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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Dimethyl 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-Dimethyl Methylene Triphosphate, PDB code: 3jpr 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) 25.46 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.630, 80.100, 55.330, 90.00, 108.07, 90.00
R / Rfree (%) 20.1 / 25.3

Other elements in 3jpr:

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

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-Dimethyl Methylene Triphosphate (pdb code 3jpr). 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-Dimethyl Methylene Triphosphate, PDB code: 3jpr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3jpr

Go back to Sodium Binding Sites List in 3jpr
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-Dimethyl 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-Dimethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:21.4
occ:1.00
 OD2 A:ASP190 2.0 26.6 1.0
OD1 A:ASP192 2.1 24.0 1.0
O P:HOH328 2.1 32.8 1.0
OD2 A:ASP256 2.2 26.7 1.0
O1A A:G2M338 2.6 11.8 1.0
CG A:ASP190 3.0 22.3 1.0
CG A:ASP192 3.1 20.0 1.0
OD1 A:ASP190 3.2 22.4 1.0
MG A:MG339 3.3 16.5 1.0
CG A:ASP256 3.4 26.6 1.0
OD2 A:ASP192 3.5 18.3 1.0
PA A:G2M338 3.5 19.7 1.0
C3' P:DOC10 3.6 37.1 1.0
O5' A:G2M338 3.7 19.1 1.0
O2A A:G2M338 4.0 20.0 1.0
CB A:ASP256 4.0 23.8 1.0
C5' A:G2M338 4.1 19.4 1.0
O A:HOH513 4.4 21.0 1.0
CB A:ASP190 4.4 20.9 1.0
OD1 A:ASP256 4.4 26.8 1.0
CB A:ASP192 4.4 21.5 1.0
C5' P:DOC10 4.5 35.7 1.0
OP1 P:DOC10 4.5 31.0 1.0
C4' P:DOC10 4.5 36.2 1.0
O1G A:G2M338 4.5 19.9 1.0
C2' P:DOC10 4.6 35.5 1.0
O A:MET191 4.7 20.0 1.0
O5' P:DOC10 4.7 35.0 1.0
NH2 A:ARG254 4.7 21.5 1.0
O3A A:G2M338 4.9 18.2 1.0
O2B A:G2M338 4.9 16.4 1.0
CA A:ASP192 5.0 20.2 1.0

Sodium binding site 2 out of 3 in 3jpr

Go back to Sodium Binding Sites List in 3jpr
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-Dimethyl 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-Dimethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:27.4
occ:1.00
 O A:THR101 2.4 23.8 1.0
O P:HOH87 2.4 38.9 1.0
O A:VAL103 2.5 17.8 1.0
OP1 P:DG9 2.5 27.8 1.0
O A:HOH551 2.6 34.6 1.0
O A:ILE106 2.6 23.4 1.0
C A:THR101 3.3 23.4 1.0
C A:VAL103 3.4 18.3 1.0
P P:DG9 3.6 26.9 1.0
C A:ILE106 3.6 21.3 1.0
OP2 P:DG9 3.7 27.2 1.0
N A:ILE106 3.8 22.0 1.0
O A:HOH547 3.8 37.6 1.0
N A:GLY105 4.0 19.7 1.0
CA A:THR101 4.0 24.4 1.0
CA A:SER104 4.0 19.0 1.0
N A:VAL103 4.1 21.2 1.0
N A:SER104 4.1 19.5 1.0
CA A:ILE106 4.2 21.0 1.0
C A:ARG102 4.3 22.3 1.0
N A:ARG102 4.3 21.1 1.0
C A:SER104 4.3 19.3 1.0
CA A:VAL103 4.4 19.1 1.0
O3' P:DC8 4.5 26.0 1.0
N A:GLY107 4.5 21.1 1.0
CA A:ARG102 4.5 23.0 1.0
CB A:ILE106 4.6 20.8 1.0
CB A:THR101 4.6 25.5 1.0
C A:GLY105 4.7 22.0 1.0
O A:ARG102 4.8 22.8 1.0
CA A:GLY107 4.8 21.7 1.0
O5' P:DG9 4.8 28.9 1.0
O A:LEU100 4.8 24.6 1.0
CA A:GLY105 4.9 22.2 1.0
O A:HOH502 4.9 41.1 1.0

Sodium binding site 3 out of 3 in 3jpr

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

b:42.2
occ:1.00
 O A:VAL65 2.4 31.2 1.0
O A:LYS60 2.4 36.3 1.0
O D:HOH329 2.5 36.9 1.0
OP1 D:DC3 2.6 33.6 1.0
O A:LEU62 2.6 35.3 1.0
C A:LYS60 3.4 36.5 1.0
C A:VAL65 3.5 30.2 1.0
C A:LEU62 3.7 36.1 1.0
P D:DC3 3.7 35.2 1.0
OP2 D:DC3 3.9 35.3 1.0
N A:VAL65 4.0 29.8 1.0
CA A:LYS60 4.2 35.0 1.0
CA A:PRO63 4.2 35.5 1.0
C A:LYS61 4.2 38.5 1.0
CA A:VAL65 4.2 30.1 1.0
CG A:LYS60 4.2 36.5 1.0
N A:GLY64 4.2 31.5 1.0
N A:PRO63 4.3 36.2 1.0
N A:LEU62 4.3 37.2 1.0
O A:LYS61 4.3 39.3 1.0
N A:LYS61 4.4 37.8 1.0
CB A:VAL65 4.4 28.9 1.0
CA A:LYS61 4.6 38.8 1.0
N A:GLY66 4.6 28.3 1.0
C A:PRO63 4.6 34.1 1.0
O3' D:DT2 4.7 35.1 1.0
CA A:LEU62 4.7 35.6 1.0
CA A:GLY66 4.8 28.8 1.0
CB A:LYS60 4.8 34.8 1.0
O5' D:DC3 4.8 38.7 1.0
NZ A:LYS60 4.9 40.0 1.0
C A:GLY64 4.9 30.7 1.0
O A:ALA59 5.0 30.5 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: Tue Dec 15 06:15:38 2020

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