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Manganese in PDB 5tbb: Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi.

Enzymatic activity of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi.

All present enzymatic activity of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi.:
2.7.7.7;

Protein crystallography data

The structure of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi., PDB code: 5tbb was solved by R.Vyas, Z.Suo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.52 / 2.39
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 55.170, 79.330, 55.460, 90.00, 107.20, 90.00
R / Rfree (%) 21.3 / 26.9

Other elements in 5tbb:

The structure of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi. also contains other interesting chemical elements:

Fluorine (F) 1 atom
Sodium (Na) 4 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi. (pdb code 5tbb). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total only one binding site of Manganese was determined in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi., PDB code: 5tbb:

Manganese binding site 1 out of 1 in 5tbb

Go back to Manganese Binding Sites List in 5tbb
Manganese binding site 1 out of 1 in the Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Postcatalytic Ternary Complex of Human Dna Polymerase Beta with Gapped Dna Substrate, Incorporated (-)Ftc and Ppi. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:72.5
occ:1.00
 O11 A:PPV407 1.9 86.7 1.0
O3A P:43X101 1.9 60.5 1.0
OD2 A:ASP192 1.9 57.4 1.0
OD1 A:ASP190 1.9 57.2 1.0
CG A:ASP190 3.0 45.5 1.0
CG A:ASP192 3.1 45.9 1.0
NA A:NA404 3.2 47.0 1.0
PA P:43X101 3.4 59.3 1.0
OD2 A:ASP190 3.4 49.2 1.0
P1 A:PPV407 3.4 96.3 1.0
OD1 A:ASP192 3.6 52.1 1.0
O31 A:PPV407 3.9 99.6 1.0
O32 A:PPV407 3.9 88.8 1.0
O5' P:43X101 4.0 50.1 1.0
C5' P:43X101 4.1 49.5 1.0
O2A P:43X101 4.1 48.4 1.0
OPP A:PPV407 4.3 93.0 1.0
CB A:ASP192 4.4 39.9 1.0
O3' P:DC10 4.4 46.7 1.0
CB A:ASP190 4.4 43.3 1.0
O21 A:PPV407 4.5 77.7 1.0
N A:ASP190 4.6 41.3 1.0
O A:ASP190 4.6 36.8 1.0
P2 A:PPV407 4.7 98.7 1.0
C A:ASP190 4.8 37.4 1.0
CA A:ASP190 4.9 38.5 1.0

Reference:

A.J.Reed, R.Vyas, A.T.Raper, Z.Suo. Structural Insights Into the Post-Chemistry Steps of Nucleotide Incorporation Catalyzed By A Dna Polymerase. J. Am. Chem. Soc. V. 139 465 2017.
ISSN: ESSN 1520-5126
PubMed: 27959534
DOI: 10.1021/JACS.6B11258
Page generated: Sun Oct 6 02:56:15 2024

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