Atomistry » Sodium » PDB 4def-4dxz » 4doc
Atomistry »
  Sodium »
    PDB 4def-4dxz »
      4doc »

Sodium in PDB 4doc: Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate:Binding of S-Isomer

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate:Binding of S-Isomer

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with A Dideoxy Terminated Primer and 2'-Deoxyguanosine 5'-Beta, Gamma-Monochlororomethylene Triphosphate:Binding of S-Isomer:
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-Monochlororomethylene Triphosphate:Binding of S-Isomer, PDB code: 4doc was solved by V.K.Batra, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.22 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.688, 80.019, 55.716, 90.00, 107.68, 90.00
R / Rfree (%) 20 / 24.9

Other elements in 4doc:

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

Magnesium (Mg) 1 atom
Chlorine (Cl) 6 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-Monochlororomethylene Triphosphate:Binding of S-Isomer (pdb code 4doc). 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-Monochlororomethylene Triphosphate:Binding of S-Isomer, PDB code: 4doc:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4doc

Go back to Sodium Binding Sites List in 4doc
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-Monochlororomethylene Triphosphate:Binding of S-Isomer


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-Monochlororomethylene Triphosphate:Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na402

b:27.4
occ:1.00
OD2 A:ASP256 2.3 29.6 1.0
OD1 A:ASP192 2.3 19.4 1.0
OD2 A:ASP190 2.3 23.3 1.0
O1A A:G1C410 3.1 17.7 1.0
CG A:ASP256 3.2 22.1 1.0
CG A:ASP190 3.2 18.9 1.0
CG A:ASP192 3.3 16.1 1.0
OD1 A:ASP190 3.5 16.7 1.0
OD2 A:ASP192 3.6 14.4 1.0
CB A:ASP256 3.8 21.8 1.0
C3' P:DOC10 3.8 27.2 1.0
C5' P:DOC10 3.9 32.5 1.0
MG A:MG401 4.0 17.6 1.0
C4' P:DOC10 4.0 32.3 1.0
OD1 A:ASP256 4.0 20.0 1.0
PA A:G1C410 4.1 17.5 1.0
O5' A:G1C410 4.2 17.9 1.0
O5' P:DOC10 4.2 33.2 1.0
C5' A:G1C410 4.3 18.4 1.0
CB A:ASP190 4.4 16.1 1.0
O P:HOH106 4.4 27.4 1.0
NH2 A:ARG254 4.5 18.8 1.0
CB A:ASP192 4.6 16.3 1.0
O A:MET191 4.6 15.4 1.0
N A:ASP256 4.7 16.5 1.0
OP1 P:DOC10 4.7 34.5 1.0
O2A A:G1C410 4.8 19.5 1.0
CA A:ASP256 4.9 17.1 1.0
C2' P:DOC10 4.9 27.2 1.0
O A:HOH620 5.0 32.2 1.0
CA A:ASP192 5.0 17.6 1.0
C A:MET191 5.0 14.9 1.0

Sodium binding site 2 out of 3 in 4doc

Go back to Sodium Binding Sites List in 4doc
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-Monochlororomethylene Triphosphate:Binding of S-Isomer


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-Monochlororomethylene Triphosphate:Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na403

b:23.0
occ:1.00
O A:ILE106 2.3 19.7 1.0
OP1 P:DG9 2.4 22.7 1.0
O A:THR101 2.4 23.3 1.0
O P:HOH115 2.5 26.5 1.0
O A:VAL103 2.5 18.1 1.0
O P:HOH101 2.5 30.3 1.0
C A:THR101 3.3 22.4 1.0
C A:ILE106 3.3 22.6 1.0
C A:VAL103 3.4 19.8 1.0
P P:DG9 3.5 23.8 1.0
OP2 P:DG9 3.7 23.0 1.0
N A:ILE106 3.8 19.1 1.0
CA A:THR101 3.9 21.1 1.0
O A:HOH756 3.9 33.6 1.0
N A:GLY105 4.0 19.2 1.0
CA A:SER104 4.0 19.7 1.0
CA A:ILE106 4.1 20.5 1.0
N A:SER104 4.1 19.7 1.0
N A:VAL103 4.2 18.7 1.0
N A:ARG102 4.3 21.2 1.0
N A:GLY107 4.3 18.8 1.0
C A:ARG102 4.3 21.0 1.0
C A:SER104 4.3 16.9 1.0
CA A:VAL103 4.4 21.2 1.0
O3' P:DC8 4.5 21.1 1.0
CB A:THR101 4.5 25.0 1.0
CB A:ILE106 4.5 21.1 1.0
CA A:GLY107 4.6 19.7 1.0
CA A:ARG102 4.6 25.6 1.0
C A:GLY105 4.6 24.1 1.0
O5' P:DG9 4.6 25.4 1.0
O A:LEU100 4.7 21.1 1.0
O A:ARG102 4.8 23.4 1.0
CA A:GLY105 4.9 22.8 1.0

Sodium binding site 3 out of 3 in 4doc

Go back to Sodium Binding Sites List in 4doc
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-Monochlororomethylene Triphosphate:Binding of S-Isomer


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-Monochlororomethylene Triphosphate:Binding of S-Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na404

b:34.6
occ:1.00
O A:LYS60 2.0 28.5 1.0
O A:VAL65 2.4 29.2 1.0
O A:LEU62 2.4 32.3 1.0
O A:HOH812 2.5 32.7 1.0
C A:LYS60 3.1 30.4 1.0
C A:LEU62 3.3 32.5 1.0
OP1 D:DC3 3.3 32.8 1.0
O A:HOH868 3.3 43.2 1.0
C A:VAL65 3.6 31.5 1.0
N A:LEU62 3.7 32.4 1.0
C A:LYS61 3.8 35.3 1.0
CA A:LYS60 3.9 28.1 1.0
N A:LYS61 4.0 31.6 1.0
N A:VAL65 4.1 29.7 1.0
N A:PRO63 4.1 33.1 1.0
O A:LYS61 4.1 36.9 1.0
CA A:LEU62 4.1 31.5 1.0
OP2 D:DC3 4.2 30.4 1.0
CG A:LYS60 4.2 31.3 1.0
CA A:VAL65 4.2 27.4 1.0
CA A:LYS61 4.2 33.3 1.0
CA A:PRO63 4.2 33.4 1.0
P D:DC3 4.2 36.8 1.0
CB A:VAL65 4.4 25.9 1.0
N A:GLY64 4.5 34.0 1.0
O A:ALA59 4.6 25.4 1.0
CB A:LYS60 4.6 28.8 1.0
N A:GLY66 4.6 29.2 1.0
C A:PRO63 4.7 33.7 1.0
CA A:GLY66 4.9 29.9 1.0
NZ A:LYS60 5.0 34.5 1.0

Reference:

Y.Wu, V.M.Zakharova, B.A.Kashemirov, M.F.Goodman, V.K.Batra, S.H.Wilson, C.E.Mckenna. Beta,Gamma-Chf- and Beta,Gamma-Chcl-Dgtp Diastereomers: Synthesis, Discrete (31)P uc(Nmr) Signatures, and Absolute Configurations of New Stereochemical Probes For Dna Polymerases J.Am.Chem.Soc. V. 134 8734 2012.
ISSN: ISSN 0002-7863
PubMed: 22397499
DOI: 10.1021/JA300218X
Page generated: Mon Oct 7 14:58:34 2024

Last articles

Zn in 9FS1
Zn in 9FS3
Zn in 9FS2
Zn in 9H3H
Zn in 9F29
Zn in 9F2A
Zn in 9EY2
Zn in 9F26
Zn in 9E8J
Zn in 9E8N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy