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Sodium in PDB 2pxi: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene Triphosphate

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma- Monofluoromethylene 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- Monofluoromethylene Triphosphate, PDB code: 2pxi was solved by C.E.Mckenna, V.K.Batra, W.A.Beard, L.C.Pedersen, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.09 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.600, 80.200, 55.400, 90.00, 107.80, 90.00
R / Rfree (%) 20.6 / 27

Other elements in 2pxi:

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

Sodium binding site 1 out of 3 in 2pxi

Go back to Sodium Binding Sites List in 2pxi
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


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

b:26.4
occ:1.00
OD1 A:ASP192 2.1 20.5 1.0
OD2 A:ASP256 2.3 27.5 1.0
OD2 A:ASP190 2.3 24.8 1.0
O1A A:GFH338 2.7 16.2 1.0
CG A:ASP190 3.0 22.0 1.0
OD1 A:ASP190 3.1 20.9 1.0
CG A:ASP192 3.2 17.5 1.0
CG A:ASP256 3.4 25.1 1.0
MG A:MG339 3.4 18.2 1.0
OD2 A:ASP192 3.5 16.7 1.0
C3' P:DOC10 3.5 37.3 1.0
PA A:GFH338 3.8 22.6 1.0
O5' A:GFH338 4.0 19.4 1.0
CB A:ASP256 4.0 22.6 1.0
O2A A:GFH338 4.3 20.5 1.0
C5' A:GFH338 4.3 20.7 1.0
CB A:ASP190 4.3 17.1 1.0
O A:MET191 4.4 20.5 1.0
OD1 A:ASP256 4.4 25.1 1.0
C4' P:DOC10 4.5 37.8 1.0
CB A:ASP192 4.5 20.8 1.0
C5' P:DOC10 4.5 34.6 1.0
O1G A:GFH338 4.6 22.2 1.0
C2' P:DOC10 4.7 37.0 1.0
OP1 P:DOC10 4.7 29.6 1.0
NH2 A:ARG254 4.7 21.9 1.0
O5' P:DOC10 4.8 35.3 1.0
O A:HOH400 4.8 36.5 1.0
C A:MET191 4.9 21.1 1.0
CA A:ASP192 5.0 19.7 1.0
N A:ASP256 5.0 21.6 1.0

Sodium binding site 2 out of 3 in 2pxi

Go back to Sodium Binding Sites List in 2pxi
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


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

b:23.6
occ:1.00
O A:THR101 2.3 26.3 1.0
OP1 P:DG9 2.4 24.3 1.0
O P:HOH11 2.5 33.7 1.0
O A:ILE106 2.5 19.0 1.0
O A:HOH484 2.6 32.1 1.0
O A:VAL103 2.7 20.8 1.0
C A:THR101 3.2 24.3 1.0
P P:DG9 3.5 23.8 1.0
C A:ILE106 3.5 21.1 1.0
C A:VAL103 3.5 20.9 1.0
OP2 P:DG9 3.6 26.2 1.0
N A:ILE106 3.8 21.0 1.0
CA A:THR101 3.9 24.9 1.0
O A:HOH424 3.9 46.0 1.0
N A:VAL103 4.0 21.8 1.0
CA A:SER104 4.1 21.6 1.0
N A:GLY105 4.1 20.1 1.0
CA A:ILE106 4.1 21.1 1.0
N A:SER104 4.1 20.8 1.0
N A:ARG102 4.2 22.6 1.0
C A:ARG102 4.2 22.5 1.0
C A:SER104 4.4 20.6 1.0
O3' P:DC8 4.4 23.9 1.0
CA A:VAL103 4.5 20.9 1.0
CA A:ARG102 4.5 23.3 1.0
N A:GLY107 4.5 20.0 1.0
CB A:ILE106 4.5 22.5 1.0
CB A:THR101 4.5 24.1 1.0
O5' P:DG9 4.7 27.9 1.0
O A:LEU100 4.7 26.5 1.0
CA A:GLY107 4.7 23.6 1.0
O A:ARG102 4.7 22.1 1.0
C A:GLY105 4.8 21.6 1.0
O P:HOH23 5.0 39.1 1.0

Sodium binding site 3 out of 3 in 2pxi

Go back to Sodium Binding Sites List in 2pxi
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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:37.4
occ:1.00
O A:LEU62 2.3 35.8 1.0
O A:LYS60 2.3 31.9 1.0
O A:VAL65 2.4 29.0 1.0
OP1 D:DC3 2.6 34.7 1.0
O A:HOH380 2.8 27.9 1.0
C A:LEU62 3.3 34.5 1.0
C A:VAL65 3.3 30.4 1.0
C A:LYS60 3.4 33.2 1.0
N A:VAL65 3.6 30.5 1.0
P D:DC3 3.6 33.8 1.0
OP2 D:DC3 3.8 35.2 1.0
CA A:PRO63 3.9 34.2 1.0
CA A:VAL65 3.9 29.6 1.0
N A:GLY64 4.0 31.2 1.0
N A:PRO63 4.0 34.6 1.0
CA A:LYS60 4.1 32.1 1.0
C A:LYS61 4.1 33.7 1.0
N A:LEU62 4.1 33.5 1.0
CB A:VAL65 4.1 29.3 1.0
CG A:LYS60 4.3 33.2 1.0
O A:LYS61 4.3 33.6 1.0
C A:PRO63 4.3 33.1 1.0
CA A:LEU62 4.4 33.0 1.0
N A:GLY66 4.4 29.9 1.0
N A:LYS61 4.4 32.7 1.0
O3' D:DT2 4.5 34.5 1.0
CA A:LYS61 4.6 34.2 1.0
C A:GLY64 4.6 31.8 1.0
CA A:GLY66 4.7 31.8 1.0
O A:ALA59 4.8 28.7 1.0
CB A:LYS60 4.8 32.3 1.0
O5' D:DC3 4.9 38.2 1.0
CA A:GLY64 5.0 31.4 1.0

Reference:

C.E.Mckenna, B.A.Kashemirov, T.G.Upton, V.K.Batra, M.F.Goodman, L.C.Pedersen, W.A.Beard, S.H.Wilson. (R)-Beta,Gamma-Fluoromethylene-Dgtp-Dna Ternary Complex with Dna Polymerase Beta. J.Am.Chem.Soc. V. 129 15412 2007.
ISSN: ISSN 0002-7863
PubMed: 18031037
DOI: 10.1021/JA072127V
Page generated: Tue Dec 15 05:54:17 2020

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