Magnesium in PDB 6c2c: The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme

The structure of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme, PDB code: 6c2c was solved by N.-S.Hong, C.J.Jackson, P.D.Carr, N.Tokuriki, F.Baier, G.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.38 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.600, 88.150, 119.800, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.4

The structure of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Magnesium atom in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme (pdb code 6c2c). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme, PDB code: 6c2c:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg403 b:38.1 occ:1.00 O B:HOH646 2.1 32.8 1.0 O A:HOH552 2.1 30.9 1.0 O A:HOH575 2.1 27.9 1.0 OE1 A:GLU61 3.9 16.1 1.0 O A:HOH682 4.0 31.2 1.0 CD A:GLU61 4.2 14.8 1.0 OE2 A:GLU61 4.3 15.2 1.0 O A:HOH696 4.3 24.6 1.0 OD1 A:ASP33 4.4 20.9 1.0 OD2 A:ASP33 4.5 27.7 1.0 O B:VAL293 4.8 26.2 1.0 CG A:ASP33 4.9 26.9 1.0 OG B:SER292 4.9 16.4 1.0 CG A:GLU61 5.0 12.3 1.0

Magnesium binding site 2 out of 2 in the The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Molecular Basis For the Functional Evolution of An Organophosphate Hydrolysing Enzyme within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg403 b:42.5 occ:1.00 O A:HOH515 2.1 27.5 1.0 O B:HOH555 2.2 23.2 1.0 O B:HOH605 2.5 30.3 1.0 O B:HOH672 3.9 29.5 1.0 OE1 B:GLU61 4.0 15.5 1.0 CD B:GLU61 4.2 12.9 1.0 OD2 B:ASP33 4.3 23.2 1.0 OD1 B:ASP33 4.3 21.6 1.0 OE2 B:GLU61 4.4 14.9 1.0 O B:HOH648 4.5 23.6 1.0 O A:VAL293 4.5 25.9 1.0 CG B:ASP33 4.7 20.9 1.0 CG B:GLU61 4.9 11.8 1.0 O A:HOH736 4.9 35.2 1.0

G.Yang, D.W.Anderson, F.Baier, E.Dohmen, N.Hong, P.D.Carr, S.C.L.Kamerlin, C.J.Jackson, E.Bornberg-Bauer, N.Tokuriki. Higher-Order Epistasis Shapes the Fitness Landscape of A Xenobiotic-Degrading Enzyme. Nat.Chem.Biol. V. 15 1120 2019.
ISSN: ESSN 1552-4469
PubMed: 31636435
DOI: 10.1038/S41589-019-0386-3