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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochloromethylene 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-Monochloromethylene Triphosphate, PDB code: 3jpo 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) 22.30 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.460, 79.990, 55.430, 90.00, 107.91, 90.00
R / Rfree (%) 19.4 / 24.7

Other elements in 3jpo:

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

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

Sodium binding site 1 out of 3 in 3jpo

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

b:19.5
occ:1.00
 OD2 A:ASP190 2.1 27.5 1.0
OD1 A:ASP192 2.1 16.2 1.0
OD2 A:ASP256 2.3 25.2 1.0
O P:HOH11 2.4 46.4 1.0
O1A A:G1C338 2.6 15.3 0.5
O1A A:G1C338 2.7 18.9 0.5
CG A:ASP190 2.9 23.8 1.0
OD1 A:ASP190 3.1 23.8 1.0
CG A:ASP192 3.1 17.1 1.0
MG A:MG339 3.3 17.5 1.0
OD2 A:ASP192 3.4 18.9 1.0
CG A:ASP256 3.4 22.1 1.0
C3' P:DOC10 3.5 35.5 1.0
PA A:G1C338 3.6 17.9 0.5
PA A:G1C338 3.7 20.3 0.5
O5' A:G1C338 3.8 17.6 0.5
O5' A:G1C338 3.8 15.2 0.5
CB A:ASP256 4.1 20.9 1.0
C5' A:G1C338 4.1 17.1 0.5
O2A A:G1C338 4.1 15.3 0.5
C5' A:G1C338 4.2 16.2 0.5
O2A A:G1C338 4.3 19.7 0.5
CB A:ASP190 4.3 20.5 1.0
OD1 A:ASP256 4.4 21.2 1.0
O1G A:G1C338 4.4 21.0 0.5
CB A:ASP192 4.5 19.1 1.0
C4' P:DOC10 4.5 33.5 1.0
C5' P:DOC10 4.5 33.2 1.0
O A:MET191 4.5 17.6 1.0
O1G A:G1C338 4.5 21.9 0.5
C2' P:DOC10 4.6 33.7 1.0
O A:HOH488 4.6 30.3 1.0
O P:HOH321 4.7 38.5 1.0
O5' P:DOC10 4.7 30.9 1.0
O2B A:G1C338 4.7 17.2 0.5
NH2 A:ARG254 4.8 19.2 1.0
OP1 P:DOC10 4.8 26.8 1.0
C A:MET191 4.9 19.0 1.0
CA A:ASP192 4.9 19.0 1.0
O3A A:G1C338 4.9 17.1 0.5
O2B A:G1C338 5.0 15.9 0.5

Sodium binding site 2 out of 3 in 3jpo

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

b:23.7
occ:1.00
 O A:THR101 2.2 21.9 1.0
OP1 P:DG9 2.4 22.3 1.0
O A:ILE106 2.4 17.6 1.0
O A:VAL103 2.5 18.9 1.0
O P:HOH88 2.5 30.9 1.0
O A:HOH492 2.6 33.1 1.0
C A:THR101 3.2 22.7 1.0
C A:ILE106 3.4 18.6 1.0
P P:DG9 3.4 22.7 1.0
C A:VAL103 3.5 18.8 1.0
OP2 P:DG9 3.7 20.8 1.0
N A:ILE106 3.7 20.0 1.0
O A:HOH560 3.9 47.3 1.0
CA A:THR101 3.9 22.7 1.0
N A:GLY105 3.9 18.4 1.0
CA A:SER104 4.0 19.1 1.0
CA A:ILE106 4.0 18.8 1.0
N A:VAL103 4.1 20.4 1.0
N A:SER104 4.1 20.1 1.0
C A:ARG102 4.3 22.0 1.0
N A:ARG102 4.3 22.3 1.0
C A:SER104 4.3 19.9 1.0
N A:GLY107 4.4 18.8 1.0
O A:HOH612 4.4 46.6 1.0
O3' P:DC8 4.4 21.4 1.0
CA A:VAL103 4.4 19.6 1.0
CB A:ILE106 4.5 19.9 1.0
CB A:THR101 4.5 23.5 1.0
CA A:ARG102 4.5 23.1 1.0
C A:GLY105 4.6 22.2 1.0
CA A:GLY107 4.6 19.8 1.0
O5' P:DG9 4.6 25.4 1.0
O A:ARG102 4.7 21.7 1.0
O A:LEU100 4.8 24.5 1.0
CA A:GLY105 4.9 20.5 1.0

Sodium binding site 3 out of 3 in 3jpo

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

b:32.8
occ:1.00
 O A:LYS60 2.2 31.8 1.0
O A:LEU62 2.3 32.8 1.0
O A:HOH521 2.3 36.5 1.0
O A:VAL65 2.4 31.6 1.0
OP1 D:DC3 2.7 36.6 1.0
O D:HOH157 2.9 36.6 1.0
C A:LEU62 3.2 32.6 1.0
C A:LYS60 3.3 33.4 1.0
C A:VAL65 3.5 31.1 1.0
P D:DC3 3.8 36.5 1.0
C A:LYS61 3.9 34.7 1.0
N A:VAL65 3.9 30.1 1.0
N A:LEU62 3.9 33.3 1.0
O D:HOH417 3.9 37.1 1.0
N A:PRO63 3.9 33.4 1.0
CA A:PRO63 3.9 33.1 1.0
O A:LYS61 4.0 33.6 1.0
CA A:LYS60 4.0 32.0 1.0
OP2 D:DC3 4.1 35.2 1.0
CA A:VAL65 4.1 30.6 1.0
CA A:LEU62 4.2 32.6 1.0
N A:GLY64 4.2 32.4 1.0
N A:LYS61 4.2 33.4 1.0
CG A:LYS60 4.3 34.8 1.0
CB A:VAL65 4.4 28.6 1.0
CA A:LYS61 4.4 35.0 1.0
C A:PRO63 4.4 32.9 1.0
N A:GLY66 4.6 31.7 1.0
O3' D:DT2 4.7 35.9 1.0
O A:ALA59 4.7 31.4 1.0
CB A:LYS60 4.8 33.1 1.0
CA A:GLY66 4.9 31.6 1.0
C A:GLY64 4.9 31.1 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 11:04:13 2024

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