Magnesium in PDB 3hsd: Crystal Structure of E. Coli Hppk(Y53A)

All present enzymatic activity of Crystal Structure of E. Coli Hppk(Y53A):
2.7.6.3;

The structure of Crystal Structure of E. Coli Hppk(Y53A), PDB code: 3hsd was solved by J.Blaszczyk, Y.Li, H.Yan, X.Ji, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.61 / 1.65
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	42.040, 47.470, 72.530, 90.00, 108.89, 90.00
R / Rfree (%)	16 / 21.5

The structure of Crystal Structure of E. Coli Hppk(Y53A) also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of E. Coli Hppk(Y53A) (pdb code 3hsd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of E. Coli Hppk(Y53A), PDB code: 3hsd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Crystal Structure of E. Coli Hppk(Y53A)


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 E. Coli Hppk(Y53A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg161 b:19.2 occ:1.00 OD1 A:ASP97 2.2 11.4 1.0 O A:HOH202 2.3 13.3 1.0 OD1 A:ASP95 2.3 13.6 1.0 O A:HOH204 2.3 32.7 1.0 O A:HOH201 2.3 23.9 1.0 O A:HOH203 2.4 25.9 1.0 CG A:ASP97 3.1 13.9 1.0 MG A:MG162 3.2 17.9 1.0 CG A:ASP95 3.3 17.7 1.0 OD2 A:ASP97 3.3 16.2 1.0 OD2 A:ASP95 3.6 21.1 1.0 OE2 A:GLU77 4.1 10.5 1.0 O A:LEU96 4.2 11.7 1.0 O A:HOH205 4.3 25.9 1.0 O A:HOH491 4.4 38.9 1.0 CB A:ASP97 4.4 8.6 1.0 O A:HOH540 4.5 31.0 1.0 C A:LEU96 4.6 7.9 1.0 CB A:ASP95 4.6 11.2 1.0 O A:HOH482 4.7 36.7 1.0 N A:LEU96 4.7 5.2 1.0 O A:HOH207 4.7 32.2 1.0 CA A:ASP97 4.8 7.1 1.0 CE1 A:HIS115 4.8 12.1 1.0 CA A:ASP95 4.9 6.6 1.0 N A:ASP97 4.9 6.9 1.0 O A:HOH321 4.9 19.6 1.0

Magnesium binding site 2 out of 5 in the Crystal Structure of E. Coli Hppk(Y53A)


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 E. Coli Hppk(Y53A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg162 b:17.9 occ:1.00 OD2 A:ASP97 2.2 16.2 1.0 OD2 A:ASP95 2.3 21.1 1.0 O A:HOH204 2.4 32.7 1.0 O A:HOH207 2.5 32.2 1.0 O A:HOH206 2.5 32.3 1.0 O A:HOH205 2.5 25.9 1.0 CG A:ASP95 3.1 17.7 1.0 CG A:ASP97 3.2 13.9 1.0 MG A:MG161 3.2 19.2 1.0 OD1 A:ASP95 3.3 13.6 1.0 OD1 A:ASP97 3.5 11.4 1.0 O A:HOH302 4.0 18.8 1.0 O A:HOH364 4.0 29.0 1.0 O A:HOH512 4.1 35.0 1.0 NH2 A:ARG92 4.3 19.7 0.3 NH1 A:ARG121 4.3 21.2 1.0 NE2 A:HIS115 4.4 15.8 1.0 CE A:MET124 4.4 13.8 1.0 CB A:ASP97 4.5 8.6 1.0 CB A:ASP95 4.5 11.2 1.0 O A:HOH201 4.5 23.9 1.0 NH2 A:ARG92 4.6 20.4 0.7 CE1 A:HIS115 4.7 12.1 1.0 O A:HOH203 4.9 25.9 1.0

Magnesium binding site 3 out of 5 in the Crystal Structure of E. Coli Hppk(Y53A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of E. Coli Hppk(Y53A) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg163 b:13.4 occ:1.00 O B:HOH217 2.1 11.5 1.0 O A:HOH215 2.1 10.6 1.0 O A:HOH214 2.2 12.1 1.0 O A:HOH219 2.2 13.4 1.0 O B:HOH216 2.2 15.4 1.0 O A:HOH218 2.3 18.4 1.0 O A:GLY26 4.1 20.8 1.0 OD2 B:ASP49 4.1 9.5 1.0 OD1 B:ASP49 4.1 13.0 1.0 O A:SER31 4.2 12.1 1.0 O A:HOH591 4.2 38.6 1.0 O B:HOH257 4.3 14.2 1.0 O A:ILE28 4.3 9.3 1.0 O A:HOH256 4.3 14.7 1.0 O A:ASP27 4.5 14.6 0.8 CG B:ASP49 4.6 12.8 1.0 CA A:ASP27 4.6 15.2 0.2 O A:ASP27 4.7 14.6 0.2 CG B:PRO47 4.7 10.6 1.0 O A:HOH549 4.7 36.7 1.0 C A:ASP27 4.8 15.1 0.8 C A:ASP27 4.8 15.0 0.2 CA A:ASP27 4.8 15.0 0.8 NE2 B:GLN50 4.8 23.7 1.0 CB B:PRO47 4.9 11.2 1.0

Magnesium binding site 4 out of 5 in the Crystal Structure of E. Coli Hppk(Y53A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of E. Coli Hppk(Y53A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg161 b:17.8 occ:1.00 OD2 B:ASP97 2.2 13.9 1.0 OD2 B:ASP95 2.2 20.3 1.0 O A:HOH211 2.2 14.2 1.0 O B:HOH208 2.3 19.4 1.0 O B:HOH209 2.3 22.3 1.0 O B:HOH210 2.5 25.6 1.0 CG B:ASP97 3.2 13.9 1.0 CG B:ASP95 3.2 19.7 1.0 OD1 B:ASP97 3.5 13.4 1.0 OD1 B:ASP95 3.7 16.0 1.0 MG B:MG162 3.7 14.3 1.0 O B:HOH311 4.0 18.9 1.0 O B:HOH438 4.2 31.0 1.0 NE2 B:HIS115 4.2 10.6 1.0 NH1 B:ARG121 4.3 34.7 1.0 O B:HOH502 4.3 35.1 1.0 O A:HOH359 4.4 25.6 1.0 OE1 A:GLU16 4.4 24.0 1.0 CE B:MET124 4.4 16.4 1.0 CB B:ASP95 4.5 12.6 1.0 CB B:ASP97 4.5 7.7 1.0 CE1 B:HIS115 4.7 17.7 1.0 O B:HOH510 4.8 34.3 1.0 O A:HOH212 4.9 16.5 1.0

Magnesium binding site 5 out of 5 in the Crystal Structure of E. Coli Hppk(Y53A)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of E. Coli Hppk(Y53A) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg162 b:14.3 occ:1.00 OD1 B:ASP97 2.1 13.4 1.0 O A:HOH211 2.2 14.2 1.0 OD1 B:ASP95 2.2 16.0 1.0 O B:HOH213 2.2 13.0 1.0 OE2 A:GLU16 2.2 19.5 1.0 O A:HOH212 2.3 16.5 1.0 CD A:GLU16 3.1 21.8 1.0 CG B:ASP97 3.1 13.9 1.0 CG B:ASP95 3.2 19.7 1.0 OE1 A:GLU16 3.3 24.0 1.0 OD2 B:ASP95 3.4 20.3 1.0 OD2 B:ASP97 3.5 13.9 1.0 MG B:MG161 3.7 17.8 1.0 O A:HOH401 4.1 26.0 1.0 O B:LEU96 4.2 12.2 1.0 OE2 B:GLU77 4.3 10.1 1.0 O A:HOH359 4.3 25.6 1.0 CB B:ASP97 4.4 7.7 1.0 CG A:GLU16 4.5 17.5 1.0 CB B:ASP95 4.6 12.6 1.0 C B:LEU96 4.6 8.3 1.0 CA B:ASP97 4.7 8.1 1.0 N B:LEU96 4.8 8.5 1.0 N B:ASP97 4.8 5.9 1.0 CA B:ASP95 4.9 9.5 1.0 O B:HOH208 4.9 19.4 1.0 O B:HOH210 5.0 25.6 1.0

Y.Li, J.Blaszczyk, X.Ji, H.Yan. Pterin-Binding Site Mutation Y53A, N55A or F123A and Activity of E. Coli Hppk. To Be Published.