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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

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