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Magnesium 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
Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3tfr

Go back to Magnesium Binding Sites List in 3tfr
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg339

b:14.0
occ:1.00
 O2B A:F3A338 2.1 9.6 1.0
OD2 A:ASP192 2.1 11.1 1.0
O1A A:F3A338 2.1 7.4 1.0
OD1 A:ASP190 2.2 11.4 1.0
O3G A:F3A338 2.2 11.4 1.0
O A:HOH350 2.3 10.6 1.0
PB A:F3A338 3.1 12.2 1.0
CG A:ASP192 3.1 16.7 1.0
CG A:ASP190 3.3 16.9 1.0
PG A:F3A338 3.3 14.4 1.0
PA A:F3A338 3.3 13.5 1.0
OD1 A:ASP192 3.5 15.0 1.0
O3B A:F3A338 3.6 14.8 1.0
C3A A:F3A338 3.6 19.0 1.0
MG A:MG340 3.6 22.4 1.0
OD2 A:ASP190 3.7 18.4 1.0
O2G A:F3A338 3.7 20.3 1.0
C5' A:F3A338 3.8 13.0 1.0
O A:ASP190 4.0 12.6 1.0
F2A A:F3A338 4.0 13.7 1.0
O5' A:F3A338 4.1 16.2 1.0
O A:HOH494 4.1 14.5 1.0
O A:HOH405 4.2 13.0 1.0
C A:ASP190 4.3 14.5 1.0
N A:ASP190 4.3 10.6 1.0
CA A:GLY179 4.4 10.7 1.0
CB A:ASP192 4.4 14.1 1.0
O1B A:F3A338 4.4 13.2 1.0
O2A A:F3A338 4.5 15.2 1.0
CB A:ASP190 4.5 13.2 1.0
O1G A:F3A338 4.6 16.0 1.0
N A:SER180 4.6 12.7 1.0
CA A:ASP190 4.7 11.4 1.0
F1A A:F3A338 4.9 15.2 1.0
N A:ASP192 4.9 14.9 1.0
N A:MET191 5.0 13.8 1.0

Magnesium binding site 2 out of 2 in 3tfr

Go back to Magnesium Binding Sites List in 3tfr
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg340

b:22.4
occ:1.00
 OD2 A:ASP190 2.1 18.4 1.0
OD1 A:ASP192 2.3 15.0 1.0
O3' P:DC10 2.3 17.6 1.0
O1A A:F3A338 2.4 7.4 1.0
OD2 A:ASP256 2.4 22.2 1.0
CG A:ASP190 3.0 16.9 1.0
C3' P:DC10 3.2 16.3 1.0
CG A:ASP192 3.3 16.7 1.0
OD1 A:ASP190 3.3 11.4 1.0
CG A:ASP256 3.4 19.3 1.0
PA A:F3A338 3.5 13.5 1.0
OD2 A:ASP192 3.6 11.1 1.0
MG A:MG339 3.6 14.0 1.0
O2A A:F3A338 3.7 15.2 1.0
C4' P:DC10 3.9 17.1 1.0
O5' A:F3A338 3.9 16.2 1.0
CB A:ASP256 3.9 14.3 1.0
C5' P:DC10 4.0 18.5 1.0
C5' A:F3A338 4.2 13.0 1.0
OD1 A:ASP256 4.3 23.0 1.0
O A:HOH494 4.3 14.5 1.0
O A:HOH458 4.4 21.5 1.0
CB A:ASP190 4.4 13.2 1.0
O5' P:DC10 4.4 15.4 1.0
OP1 P:DC10 4.5 20.6 1.0
C2' P:DC10 4.5 15.2 1.0
CB A:ASP192 4.6 14.1 1.0
O3G A:F3A338 4.8 11.4 1.0
NH2 A:ARG254 4.9 25.3 1.0
O A:MET191 4.9 14.9 1.0
O A:HOH483 5.0 22.4 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: Mon Dec 14 08:54:15 2020

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