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Magnesium 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
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(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 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(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer, PDB code: 3tfs:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3tfs

Go back to Magnesium Binding Sites List in 3tfs
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(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer


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(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg339

b:14.9
occ:1.00
 OD2 A:ASP192 2.1 12.2 1.0
O2B A:FHA338 2.1 13.8 1.0
OD1 A:ASP190 2.1 14.8 1.0
O1A A:FHA338 2.1 10.8 1.0
O3G A:FHA338 2.1 13.5 1.0
O A:HOH348 2.3 13.1 1.0
CG A:ASP192 3.1 11.9 1.0
PB A:FHA338 3.1 12.4 1.0
CG A:ASP190 3.2 15.0 1.0
PG A:FHA338 3.4 14.9 1.0
PA A:FHA338 3.4 16.0 1.0
OD1 A:ASP192 3.5 12.7 1.0
MG A:MG340 3.6 13.0 1.0
O3B A:FHA338 3.6 13.3 1.0
OD2 A:ASP190 3.6 15.4 1.0
C3A A:FHA338 3.6 16.4 1.0
O A:HOH366 3.8 16.6 1.0
O2G A:FHA338 4.0 17.8 1.0
C5' A:FHA338 4.1 13.7 1.0
O A:ASP190 4.1 16.9 1.0
O5' A:FHA338 4.2 15.3 1.0
O A:HOH367 4.3 15.0 1.0
C A:ASP190 4.4 14.4 1.0
N A:ASP190 4.4 14.4 1.0
CB A:ASP192 4.4 13.8 1.0
CA A:GLY179 4.4 13.9 1.0
CB A:ASP190 4.5 14.1 1.0
O2A A:FHA338 4.5 15.1 1.0
N A:SER180 4.5 16.3 1.0
O1B A:FHA338 4.6 14.1 1.0
OG A:SER180 4.6 18.0 1.0
O P:HOH235 4.7 15.4 1.0
CA A:ASP190 4.7 12.9 1.0
O1G A:FHA338 4.7 19.6 1.0
N A:ASP192 4.7 17.1 1.0
N A:MET191 4.9 12.8 1.0
F1A A:FHA338 5.0 17.5 1.0

Magnesium binding site 2 out of 2 in 3tfs

Go back to Magnesium Binding Sites List in 3tfs
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(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer


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(Cfh)Pp in the Active Site: Stereoselective Binding of (S) Isomer within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg340

b:13.0
occ:1.00
 OD2 A:ASP256 2.1 17.1 1.0
OD1 A:ASP192 2.1 12.7 1.0
OD2 A:ASP190 2.2 15.4 1.0
O3' P:DC10 2.3 15.1 1.0
O P:HOH235 2.3 15.4 1.0
O1A A:FHA338 2.3 10.8 1.0
CG A:ASP192 3.1 11.9 1.0
CG A:ASP190 3.1 15.0 1.0
CG A:ASP256 3.2 19.9 1.0
C3' P:DC10 3.3 15.6 1.0
OD1 A:ASP190 3.4 14.8 1.0
OD2 A:ASP192 3.5 12.2 1.0
PA A:FHA338 3.5 16.0 1.0
MG A:MG339 3.6 14.9 1.0
O2A A:FHA338 3.7 15.1 1.0
CB A:ASP256 3.8 18.9 1.0
O5' A:FHA338 3.9 15.3 1.0
C4' P:DC10 4.0 19.4 1.0
C5' P:DC10 4.2 17.9 1.0
C5' A:FHA338 4.2 13.7 1.0
O A:HOH366 4.2 16.6 1.0
OD1 A:ASP256 4.2 21.1 1.0
CB A:ASP192 4.4 13.8 1.0
CB A:ASP190 4.5 14.1 1.0
OP1 P:DC10 4.5 21.3 1.0
C2' P:DC10 4.6 19.1 1.0
O5' P:DC10 4.6 20.6 1.0
O A:MET191 4.8 13.9 1.0
O3G A:FHA338 4.8 13.5 1.0
NH2 A:ARG254 4.8 19.1 1.0
CA A:ASP192 5.0 13.3 1.0
N A:ASP256 5.0 15.0 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: Mon Dec 14 08:54:16 2020

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