Magnesium in PDB 9iqw: Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf

The structure of Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf, PDB code: 9iqw was solved by H.Yu, W.Lianrong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.77 / 1.64
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	96.75, 115.54, 54.29, 90, 90, 90
R / Rfree (%)	17.5 / 19.1

The binding sites of Magnesium atom in the Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf (pdb code 9iqw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf, PDB code: 9iqw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:17.6 occ:1.00 OD2 C:ASP13 2.0 18.5 1.0 O A:HOH313 2.1 17.4 1.0 O C:HOH322 2.1 18.1 1.0 OD1 A:ASP101 2.1 19.2 1.0 O A:HOH363 2.1 18.7 1.0 O C:HOH402 2.1 18.1 1.0 CG A:ASP101 3.1 16.5 1.0 CG C:ASP13 3.2 15.6 1.0 OD2 A:ASP101 3.5 19.6 1.0 OD1 A:ASP100 3.8 20.1 1.0 NZ C:LYS92 3.8 22.3 1.0 O C:HOH480 4.1 28.1 1.0 CB C:ASP13 4.1 18.1 1.0 OD1 C:ASP13 4.1 20.4 1.0 O C:HOH415 4.1 18.4 1.0 O C:HOH351 4.1 25.9 1.0 O C:ASP15 4.3 18.7 1.0 N A:ASP101 4.4 17.2 1.0 CB A:ASP101 4.4 18.1 1.0 CG A:ASP100 4.5 19.0 1.0 O A:HOH501 4.7 40.0 1.0 O A:HOH395 4.8 34.7 1.0 N A:LYS102 4.9 18.3 1.0 OD2 A:ASP100 4.9 19.9 1.0 CA A:ASP101 4.9 20.2 1.0

Magnesium binding site 2 out of 4 in the Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg203 b:17.8 occ:1.00 O C:HOH327 2.0 19.4 1.0 OD2 A:ASP13 2.0 21.5 1.0 OD1 C:ASP101 2.0 18.9 1.0 O C:HOH369 2.1 18.7 1.0 O A:HOH414 2.1 19.0 1.0 O A:HOH329 2.1 18.8 1.0 CG C:ASP101 3.1 22.1 1.0 CG A:ASP13 3.2 19.1 1.0 OD2 C:ASP101 3.5 20.1 1.0 NZ A:LYS92 3.8 22.7 1.0 OD1 C:ASP100 3.8 19.9 1.0 CB A:ASP13 4.1 17.3 1.0 O A:HOH479 4.1 29.5 1.0 O A:HOH442 4.1 17.7 1.0 OD1 A:ASP13 4.1 22.4 1.0 O A:HOH402 4.2 29.7 1.0 O A:HOH321 4.2 26.1 1.0 O A:ASP15 4.3 18.7 1.0 N C:ASP101 4.4 16.7 1.0 CB C:ASP101 4.4 20.1 1.0 CG C:ASP100 4.5 19.7 1.0 N C:LYS102 4.9 18.7 1.0 OD2 C:ASP100 4.9 22.4 1.0 CA C:ASP101 4.9 18.0 1.0

Magnesium binding site 3 out of 4 in the Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:18.0 occ:1.00 OD2 E:ASP13 2.0 19.0 1.0 O B:HOH320 2.0 16.9 1.0 OD1 B:ASP101 2.1 17.0 1.0 O B:HOH347 2.1 18.3 1.0 O E:HOH333 2.1 17.4 1.0 O E:HOH436 2.1 18.8 1.0 CG B:ASP101 3.1 16.6 1.0 CG E:ASP13 3.3 19.2 1.0 OD2 B:ASP101 3.5 17.6 1.0 NZ E:LYS92 3.8 20.6 1.0 OD1 B:ASP100 3.8 18.3 1.0 O E:HOH498 4.1 28.0 1.0 CB E:ASP13 4.1 16.1 1.0 O E:HOH430 4.1 16.3 1.0 OD1 E:ASP13 4.2 20.3 1.0 O E:HOH419 4.2 31.0 1.0 O E:HOH323 4.3 24.9 1.0 O E:ASP15 4.3 17.0 1.0 N B:ASP101 4.4 14.8 1.0 CB B:ASP101 4.4 16.6 1.0 CG B:ASP100 4.6 17.1 1.0 O B:HOH421 4.6 33.2 1.0 OD2 B:ASP100 4.9 20.3 1.0 N B:LYS102 4.9 15.6 1.0 CA B:ASP101 4.9 14.6 1.0 O E:HOH408 5.0 18.8 1.0

Magnesium binding site 4 out of 4 in the Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Phage HY126 Encoded D-Arabinose 1,5-Diphosphate Phosphatase Afhf within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg203 b:17.3 occ:1.00 O E:HOH324 2.0 17.4 1.0 OD2 B:ASP13 2.0 19.4 1.0 OD1 E:ASP101 2.1 17.1 1.0 O E:HOH378 2.1 19.4 1.0 O B:HOH339 2.1 17.8 1.0 O B:HOH434 2.1 18.6 1.0 CG E:ASP101 3.1 16.8 1.0 CG B:ASP13 3.3 19.6 1.0 OD2 E:ASP101 3.5 19.6 1.0 NZ B:LYS92 3.8 22.6 1.0 OD1 E:ASP100 3.8 18.2 1.0 O B:HOH509 4.0 30.5 1.0 O B:HOH449 4.1 20.7 1.0 O B:HOH345 4.1 25.0 1.0 CB B:ASP13 4.1 15.2 1.0 OD1 B:ASP13 4.1 20.6 1.0 O B:HOH450 4.2 29.2 1.0 O B:ASP15 4.3 19.0 1.0 N E:ASP101 4.4 17.1 1.0 CB E:ASP101 4.4 14.7 1.0 CG E:ASP100 4.5 18.0 1.0 O E:HOH520 4.8 42.7 1.0 OD2 E:ASP100 4.8 19.7 1.0 N E:LYS102 4.9 14.1 1.0 CA E:ASP101 4.9 16.3 1.0

H.Yu, H.Yu, W.Lianrong. N/A N/A.