Magnesium in PDB 5tk6: Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Diphosphate Bound

The structure of Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Diphosphate Bound, PDB code: 5tk6 was solved by J.Bridwell-Rabb, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.41 / 1.92
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	142.588, 142.588, 53.800, 90.00, 90.00, 120.00
R / Rfree (%)	17.9 / 21.8

The binding sites of Magnesium atom in the Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Diphosphate Bound (pdb code 5tk6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Diphosphate Bound, PDB code: 5tk6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Diphosphate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Diphosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:34.2 occ:1.00 OD1 A:ASP132 2.0 39.2 1.0 O A:HOH342 2.1 40.9 1.0 OD2 A:ASP67 2.1 37.6 1.0 NE2 A:HIS66 2.1 35.1 1.0 O A:HOH325 2.1 39.9 1.0 NE2 A:HIS31 2.3 34.8 1.0 CD2 A:HIS66 2.9 40.0 1.0 CG A:ASP132 3.0 43.4 1.0 CG A:ASP67 3.0 42.4 1.0 CE1 A:HIS31 3.1 33.8 1.0 CE1 A:HIS66 3.2 36.8 1.0 CD2 A:HIS31 3.3 33.1 1.0 OD1 A:ASP67 3.4 41.6 1.0 OD2 A:ASP132 3.4 46.9 1.0 O A:HOH336 4.1 37.7 1.0 CG A:HIS66 4.1 36.5 1.0 ND1 A:HIS66 4.2 38.5 1.0 O A:HOH349 4.3 44.6 1.0 NH1 A:ARG16 4.3 34.0 1.0 CB A:ASP132 4.3 40.4 1.0 CB A:ASP67 4.3 35.4 1.0 ND1 A:HIS31 4.3 32.5 1.0 CG A:HIS31 4.4 31.3 1.0 O A:HOH338 4.6 42.9 1.0 O A:HOH315 4.6 59.8 1.0 CG2 A:VAL35 4.8 28.6 1.0

Magnesium binding site 2 out of 2 in the Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Diphosphate Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Diphosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:55.4 occ:1.00 O A:HOH315 2.0 59.8 1.0 O A:HOH331 2.1 52.7 1.0 O A:HOH343 2.1 53.1 1.0 OD2 A:ASP132 2.1 46.9 1.0 O19 A:7D3203 2.2 56.9 1.0 O23 A:7D3203 2.2 65.2 1.0 CG A:ASP132 3.2 43.4 1.0 P21 A:7D3203 3.3 69.2 1.0 P17 A:7D3203 3.5 61.0 1.0 O22 A:7D3203 3.5 65.2 1.0 CB A:ASP132 3.7 40.4 1.0 O20 A:7D3203 3.8 68.3 1.0 O A:HOH338 4.2 42.9 1.0 O18 A:7D3203 4.3 57.1 1.0 OD1 A:ASP132 4.3 39.2 1.0 O A:HOH342 4.3 40.9 1.0 O A:HOH307 4.3 65.3 1.0 O A:HOH325 4.5 39.9 1.0 C A:ASP132 4.5 37.7 1.0 O16 A:7D3203 4.5 59.9 1.0 C15 A:7D3203 4.6 47.5 1.0 O24 A:7D3203 4.7 70.6 1.0 N A:HIS133 4.7 34.5 1.0 CA A:ASP132 4.7 36.5 1.0 O A:ASP132 4.8 33.1 1.0 O A:GLU129 4.8 35.5 1.0

J.Bridwell-Rabb, G.Kang, A.Zhong, H.W.Liu, C.L.Drennan. An Hd Domain Phosphohydrolase Active Site Tailored For Oxetanocin-A Biosynthesis. Proc. Natl. Acad. Sci. V. 113 13750 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 27849620
DOI: 10.1073/PNAS.1613610113