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

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Fluoro Methyl 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 Methyl 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 Methyl Methylene Triphosphate, PDB code: 3jps 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) 24.98 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.570, 79.860, 55.550, 90.00, 107.84, 90.00
R / Rfree (%) 19.1 / 23.7

Other elements in 3jps:

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

Fluorine (F) 1 atom
Magnesium (Mg) 1 atom
Chlorine (Cl) 3 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 Methyl Methylene Triphosphate (pdb code 3jps). 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 Methyl Methylene Triphosphate, PDB code: 3jps:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3jps

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

b:33.5
occ:1.00
 OD2 A:ASP190 2.1 17.1 1.0
OD1 A:ASP192 2.2 14.7 1.0
OD2 A:ASP256 2.4 25.0 1.0
O1A A:GFM338 2.7 13.2 1.0
CG A:ASP190 3.2 16.7 1.0
CG A:ASP192 3.3 12.3 1.0
OD1 A:ASP190 3.5 16.3 1.0
CG A:ASP256 3.5 20.9 1.0
OD2 A:ASP192 3.6 11.0 1.0
PA A:GFM338 3.7 16.0 1.0
MG A:MG339 3.7 15.2 1.0
O5' A:GFM338 3.8 14.7 1.0
O P:HOH74 3.9 26.8 1.0
C5' P:DOC10 4.0 34.1 1.0
O2A A:GFM338 4.1 16.5 1.0
CB A:ASP256 4.2 20.1 1.0
C5' A:GFM338 4.2 14.4 1.0
C3' P:DOC10 4.3 34.9 1.0
O5' P:DOC10 4.4 35.3 1.0
OP1 P:DOC10 4.4 28.4 1.0
CB A:ASP190 4.5 14.0 1.0
OD1 A:ASP256 4.5 21.5 1.0
CB A:ASP192 4.6 13.1 1.0
O A:HOH506 4.7 25.7 1.0
NH2 A:ARG254 4.7 17.2 1.0
C4' P:DOC10 4.7 36.2 1.0
O1G A:GFM338 4.8 17.8 1.0
O A:MET191 4.8 15.6 1.0

Sodium binding site 2 out of 3 in 3jps

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

b:23.1
occ:1.00
 OP1 P:DG9 2.3 20.0 1.0
O A:THR101 2.3 20.3 1.0
O A:ILE106 2.4 15.5 1.0
O P:HOH103 2.4 30.9 1.0
O A:VAL103 2.7 16.6 1.0
O A:HOH491 2.7 28.8 1.0
C A:THR101 3.3 19.9 1.0
P P:DG9 3.4 20.1 1.0
C A:ILE106 3.4 17.5 1.0
C A:VAL103 3.5 17.2 1.0
OP2 P:DG9 3.6 19.1 1.0
N A:ILE106 3.8 17.9 1.0
CA A:THR101 3.8 19.7 1.0
N A:GLY105 4.0 18.1 1.0
CA A:SER104 4.1 18.8 1.0
CA A:ILE106 4.1 17.0 1.0
N A:VAL103 4.1 18.9 1.0
N A:SER104 4.2 16.9 1.0
O A:HOH598 4.2 32.1 1.0
N A:ARG102 4.3 18.9 1.0
C A:ARG102 4.3 19.8 1.0
N A:GLY107 4.4 16.6 1.0
O3' P:DC8 4.4 18.0 1.0
C A:SER104 4.4 18.8 1.0
CB A:THR101 4.5 20.3 1.0
CB A:ILE106 4.5 17.3 1.0
O5' P:DG9 4.5 21.7 1.0
CA A:VAL103 4.5 18.1 1.0
CA A:GLY107 4.6 19.3 1.0
CA A:ARG102 4.6 21.2 1.0
C A:GLY105 4.7 19.0 1.0
O A:LEU100 4.8 17.8 1.0
O A:ARG102 4.8 20.3 1.0
CA A:GLY105 5.0 19.4 1.0

Sodium binding site 3 out of 3 in 3jps

Go back to Sodium Binding Sites List in 3jps
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 Methyl 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 Methyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:32.7
occ:1.00
 O A:LYS60 2.2 31.1 1.0
O A:VAL65 2.3 28.9 1.0
O A:LEU62 2.4 31.1 1.0
O A:HOH541 2.7 37.4 1.0
O D:HOH182 2.7 33.6 1.0
OP1 D:DC3 2.7 34.6 1.0
C A:LYS60 3.3 32.2 1.0
C A:VAL65 3.4 27.9 1.0
C A:LEU62 3.4 30.9 1.0
P D:DC3 3.8 35.9 1.0
N A:VAL65 3.8 27.3 1.0
CA A:LYS60 3.9 30.7 1.0
N A:LEU62 4.0 31.8 1.0
OP2 D:DC3 4.0 32.7 1.0
CA A:VAL65 4.0 27.6 1.0
C A:LYS61 4.1 32.9 1.0
N A:PRO63 4.1 31.6 1.0
CG A:LYS60 4.1 33.3 1.0
CA A:PRO63 4.2 31.4 1.0
CB A:VAL65 4.2 26.0 1.0
N A:GLY64 4.3 29.1 1.0
N A:LYS61 4.3 31.7 1.0
CA A:LEU62 4.3 30.9 1.0
N A:GLY66 4.4 27.8 1.0
O A:LYS61 4.5 31.3 1.0
CA A:LYS61 4.5 32.7 1.0
C A:PRO63 4.6 30.6 1.0
CB A:LYS60 4.7 32.0 1.0
CA A:GLY66 4.7 27.8 1.0
O A:ALA59 4.7 27.1 1.0
O3' D:DT2 4.8 33.9 1.0
C A:GLY64 4.9 27.5 1.0
NZ A:LYS60 4.9 40.7 1.0
O5' D:DC3 5.0 38.1 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 11:04:48 2024

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