Magnesium in PDB 5mf5: PA3825-Eal Mg-Cdg Structure

The structure of PA3825-Eal Mg-Cdg Structure, PDB code: 5mf5 was solved by S.Horrell, D.Bellini, R.Strange, A.Wagner, M.Walsh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.16 / 1.77
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	64.590, 64.590, 135.730, 90.00, 90.00, 90.00
R / Rfree (%)	19.8 / 23.2

The binding sites of Magnesium atom in the PA3825-Eal Mg-Cdg Structure (pdb code 5mf5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the PA3825-Eal Mg-Cdg Structure, PDB code: 5mf5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the PA3825-Eal Mg-Cdg Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of PA3825-Eal Mg-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:31.4 occ:1.00 O A:VAL40 2.3 22.2 1.0 O6 A:C2E301 2.4 22.2 1.0 C6 A:C2E301 3.1 21.8 1.0 N A:ASN98 3.2 18.3 1.0 ND2 A:ASN98 3.3 22.1 1.0 C A:VAL40 3.4 17.3 1.0 C5 A:C2E301 3.5 19.8 1.0 N7 A:C2E301 3.7 20.9 1.0 CB A:ASN98 3.7 19.9 1.0 CA A:PHE97 3.9 17.7 1.0 N1 A:C2E301 4.0 21.5 1.0 CD2 A:LEU74 4.0 28.6 1.0 CG A:ASN98 4.0 21.4 1.0 CA A:ASN98 4.0 19.7 1.0 C A:PHE97 4.1 19.4 1.0 CA A:LEU41 4.1 17.2 1.0 N A:LEU41 4.1 17.7 1.0 O A:ASN98 4.2 20.5 1.0 N A:MET42 4.4 18.8 1.0 CB A:VAL40 4.4 18.7 1.0 CB A:PHE97 4.4 18.2 1.0 CA A:VAL40 4.5 17.9 1.0 CG1 A:VAL40 4.5 19.6 1.0 CD2 A:PHE97 4.5 18.6 1.0 C A:ASN98 4.6 21.3 1.0 C4 A:C2E301 4.6 21.5 1.0 C A:LEU41 4.6 19.4 1.0 C8 A:C2E301 4.8 21.6 1.0 CG A:PHE97 4.9 18.3 1.0 O A:GLY96 4.9 19.3 1.0 C2 A:C2E301 4.9 21.8 1.0

Magnesium binding site 2 out of 3 in the PA3825-Eal Mg-Cdg Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of PA3825-Eal Mg-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:22.5 occ:1.00 O21 A:C2E301 2.2 26.1 1.0 OE1 A:GLU130 2.2 26.9 1.0 O A:HOH459 2.2 27.8 1.0 OD2 A:ASP160 2.2 30.2 1.0 OE2 A:GLU39 2.2 24.8 1.0 OD1 A:ASN98 2.3 21.9 1.0 CD A:GLU39 3.2 24.3 1.0 CG A:ASN98 3.2 21.4 1.0 CD A:GLU130 3.3 26.1 1.0 CG A:ASP160 3.3 30.8 1.0 P11 A:C2E301 3.4 28.5 1.0 ND2 A:ASN98 3.5 22.1 1.0 OE1 A:GLU39 3.5 24.9 1.0 O5A A:C2E301 3.7 28.5 1.0 O A:HOH509 3.9 25.5 1.0 CB A:ASP160 3.9 29.5 1.0 O A:HOH484 4.0 23.7 1.0 OE2 A:GLU130 4.0 29.1 1.0 O11 A:C2E301 4.2 32.6 1.0 O A:HOH401 4.2 33.0 1.0 CB A:GLU130 4.2 21.6 1.0 OD1 A:ASP160 4.3 30.7 1.0 CG A:GLU130 4.4 23.6 1.0 OE2 A:GLU217 4.5 39.8 1.0 CG A:GLU39 4.5 23.2 1.0 NZ A:LYS181 4.6 29.4 1.0 CB A:ASN98 4.6 19.9 1.0 O3' A:C2E301 4.7 26.2 1.0 C5A A:C2E301 4.8 27.8 1.0 C2' A:C2E301 4.9 23.3 1.0

Magnesium binding site 3 out of 3 in the PA3825-Eal Mg-Cdg Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of PA3825-Eal Mg-Cdg Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg304 b:35.8 occ:1.00 O A:HOH401 2.2 33.0 1.0 O A:HOH468 2.2 33.7 1.0 OD1 A:ASP161 2.2 35.7 1.0 OD1 A:ASP183 2.3 33.1 1.0 O11 A:C2E301 2.3 32.6 1.0 O A:HOH511 3.4 35.9 1.0 CG A:ASP161 3.4 30.9 1.0 CG A:ASP183 3.5 31.3 1.0 OE1 A:GLU217 3.6 37.8 1.0 P11 A:C2E301 3.9 28.5 1.0 CA A:ASP161 4.1 26.7 1.0 CB A:ASP161 4.2 28.7 1.0 N A:ASP161 4.3 24.6 1.0 OD2 A:ASP183 4.3 29.1 1.0 OD2 A:ASP161 4.5 32.5 1.0 CB A:ASP183 4.5 29.4 1.0 O A:HOH449 4.5 45.0 1.0 NH2 A:ARG134 4.5 60.0 1.0 CA A:ASP183 4.6 25.4 1.0 O3' A:C2E301 4.6 26.2 1.0 N A:GLN184 4.6 23.2 1.0 NE2 A:GLN184 4.7 39.1 1.0 CD A:GLU217 4.7 37.9 1.0 O A:HOH509 4.8 25.5 1.0 O21 A:C2E301 4.9 26.1 1.0 C5A A:C2E301 4.9 27.8 1.0 O5A A:C2E301 4.9 28.5 1.0 CG A:GLN184 5.0 35.6 1.0

D.Bellini, S.Horrell, A.Hutchin, C.W.Phippen, R.W.Strange, Y.Cai, A.Wagner, J.S.Webb, I.Tews, M.A.Walsh. Dimerisation Induced Formation of the Active Site and the Identification of Three Metal Sites in Eal-Phosphodiesterases. Sci Rep V. 7 42166 2017.
ISSN: ESSN 2045-2322
PubMed: 28186120
DOI: 10.1038/SREP42166