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

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

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl 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-Monomethyl Methylene Triphosphate, PDB code: 3jpp 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) 26.42 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.700, 80.110, 55.550, 90.00, 107.95, 90.00
R / Rfree (%) 19.8 / 25

Other elements in 3jpp:

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

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-Monomethyl Methylene Triphosphate (pdb code 3jpp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 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-Monomethyl Methylene Triphosphate, PDB code: 3jpp:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3jpp

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Sodium binding site 1 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl 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-Monomethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:24.1
occ:1.00
 OD1 A:ASP192 2.0 18.5 1.0
O P:HOH273 2.1 35.2 1.0
OD2 A:ASP190 2.1 19.5 1.0
OD2 A:ASP256 2.2 25.8 1.0
O1A A:G1M338 2.6 20.6 0.5
O1A A:G1M338 2.6 15.2 0.5
CG A:ASP190 3.0 20.1 1.0
CG A:ASP192 3.1 17.0 1.0
OD1 A:ASP190 3.3 19.1 1.0
CG A:ASP256 3.4 21.9 1.0
OD2 A:ASP192 3.4 17.7 1.0
PA A:G1M338 3.5 21.5 0.5
PA A:G1M338 3.5 15.8 0.5
MG A:MG339 3.6 18.6 1.0
O5' A:G1M338 3.6 20.0 0.5
O5' A:G1M338 3.7 15.4 0.5
C3' P:DOC10 3.7 41.1 1.0
O2A A:G1M338 4.0 15.2 0.5
O2A A:G1M338 4.0 20.9 0.5
C5' A:G1M338 4.0 19.9 0.5
CB A:ASP256 4.1 20.8 1.0
C5' A:G1M338 4.1 16.8 0.5
O P:HOH196 4.2 36.0 1.0
C5' P:DOC10 4.3 38.0 1.0
OD1 A:ASP256 4.4 20.4 1.0
O A:HOH578 4.4 27.9 1.0
CB A:ASP192 4.4 18.1 1.0
CB A:ASP190 4.4 16.8 1.0
O5' P:DOC10 4.5 36.3 1.0
C4' P:DOC10 4.5 39.7 1.0
O1G A:G1M338 4.6 24.7 0.5
O1G A:G1M338 4.6 16.1 0.5
O A:MET191 4.7 19.8 1.0
OP1 P:DOC10 4.7 29.9 1.0
C2' P:DOC10 4.7 39.8 1.0
O3A A:G1M338 4.9 21.0 0.5
O3A A:G1M338 4.9 14.5 0.5
O2B A:G1M338 4.9 11.0 0.5
O2B A:G1M338 4.9 18.4 0.5
NH2 A:ARG254 4.9 18.0 1.0
CA A:ASP192 5.0 17.8 1.0

Sodium binding site 2 out of 4 in 3jpp

Go back to Sodium Binding Sites List in 3jpp
Sodium binding site 2 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl 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-Monomethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:27.0
occ:1.00
 OP1 P:DG9 2.3 22.6 1.0
O A:THR101 2.3 26.1 1.0
O P:HOH33 2.4 25.1 1.0
O A:ILE106 2.5 20.0 1.0
O A:HOH524 2.6 29.6 1.0
O A:VAL103 2.7 18.4 1.0
P P:DG9 3.3 22.7 1.0
C A:THR101 3.3 24.1 1.0
OP2 P:DG9 3.4 23.3 1.0
C A:ILE106 3.5 20.2 1.0
C A:VAL103 3.6 19.1 1.0
N A:ILE106 3.8 20.5 1.0
CA A:THR101 4.0 24.3 1.0
N A:GLY105 4.0 19.9 1.0
O A:HOH525 4.0 35.1 1.0
CA A:SER104 4.1 20.3 1.0
CA A:ILE106 4.2 19.8 1.0
N A:VAL103 4.2 21.4 1.0
N A:SER104 4.2 19.6 1.0
O3' P:DC8 4.3 24.0 1.0
N A:ARG102 4.4 23.7 1.0
C A:ARG102 4.4 22.5 1.0
C A:SER104 4.4 19.6 1.0
N A:GLY107 4.5 20.5 1.0
O5' P:DG9 4.5 25.8 1.0
CB A:THR101 4.6 23.9 1.0
CA A:VAL103 4.6 20.0 1.0
CB A:ILE106 4.6 19.9 1.0
CA A:ARG102 4.6 24.8 1.0
C A:GLY105 4.7 21.9 1.0
CA A:GLY107 4.7 22.7 1.0
O A:ARG102 4.9 23.7 1.0
O A:LEU100 4.9 21.0 1.0
CA A:GLY105 4.9 22.1 1.0
O P:HOH219 5.0 34.2 1.0

Sodium binding site 3 out of 4 in 3jpp

Go back to Sodium Binding Sites List in 3jpp
Sodium binding site 3 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl 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-Monomethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:38.1
occ:1.00
 O A:LYS60 2.4 32.7 1.0
O A:LEU62 2.4 36.8 1.0
O A:HOH481 2.5 31.6 1.0
O A:VAL65 2.5 30.6 1.0
OP1 D:DC3 2.6 36.2 1.0
O D:HOH337 2.9 36.8 1.0
C A:LEU62 3.3 36.5 1.0
C A:LYS60 3.4 34.0 1.0
C A:VAL65 3.4 30.6 1.0
N A:VAL65 3.7 30.2 1.0
P D:DC3 3.7 35.4 1.0
CA A:PRO63 3.9 35.9 1.0
OP2 D:DC3 4.0 36.3 1.0
N A:PRO63 4.0 36.6 1.0
N A:GLY64 4.0 33.1 1.0
CA A:VAL65 4.0 28.9 1.0
C A:LYS61 4.0 37.5 1.0
CA A:LYS60 4.1 32.2 1.0
N A:LEU62 4.1 36.8 1.0
O A:LYS61 4.2 35.9 1.0
CB A:VAL65 4.3 26.6 1.0
C A:PRO63 4.3 34.6 1.0
N A:LYS61 4.3 36.1 1.0
CG A:LYS60 4.3 34.6 1.0
CA A:LEU62 4.4 36.4 1.0
N A:GLY66 4.5 30.4 1.0
CA A:LYS61 4.6 37.4 1.0
O3' D:DT2 4.6 37.3 1.0
C A:GLY64 4.7 31.7 1.0
O A:ALA59 4.7 27.8 1.0
CA A:GLY66 4.8 30.7 1.0
CB A:LYS60 4.8 33.3 1.0
O5' D:DC3 5.0 40.5 1.0
CA A:GLY64 5.0 32.2 1.0

Sodium binding site 4 out of 4 in 3jpp

Go back to Sodium Binding Sites List in 3jpp
Sodium binding site 4 out of 4 in the Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monomethyl Methylene Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na347

b:51.9
occ:1.00
 O A:HOH404 1.9 33.7 1.0
O A:HOH578 2.0 27.9 1.0
O A:HOH528 2.2 46.3 1.0
O A:HOH440 2.4 39.7 1.0
O2G A:G1M338 3.9 28.3 0.5
O2G A:G1M338 4.0 21.4 0.5
O P:HOH196 4.0 36.0 1.0
O1G A:G1M338 4.2 16.1 0.5
O1G A:G1M338 4.3 24.7 0.5
O A:HOH422 4.4 32.3 1.0
PG A:G1M338 4.6 27.3 0.5
PG A:G1M338 4.6 19.4 0.5
C3B2 A:G1M338 4.7 11.0 0.5
O2A A:G1M338 4.7 15.2 0.5
O2A A:G1M338 4.7 20.9 0.5
CA A:GLY189 4.7 18.3 1.0
C A:GLY189 4.8 19.5 1.0
O A:GLY189 4.8 20.3 1.0
OD2 A:ASP190 4.9 19.5 1.0
O P:HOH273 4.9 35.2 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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