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Sodium in PDB 3tfr: Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site

Enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site

All present enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site, PDB code: 3tfr was solved by B.T.Chamberlain, V.K.Batra, W.A.Beard, A.P.Kadina, D.D.Shock, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.69 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.890, 79.380, 55.650, 90.00, 107.64, 90.00
R / Rfree (%) 18.8 / 25.1

Other elements in 3tfr:

The structure of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site also contains other interesting chemical elements:

Fluorine (F) 2 atoms
Magnesium (Mg) 2 atoms
Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site (pdb code 3tfr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site, PDB code: 3tfr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3tfr

Go back to Sodium Binding Sites List in 3tfr
Sodium binding site 1 out of 2 in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:15.3
occ:1.00
 OP1 P:DG9 2.5 13.3 1.0
O A:VAL103 2.6 11.7 1.0
O A:THR101 2.6 17.0 1.0
O A:ILE106 2.6 12.9 1.0
O A:HOH561 2.7 17.6 1.0
O P:HOH94 2.8 19.9 1.0
C A:THR101 3.4 13.6 1.0
C A:VAL103 3.4 14.2 1.0
P P:DG9 3.4 15.8 1.0
OP2 P:DG9 3.5 16.2 1.0
C A:ILE106 3.5 15.8 1.0
O A:HOH539 3.7 26.7 1.0
N A:ILE106 3.7 14.3 1.0
CA A:THR101 3.9 17.0 1.0
CA A:SER104 4.0 12.1 1.0
N A:GLY105 4.0 15.0 1.0
N A:SER104 4.1 14.3 1.0
N A:VAL103 4.1 14.3 1.0
CA A:ILE106 4.1 14.0 1.0
C A:ARG102 4.3 17.0 1.0
C A:SER104 4.3 14.0 1.0
N A:ARG102 4.3 14.5 1.0
CB A:THR101 4.3 14.2 1.0
CA A:VAL103 4.4 15.0 1.0
O3' P:DC8 4.4 13.7 1.0
CB A:ILE106 4.5 13.0 1.0
N A:GLY107 4.5 17.3 1.0
CA A:ARG102 4.6 17.5 1.0
C A:GLY105 4.7 15.7 1.0
O5' P:DG9 4.7 12.6 1.0
O A:ARG102 4.7 13.8 1.0
CA A:GLY107 4.8 15.1 1.0
O A:HOH653 4.8 26.7 1.0
O A:LEU100 4.9 14.6 1.0
CA A:GLY105 4.9 17.5 1.0

Sodium binding site 2 out of 2 in 3tfr

Go back to Sodium Binding Sites List in 3tfr
Sodium binding site 2 out of 2 in the Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(CF2)Pp in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:25.9
occ:1.00
 O A:LYS60 2.6 21.9 1.0
O A:VAL65 2.6 20.5 1.0
O A:LEU62 2.7 21.3 1.0
OP1 D:DC3 2.7 19.4 1.0
O A:HOH476 2.7 21.4 1.0
O A:HOH725 2.9 26.2 1.0
C A:LEU62 3.4 21.2 1.0
C A:LYS60 3.6 22.4 1.0
C A:VAL65 3.6 21.0 1.0
O D:HOH164 3.7 24.2 1.0
P D:DC3 3.7 25.8 1.0
OP2 D:DC3 3.8 18.4 1.0
N A:VAL65 3.9 17.1 1.0
N A:PRO63 4.0 22.9 1.0
CA A:PRO63 4.0 20.6 1.0
N A:LEU62 4.0 20.0 1.0
C A:LYS61 4.1 21.6 1.0
N A:GLY64 4.2 18.8 1.0
CA A:VAL65 4.2 18.1 1.0
O A:LYS61 4.3 21.7 1.0
CA A:LYS60 4.3 18.0 1.0
CA A:LEU62 4.3 18.3 1.0
CG A:LYS60 4.4 22.0 1.0
C A:PRO63 4.5 22.0 1.0
CB A:VAL65 4.5 18.3 1.0
N A:LYS61 4.5 21.1 1.0
O3' D:DT2 4.6 20.3 1.0
CA A:LYS61 4.7 21.9 1.0
N A:GLY66 4.7 21.2 1.0
O5' D:DC3 4.9 22.3 1.0
C A:GLY64 4.9 17.8 1.0
CA A:GLY66 4.9 20.8 1.0
O A:ALA59 4.9 18.9 1.0
NZ A:LYS60 5.0 30.9 1.0
CB A:LYS60 5.0 17.0 1.0

Reference:

B.T.Chamberlain, V.K.Batra, W.A.Beard, A.P.Kadina, D.D.Shock, B.A.Kashemirov, C.E.Mckenna, M.F.Goodman, S.H.Wilson. Stereospecific Formation of A Ternary Complex of (S)-Alpha, Beta-Fluoromethylene-Datp with Dna Pol Beta. Chembiochem V. 13 528 2012.
ISSN: ISSN 1439-4227
PubMed: 22315190
DOI: 10.1002/CBIC.201100738
Page generated: Tue Dec 15 06:26:09 2020

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