Magnesium in PDB 8oe6: Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231

The structure of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231, PDB code: 8oe6 was solved by M.Marek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.48 / 1.31
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.431, 67.998, 122.379, 90, 90, 90
R / Rfree (%)	15.4 / 16.8

The structure of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Magnesium atom in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231 (pdb code 8oe6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231, PDB code: 8oe6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:24.3 occ:1.00 O A:HOH495 2.0 25.1 1.0 O A:HOH606 2.0 33.0 1.0 O A:HOH732 2.0 29.3 1.0 O A:HOH632 2.1 27.4 1.0 O A:HOH542 2.1 25.4 1.0 NE2 A:HIS13 2.2 21.9 1.0 CE1 A:HIS13 3.2 21.5 1.0 CD2 A:HIS13 3.2 20.5 1.0 O A:HOH682 4.0 43.1 1.0 OD2 A:ASP26 4.3 22.9 1.0 ND1 A:HIS13 4.3 21.5 1.0 O A:HOH639 4.3 37.0 1.0 CG A:HIS13 4.3 18.6 1.0 O A:ASP26 4.4 19.1 1.0 O A:HOH564 4.6 32.0 1.0 NH1 A:ARG30 4.7 23.2 1.0 CG A:ASP26 4.7 20.4 1.0 CB A:ASP26 4.8 18.9 1.0 O A:HOH496 4.9 44.2 1.0

Magnesium binding site 2 out of 4 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:26.3 occ:1.00 O A:HOH462 2.0 24.5 1.0 O A:HOH450 2.1 28.2 1.0 O A:HOH801 2.1 27.5 1.0 O A:HOH434 2.1 25.1 1.0 O A:HOH731 2.1 31.6 1.0 O A:HOH700 2.1 29.7 1.0 OD2 A:ASP73 4.1 22.2 1.0 O A:HOH802 4.1 44.9 1.0 O A:HOH609 4.2 37.8 1.0 OE1 A:GLU16 4.2 26.6 1.0 OE2 A:GLU16 4.3 37.9 1.0 O A:GLY19 4.4 25.5 1.0 O A:HOH737 4.4 41.0 1.0 O A:HOH756 4.5 48.0 1.0 CD A:GLU16 4.7 29.9 1.0 N A:ARG21 5.0 20.0 1.0

Magnesium binding site 3 out of 4 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:24.6 occ:0.51 O A:HOH612 1.9 33.9 1.0 O A:HOH662 2.0 28.9 1.0 O A:HOH547 2.1 27.3 1.0 O A:HOH804 2.1 39.0 1.0 O A:HOH419 2.2 31.3 1.0 O A:HOH552 2.3 34.2 1.0 O A:LYS71 3.9 19.0 1.0 O A:HOH798 4.0 30.6 1.0 OD1 A:ASP73 4.1 23.9 1.0 O A:HOH426 4.2 40.7 1.0 O A:HOH511 4.2 30.2 1.0 O A:HOH723 4.3 43.9 1.0 O A:SER72 4.3 19.5 1.0 NH2 A:ARG21 4.3 33.1 1.0 C A:LYS71 4.6 17.6 1.0 C A:SER72 4.8 18.8 1.0 CA A:ASP73 4.9 18.7 1.0

Magnesium binding site 4 out of 4 in the Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Hyperstable Haloalkane Dehalogenase Variant DHAA231 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:41.7 occ:1.00 O A:HOH803 2.0 49.1 1.0 O A:HOH692 2.1 36.3 1.0 O A:HOH775 2.2 48.9 1.0 O A:HOH709 2.3 48.3 1.0 O A:HOH580 4.2 38.2 1.0 O A:HOH791 4.2 41.8 1.0 O A:HOH476 4.3 33.3 1.0 O A:HOH447 4.4 21.6 1.0 O A:HOH439 4.5 41.2 1.0 CD A:PRO269 4.5 20.6 1.0 CG A:PRO269 4.8 21.9 1.0

A.Kunka, S.M.Marques, M.Havlasek, M.Vasina, N.Velatova, L.Cengelova, D.Kovar, J.Damborsky, M.Marek, D.Bednar, Z.Prokop. Advancing Enzyme'S Stability and Catalytic Efficiency Through Synergy of Force-Field Calculations, Evolutionary Analysis, and Machine Learning. Acs Catalysis V. 13 12506 2023.
ISSN: ESSN 2155-5435
PubMed: 37822856
DOI: 10.1021/ACSCATAL.3C02575