Magnesium in PDB 5dk5: Crystal Structure of Crn-4-Mes Complex

The structure of Crystal Structure of Crn-4-Mes Complex, PDB code: 5dk5 was solved by Y.-Y.Hsiao, H.S.Yuan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.75 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	66.259, 67.624, 178.002, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 21.7

The structure of Crystal Structure of Crn-4-Mes Complex also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Crn-4-Mes Complex (pdb code 5dk5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Crn-4-Mes Complex, PDB code: 5dk5:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Crn-4-Mes Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Crn-4-Mes Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:38.0 occ:1.00 O A:HOH570 2.2 26.5 1.0 O A:HOH566 2.2 42.7 1.0 O A:HOH479 2.2 28.4 1.0 O A:HOH405 2.2 58.8 1.0 OD2 A:ASP15 2.8 29.8 1.0 OD2 A:ASP184 2.9 24.6 1.0 OE2 A:GLU17 3.3 25.4 1.0 O A:HOH668 3.8 34.4 1.0 H71 A:MES302 3.8 35.5 1.0 O2S A:MES302 3.9 43.4 1.0 CG A:ASP15 3.9 26.3 1.0 CG A:ASP184 3.9 25.9 1.0 H52 A:MES302 3.9 34.4 1.0 O A:HOH401 4.1 31.3 1.0 HB3 A:ASP184 4.1 29.8 1.0 H72 A:MES302 4.2 35.5 1.0 CD A:GLU17 4.3 23.6 1.0 OD1 A:ASP15 4.3 24.4 1.0 O A:PHE16 4.4 19.6 1.0 OD1 A:ASP111 4.5 33.1 1.0 CB A:ASP184 4.5 24.9 1.0 C7 A:MES302 4.5 29.5 1.0 OD2 A:ASP115 4.6 23.5 1.0 OD2 A:ASP111 4.6 38.3 1.0 HB2 A:ASP184 4.6 29.8 1.0 OE1 A:GLU17 4.7 24.3 1.0 HD12 A:ILE163 4.7 33.3 1.0 HD11 A:ILE163 4.7 33.3 1.0 OD1 A:ASP115 4.8 26.4 1.0 O A:HOH439 4.8 22.0 1.0 OD1 A:ASP184 4.9 26.6 1.0 CG A:ASP111 4.9 33.5 1.0 C5 A:MES302 4.9 28.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Crn-4-Mes Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Crn-4-Mes Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg303 b:42.3 occ:1.00 O B:HOH505 2.2 34.1 1.0 O B:HOH534 2.2 65.2 1.0 O B:HOH401 2.2 42.5 1.0 O B:HOH426 2.2 70.5 1.0 OD2 B:ASP15 2.9 44.5 1.0 OD2 B:ASP184 3.0 43.8 1.0 OE2 B:GLU17 3.4 40.9 1.0 O B:HOH405 3.8 43.6 1.0 O2S B:MES302 3.8 87.1 1.0 CG B:ASP15 3.9 42.8 1.0 H72 B:MES302 3.9 42.9 1.0 H31 B:MES302 4.1 40.5 1.0 CG B:ASP184 4.1 43.5 1.0 HB3 B:ASP184 4.1 46.9 1.0 OD1 B:ASP15 4.2 45.5 1.0 O B:PHE16 4.3 31.9 1.0 CD B:GLU17 4.4 38.6 1.0 HN4 B:MES302 4.4 43.2 1.0 OD2 B:ASP111 4.5 38.8 1.0 OD1 B:ASP111 4.5 38.8 1.0 CB B:ASP184 4.5 39.1 1.0 HB2 B:ASP184 4.6 46.9 1.0 OE1 B:GLU17 4.7 35.8 1.0 OD2 B:ASP115 4.7 35.5 1.0 C7 B:MES302 4.7 35.7 1.0 HD11 B:ILE163 4.8 42.2 1.0 O B:HOH430 4.8 26.4 1.0 OD1 B:ASP115 4.8 35.9 1.0 HD12 B:ILE163 4.8 42.2 1.0 CG B:ASP111 4.9 38.1 1.0 N4 B:MES302 4.9 36.0 1.0 C3 B:MES302 4.9 33.7 1.0 H82 B:MES302 5.0 75.4 1.0

K.-W.Huang, K.-C.Hsu, L.-Y.Chu, J.-M.Yang, H.S.Yuan, Y.-Y.Hsiao. Identification of Inhibitors For the Deddh Family of Exonucleases and A Unique Inhibition Mechanism By Crystal Structure Analysis of Crn-4 Bound with 2-Morpholin-4-Ylethanesulfonate (Mes) J.Med.Chem. V. 59 8019 2016.
ISSN: ISSN 0022-2623
PubMed: 27529560
DOI: 10.1021/ACS.JMEDCHEM.6B00794