Magnesium in PDB 6dsy: Bst Dna Polymerase I Post-Chemistry (N+1) Structure

All present enzymatic activity of Bst Dna Polymerase I Post-Chemistry (N+1) Structure:
2.7.7.7;

The structure of Bst Dna Polymerase I Post-Chemistry (N+1) Structure, PDB code: 6dsy was solved by N.Chim, L.N.Jackson, J.C.Chaput, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.09 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.199, 93.751, 105.846, 90.00, 90.00, 90.00
R / Rfree (%)	20.3 / 25.5

The binding sites of Magnesium atom in the Bst Dna Polymerase I Post-Chemistry (N+1) Structure (pdb code 6dsy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Bst Dna Polymerase I Post-Chemistry (N+1) Structure, PDB code: 6dsy:

Magnesium binding site 1 out of 1 in the Bst Dna Polymerase I Post-Chemistry (N+1) Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Bst Dna Polymerase I Post-Chemistry (N+1) Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:30.0 occ:1.00 O A:HOH1275 2.7 44.7 1.0 OD2 A:ASP830 3.2 19.4 1.0 OP1 P:DT10 3.2 0.1 1.0 CA A:HIS829 3.2 26.5 1.0 C A:HIS829 3.3 20.6 1.0 CG A:ASP830 3.5 16.3 1.0 OD1 A:ASP830 3.5 18.0 1.0 CB A:HIS829 3.6 37.0 1.0 N A:ASP830 3.6 22.2 1.0 NH2 A:ARG615 3.8 37.5 1.0 NH1 A:ARG615 3.9 32.2 1.0 O A:HIS829 3.9 24.3 1.0 OE1 A:GLU658 4.0 21.8 1.0 CZ A:ARG615 4.0 30.8 1.0 OH A:TYR714 4.3 59.5 1.0 P P:DT10 4.4 0.2 1.0 CB A:ASP830 4.4 14.2 1.0 CA A:ASP830 4.5 20.3 1.0 C5' P:DT10 4.6 0.3 1.0 CG A:HIS829 4.6 33.9 1.0 N A:HIS829 4.6 24.4 1.0 O5' P:DT10 4.6 0.6 1.0 O3' P:DT10 4.7 0.9 1.0 O A:HOH1415 4.7 50.3 1.0 O A:HOH1139 4.8 24.6 1.0 CD2 A:HIS829 4.8 36.0 1.0 NE A:ARG615 4.9 33.5 1.0

N.Chim, L.N.Jackson, A.M.Trinh, J.C.Chaput. Crystal Structures of Dna Polymerase I Capture Novel Intermediates in the Dna Synthesis Pathway. Elife V. 7 2018.
ISSN: ESSN 2050-084X
PubMed: 30338759
DOI: 10.7554/ELIFE.40444