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Sodium in PDB 3tfs: Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer

Enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer

All present enzymatic activity of Ternary Complex Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer:
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(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer, PDB code: 3tfs 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) 25.56 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.770, 79.580, 55.720, 90.00, 107.75, 90.00
R / Rfree (%) 18.8 / 24.2

Other elements in 3tfs:

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

Fluorine (F) 1 atom
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(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer (pdb code 3tfs). 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(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer, PDB code: 3tfs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 3tfs

Go back to Sodium Binding Sites List in 3tfs
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(Cfh)Pp in the Active Site: Stereoselective 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 Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:21.1
occ:1.00
 O A:THR101 2.5 21.8 1.0
OP1 P:DG9 2.5 18.3 1.0
O A:ILE106 2.6 13.3 1.0
O A:HOH513 2.6 24.9 1.0
O A:VAL103 2.7 16.2 1.0
O P:HOH78 2.7 22.4 1.0
C A:THR101 3.4 18.7 1.0
C A:VAL103 3.5 16.5 1.0
P P:DG9 3.5 19.2 1.0
OP2 P:DG9 3.5 19.2 1.0
C A:ILE106 3.6 17.9 1.0
O A:HOH485 3.8 33.4 1.0
N A:ILE106 3.9 18.1 1.0
CA A:SER104 3.9 16.4 1.0
CA A:THR101 4.0 19.5 1.0
N A:SER104 4.0 15.1 1.0
N A:GLY105 4.0 16.2 1.0
N A:VAL103 4.1 17.6 1.0
CA A:ILE106 4.3 17.1 1.0
C A:ARG102 4.3 18.8 1.0
C A:SER104 4.3 16.8 1.0
N A:ARG102 4.4 19.4 1.0
CA A:VAL103 4.4 17.1 1.0
O3' P:DC8 4.5 17.8 1.0
CB A:THR101 4.5 19.3 1.0
N A:GLY107 4.5 16.4 1.0
CA A:ARG102 4.6 18.6 1.0
CB A:ILE106 4.7 15.9 1.0
O5' P:DG9 4.7 19.4 1.0
O A:ARG102 4.7 18.1 1.0
CA A:GLY107 4.7 16.0 1.0
C A:GLY105 4.7 19.7 1.0
O A:LEU100 4.9 17.4 1.0
CA A:GLY105 4.9 15.9 1.0

Sodium binding site 2 out of 2 in 3tfs

Go back to Sodium Binding Sites List in 3tfs
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(Cfh)Pp in the Active Site: Stereoselective 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 Structure of Dna Polymerase Beta with A Gapped Dna Substrate and A, B Damp(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:29.0
occ:1.00
 O A:LEU62 2.6 28.9 1.0
O A:VAL65 2.6 24.0 1.0
O A:LYS60 2.6 28.8 1.0
OP1 D:DC3 2.7 25.9 1.0
O A:HOH617 2.7 25.6 1.0
O A:HOH506 2.9 26.2 1.0
C A:LEU62 3.4 27.6 1.0
P D:DC3 3.6 28.7 1.0
C A:VAL65 3.7 26.3 1.0
C A:LYS60 3.7 28.9 1.0
OP2 D:DC3 3.7 24.1 1.0
N A:VAL65 3.9 25.4 1.0
CA A:PRO63 4.0 27.3 1.0
N A:PRO63 4.1 29.0 1.0
N A:GLY64 4.1 24.3 1.0
C A:LYS61 4.1 27.4 1.0
N A:LEU62 4.1 25.3 1.0
O A:LYS61 4.1 27.5 1.0
CA A:VAL65 4.2 22.7 1.0
CA A:LEU62 4.4 26.6 1.0
CA A:LYS60 4.4 24.0 1.0
C A:PRO63 4.4 26.4 1.0
CB A:VAL65 4.5 24.7 1.0
CG A:LYS60 4.5 28.2 1.0
O3' D:DT2 4.6 26.7 1.0
N A:LYS61 4.6 26.8 1.0
CA A:LYS61 4.7 27.4 1.0
N A:GLY66 4.8 26.6 1.0
C A:GLY64 4.8 25.4 1.0
O5' D:DC3 4.9 28.9 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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