Atomistry » Sodium » PDB 3ma9-3mo9 » 3mby
Atomistry »
  Sodium »
    PDB 3ma9-3mo9 »
      3mby »

Sodium in PDB 3mby: Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

Enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer

All present enzymatic activity of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer, PDB code: 3mby was solved by V.K.Batra, W.A.Beard, E.W.Hou, L.C.Pedersen, R.Prasad, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.84 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.830, 80.030, 55.420, 90.00, 107.70, 90.00
R / Rfree (%) 19 / 24.6

Other elements in 3mby:

The structure of Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer also contains other interesting chemical elements:

Magnesium (Mg) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer (pdb code 3mby). 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 Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer, PDB code: 3mby:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3mby

Go back to Sodium Binding Sites List in 3mby
Sodium binding site 1 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer


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 Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:24.0
occ:1.00
 OD1 A:ASP192 2.0 21.1 1.0
O P:HOH306 2.0 37.8 1.0
OD2 A:ASP190 2.4 24.9 1.0
O1A A:8DG338 2.5 24.8 1.0
O A:HOH553 2.6 29.1 1.0
CG A:ASP190 2.9 21.7 1.0
OD1 A:ASP190 2.9 19.1 1.0
CG A:ASP192 3.0 17.3 1.0
MG A:MG339 3.3 17.6 1.0
OD2 A:ASP192 3.3 16.0 1.0
PA A:8DG338 3.6 23.2 1.0
O5' A:8DG338 3.8 20.9 1.0
OD2 A:ASP256 3.8 25.3 1.0
CG A:ASP256 4.0 20.9 1.0
C5' A:8DG338 4.1 21.8 1.0
O2A A:8DG338 4.1 22.6 1.0
CB A:ASP190 4.2 19.0 1.0
CB A:ASP256 4.3 19.6 1.0
CB A:ASP192 4.3 18.2 1.0
O A:HOH542 4.5 25.5 1.0
O A:MET191 4.5 18.0 1.0
OP1 P:DOC10 4.5 24.4 1.0
OD1 A:ASP256 4.5 18.8 1.0
C3' P:DOC10 4.6 29.9 1.0
C5' P:DOC10 4.6 29.3 1.0
O3G A:8DG338 4.6 18.6 1.0
O2B A:8DG338 4.8 16.6 1.0
C A:MET191 4.9 17.9 1.0
CA A:ASP192 4.9 17.3 1.0
C4' P:DOC10 4.9 30.4 1.0
O3A A:8DG338 4.9 21.1 1.0

Sodium binding site 2 out of 3 in 3mby

Go back to Sodium Binding Sites List in 3mby
Sodium binding site 2 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer


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 Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:18.7
occ:1.00
 O A:THR101 2.3 20.7 1.0
OP1 P:DG9 2.4 16.1 1.0
O A:VAL103 2.4 17.9 1.0
O A:ILE106 2.5 15.7 1.0
O A:HOH492 2.6 25.6 1.0
O P:HOH41 2.7 24.9 1.0
C A:THR101 3.2 20.4 1.0
C A:VAL103 3.4 18.4 1.0
P P:DG9 3.4 19.1 1.0
C A:ILE106 3.5 16.9 1.0
OP2 P:DG9 3.7 18.8 1.0
N A:ILE106 3.8 16.9 1.0
CA A:THR101 3.8 19.8 1.0
N A:VAL103 4.0 18.7 1.0
CA A:SER104 4.0 17.2 1.0
N A:GLY105 4.0 17.8 1.0
O A:HOH526 4.0 32.8 1.0
N A:SER104 4.1 17.4 1.0
CA A:ILE106 4.1 16.8 1.0
C A:ARG102 4.2 19.5 1.0
N A:ARG102 4.2 20.2 1.0
CA A:VAL103 4.3 18.5 1.0
C A:SER104 4.3 18.6 1.0
CB A:THR101 4.4 21.4 1.0
O A:HOH640 4.5 52.8 1.0
CB A:ILE106 4.5 18.0 1.0
N A:GLY107 4.5 16.9 1.0
O3' P:DC8 4.5 15.9 1.0
O5' P:DG9 4.5 19.0 1.0
CA A:ARG102 4.6 20.1 1.0
C A:GLY105 4.6 18.4 1.0
O A:LEU100 4.7 18.7 1.0
CA A:GLY107 4.7 20.1 1.0
O A:ARG102 4.8 19.0 1.0
CA A:GLY105 4.9 18.0 1.0

Sodium binding site 3 out of 3 in 3mby

Go back to Sodium Binding Sites List in 3mby
Sodium binding site 3 out of 3 in the Ternary Complex of Dna Polymerase Beta with Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer


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 Template Base A and 8OXODGTP in the Active Site with A Dideoxy Terminated Primer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:32.7
occ:1.00
 O A:LEU62 2.3 31.6 1.0
O A:VAL65 2.4 25.2 1.0
O A:LYS60 2.4 30.6 1.0
OP1 D:DC3 2.6 30.5 1.0
O A:HOH589 2.7 38.0 1.0
O D:HOH168 2.7 42.9 1.0
C A:LEU62 3.3 31.6 1.0
C A:LYS60 3.5 30.4 1.0
C A:VAL65 3.5 25.1 1.0
P D:DC3 3.7 32.3 1.0
N A:VAL65 3.8 26.7 1.0
OP2 D:DC3 3.9 29.5 1.0
N A:LEU62 4.0 31.9 1.0
N A:PRO63 4.0 31.7 1.0
C A:LYS61 4.0 32.7 1.0
CA A:PRO63 4.1 31.6 1.0
N A:GLY64 4.1 30.6 1.0
CA A:VAL65 4.1 25.9 1.0
CA A:LYS60 4.2 29.0 1.0
CA A:LEU62 4.3 30.2 1.0
O A:LYS61 4.3 33.5 1.0
CB A:VAL65 4.3 25.3 1.0
N A:LYS61 4.4 31.2 1.0
CG A:LYS60 4.4 29.9 1.0
C A:PRO63 4.5 31.2 1.0
CA A:LYS61 4.5 32.2 1.0
N A:GLY66 4.6 24.0 1.0
O3' D:DT2 4.6 32.1 1.0
C A:GLY64 4.8 28.2 1.0
CA A:GLY66 4.8 25.6 1.0
O A:ALA59 4.8 25.9 1.0
O5' D:DC3 4.9 35.0 1.0
CB A:LYS60 5.0 29.6 1.0

Reference:

V.K.Batra, W.A.Beard, E.W.Hou, L.C.Pedersen, R.Prasad, S.H.Wilson. Mutagenic Conformation of 8-Oxo-7,8-Dihydro-2'-Dgtp in the Confines of A Dna Polymerase Active Site. Nat.Struct.Mol.Biol. V. 17 889 2010.
ISSN: ISSN 1545-9993
PubMed: 20526335
DOI: 10.1038/NSMB.1852
Page generated: Mon Oct 7 11:28:07 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy