Magnesium in PDB 5tk7: Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Triphosphate Bound

The structure of Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Triphosphate Bound, PDB code: 5tk7 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)	49.34 / 1.90
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	143.031, 143.031, 53.786, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 22.4

The binding sites of Magnesium atom in the Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Triphosphate Bound (pdb code 5tk7). 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 Triphosphate Bound, PDB code: 5tk7:
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 Triphosphate 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 Triphosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg201 b:45.6 occ:1.00 O A:HOH343 2.0 46.7 1.0 O A:HOH306 2.1 53.2 1.0 OD2 A:ASP67 2.1 50.8 1.0 OD1 A:ASP132 2.1 51.0 1.0 NE2 A:HIS66 2.1 45.8 1.0 NE2 A:HIS31 2.3 43.0 1.0 CD2 A:HIS66 2.9 53.2 1.0 CG A:ASP67 3.0 51.9 1.0 CG A:ASP132 3.0 53.1 1.0 CE1 A:HIS31 3.1 40.8 1.0 CE1 A:HIS66 3.2 47.4 1.0 OD2 A:ASP132 3.3 53.1 1.0 OD1 A:ASP67 3.3 51.9 1.0 CD2 A:HIS31 3.4 38.7 1.0 CG A:HIS66 4.1 47.9 1.0 O A:HOH319 4.2 44.4 1.0 ND1 A:HIS66 4.2 50.4 1.0 O A:HOH304 4.2 54.0 1.0 NH1 A:ARG16 4.3 40.6 1.0 CB A:ASP132 4.3 47.2 1.0 CB A:ASP67 4.3 50.6 1.0 ND1 A:HIS31 4.3 39.5 1.0 CG A:HIS31 4.5 38.1 1.0 O A:HOH317 4.6 50.5 1.0 O27 A:7D4203 4.6 69.2 1.0 CG2 A:VAL35 4.8 34.5 1.0

Magnesium binding site 2 out of 2 in the Structure of the Hd-Domain Phosphohydrolase Oxsa with Oxetanocin-A Triphosphate 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 Triphosphate Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:61.6 occ:1.00 O A:HOH324 2.0 60.4 1.0 O A:HOH328 2.1 58.6 1.0 O22 A:7D4203 2.1 71.9 1.0 OD2 A:ASP132 2.1 53.1 1.0 O19 A:7D4203 2.1 60.7 1.0 O27 A:7D4203 2.2 69.2 1.0 P21 A:7D4203 3.1 70.9 1.0 CG A:ASP132 3.2 53.1 1.0 P25 A:7D4203 3.2 77.1 1.0 P17 A:7D4203 3.4 70.4 1.0 O24 A:7D4203 3.5 67.3 1.0 O20 A:7D4203 3.6 72.0 1.0 CB A:ASP132 3.7 47.2 1.0 O28 A:7D4203 3.8 77.8 1.0 O18 A:7D4203 4.2 59.3 1.0 O A:HOH343 4.3 46.7 1.0 OD1 A:ASP132 4.3 51.0 1.0 O A:HOH317 4.3 50.5 1.0 O A:HOH306 4.4 53.2 1.0 O23 A:7D4203 4.5 73.3 1.0 O16 A:7D4203 4.5 59.6 1.0 C15 A:7D4203 4.6 56.1 1.0 O26 A:7D4203 4.6 67.2 1.0 C A:ASP132 4.6 45.5 1.0 N A:HIS133 4.7 39.6 1.0 CA A:ASP132 4.8 40.5 1.0 O A:GLU129 4.8 38.5 1.0 O A:ASP132 4.9 38.6 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