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Manganese in PDB 5omq: Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site

Enzymatic activity of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site

All present enzymatic activity of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site:
2.7.7.7;

Protein crystallography data

The structure of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site, PDB code: 5omq was solved by K.Betz, A.Marx, K.Diederichs, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.84 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.793, 93.678, 158.205, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 24.8

Other elements in 5omq:

The structure of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site (pdb code 5omq). 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 Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site, PDB code: 5omq:

Manganese binding site 1 out of 1 in 5omq

Go back to Manganese Binding Sites List in 5omq
Manganese binding site 1 out of 1 in the Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Ternary Complex of 9N Dna Polymerase in the Replicative State with Three Metal Ions in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn805

b:41.8
occ:0.96
 O A:PHE405 2.1 43.9 1.0
O2B A:DTP806 2.1 47.0 1.0
OD1 A:ASP404 2.1 57.7 1.0
OD2 A:ASP542 2.2 49.1 1.0
O2A A:DTP806 2.2 35.6 1.0
O3G A:DTP806 2.3 42.4 1.0
CG A:ASP542 3.1 43.0 1.0
CG A:ASP404 3.2 53.6 1.0
PB A:DTP806 3.2 44.0 1.0
C A:PHE405 3.3 54.4 1.0
H5'2 A:DTP806 3.3 52.0 1.0
OD1 A:ASP542 3.4 47.5 1.0
PG A:DTP806 3.4 39.7 1.0
PA A:DTP806 3.4 40.8 1.0
MG A:MG804 3.4 43.6 1.0
MG A:MG803 3.5 44.5 1.0
OD2 A:ASP404 3.6 58.9 1.0
O3A A:DTP806 3.6 31.2 1.0
O3B A:DTP806 3.7 49.2 1.0
N A:PHE405 3.9 49.3 1.0
O A:HOH936 4.0 50.2 1.0
CA A:PHE405 4.0 50.2 1.0
O A:HOH923 4.1 48.4 1.0
O1G A:DTP806 4.2 35.7 1.0
C5' A:DTP806 4.3 43.2 1.0
N A:ARG406 4.3 35.0 1.0
N A:SER407 4.3 51.4 1.0
O5' A:DTP806 4.3 42.7 1.0
CB A:PHE405 4.4 45.7 1.0
C A:ASP404 4.4 50.2 1.0
CB A:ASP404 4.5 47.1 1.0
CB A:ASP542 4.5 39.7 1.0
O2G A:DTP806 4.5 39.7 1.0
CA A:ARG406 4.6 52.3 1.0
O1B A:DTP806 4.6 42.7 1.0
C A:ARG406 4.6 48.1 1.0
O1A A:DTP806 4.7 30.2 1.0
N A:LEU408 4.7 55.0 1.0
H5'1 A:DTP806 4.7 52.0 1.0
CB A:LEU408 4.9 39.6 1.0
O A:ASP542 4.9 38.0 1.0
O A:HOH951 4.9 61.5 1.0
O A:ASP404 4.9 50.7 1.0
CA A:ASP404 5.0 46.5 1.0

Reference:

H.M.Kropp, K.Betz, J.Wirth, K.Diederichs, A.Marx. Crystal Structures of Ternary Complexes of Archaeal B-Family Dna Polymerases. Plos One V. 12 88005 2017.
ISSN: ESSN 1932-6203
PubMed: 29211756
DOI: 10.1371/JOURNAL.PONE.0188005
Page generated: Sun Oct 6 02:21:32 2024

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