.0 1.0
N A:ILE106 3.8 17.4 1.0
CA A:THR101 3.9 19.4 1.0
N A:GLY105 3.9 18.0 1.0
CA A:SER104 4.1 19.3 1.0
CA A:ILE106 4.2 16.8 1.0
N A:VAL103 4.2 18.8 1.0
N A:SER104 4.2 18.1 1.0
N A:ARG102 4.3 17.8 1.0
C A:SER104 4.4 18.4 1.0
C A:ARG102 4.4 18.7 1.0
O3' P:DC8 4.4 19.8 1.0
O5' P:DG9 4.5 23.7 1.0
N A:GLY107 4.5 17.4 1.0
CB A:THR101 4.5 18.7 1.0
O P:HOH229 4.6 33.1 1.0
CA A:VAL103 4.6 16.6 1.0
CB A:ILE106 4.6 15.7 1.0
CA A:ARG102 4.6 19.8 1.0
C A:GLY105 4.6 18.5 1.0
CA A:GLY107 4.7 17.7 1.0
O A:LEU100 4.9 18.6 1.0
CA A:GLY105 4.9 18.6 1.0
O A:ARG102 4.9 18.0 1.0

Sodium binding site 3 out of 3 in 3jpt

Go back to Sodium Binding Sites List in 3jpt
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-Fluoro Chloro Methylene Triphosphate


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-Fluoro Chloro Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:30.6
occ:1.00
 O A:HOH599 2.2 48.9 1.0
O A:LYS60 2.2 28.7 1.0
O A:LEU62 2.4 31.7 1.0
O A:VAL65 2.6 28.7 1.0
O D:HOH269 2.6 34.5 1.0
OP1 D:DC3 2.7 32.7 1.0
C A:LYS60 3.2 29.2 1.0
C A:LEU62 3.4 31.5 1.0
C A:VAL65 3.6 28.2 1.0
P D:DC3 3.9 32.8 1.0
N A:VAL65 4.0 27.7 1.0
N A:LEU62 4.0 31.8 1.0
CA A:LYS60 4.0 28.2 1.0
C A:LYS61 4.0 32.5 1.0
CA A:PRO63 4.0 31.2 1.0
N A:PRO63 4.1 31.8 1.0
OP2 D:DC3 4.1 31.1 1.0
N A:LYS61 4.2 31.0 1.0
CA A:VAL65 4.2 27.4 1.0
CG A:LYS60 4.2 29.6 1.0
O A:LYS61 4.3 31.8 1.0
N A:GLY64 4.3 29.6 1.0
CA A:LEU62 4.3 31.1 1.0
CA A:LYS61 4.4 32.4 1.0
CB A:VAL65 4.4 26.5 1.0
C A:PRO63 4.5 30.1 1.0
N A:GLY66 4.7 28.1 1.0
O A:ALA59 4.7 25.5 1.0
CB A:LYS60 4.7 27.4 1.0
O3' D:DT2 4.8 31.7 1.0
CA A:GLY66 4.9 29.8 1.0

Reference:

V.K.Batra, L.C.Pedersen, W.A.Beard, S.H.Wilson, B.A.Kashemirov, T.G.Upton, M.F.Goodman, C.E.Mckenna. Halogenated Beta,Gamma-Methylene- and Ethylidene-Dgtp-Dna Ternary Complexes with Dna Polymerase Beta: Structural Evidence For Stereospecific Binding of the Fluoromethylene Analogues. J.Am.Chem.Soc. V. 132 7617 2010.
ISSN: ISSN 0002-7863
PubMed: 20465217
DOI: 10.1021/JA909370K
Page generated: Mon Oct 7 11:04:49 2024

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