Atomistry » Sodium » PDB 2ply-2qd6 » 2pxi
Atomistry »
  Sodium »
    PDB 2ply-2qd6 »
      2pxi »

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: Mon Oct 7 03:45:15 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