Atomistry » Sodium » PDB 3iwf-3k93 » 3jpp
Atomistry »
  Sodium »
    PDB 3iwf-3k93 »
      3jpp »

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

Go back to Sodium Binding Sites List in 3jpp
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy