Magnesium in PDB 2jfr: Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution

The structure of Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution, PDB code: 2jfr was solved by M.Bellinzoni, A.Wehenkel, W.Shepard, P.M.Alzari, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	6.00 / 0.83
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	76.382, 83.998, 33.478, 90.00, 90.00, 90.00
R / Rfree (%)	9.5 / 12.4

The structure of Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Chlorine	(Cl)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution (pdb code 2jfr). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution, PDB code: 2jfr:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution


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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1234 b:13.9 occ:0.99 OD1 A:ASP35 2.0 13.8 1.0 O3 A:PO41239 2.0 20.9 0.2 O A:HOH2487 2.0 14.6 0.8 O A:HOH2091 2.1 15.2 1.0 O A:GLY36 2.1 14.0 1.0 O A:HOH2131 2.1 14.2 1.0 O A:HOH2486 2.1 14.6 0.8 O4 A:PO41239 2.4 19.4 0.2 P A:PO41239 2.8 18.0 0.2 CG A:ASP35 3.1 13.2 1.0 C A:GLY36 3.2 13.8 1.0 OD2 A:ASP35 3.6 14.1 1.0 MN A:MN1235 3.7 13.8 0.6 O2 A:PO41239 3.8 24.8 0.2 O A:HOH2489 3.8 22.5 0.8 N A:GLY36 3.9 13.4 1.0 O1 A:PO41239 3.9 19.6 0.2 O A:HOH2490 3.9 16.8 1.0 O A:HOH2488 4.0 17.9 0.8 C A:ASP35 4.0 13.3 1.0 O A:HOH2491 4.1 47.5 1.0 OD1 A:ASP22 4.1 14.4 1.0 CA A:GLY36 4.2 13.8 1.0 N A:PHE37 4.2 14.2 1.0 O A:HOH2485 4.2 14.2 1.0 CB A:GLN21 4.2 14.8 1.0 OE1 A:GLN21 4.2 17.9 1.0 O A:HOH2477 4.4 17.1 1.0 CA A:PHE37 4.4 14.6 1.0 CB A:ASP35 4.4 13.6 1.0 OD1 A:ASN224 4.4 14.3 1.0 O A:ASP35 4.4 13.6 1.0 CA A:ASP35 4.5 13.4 1.0 OD1 A:ASP223 4.5 15.8 1.0 NH1 A:ARG17 4.6 20.9 0.6 CB A:PHE37 4.7 15.1 1.0 O A:GLN21 4.8 14.2 1.0 C A:GLN21 4.8 13.9 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution


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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1236 b:15.6 occ:0.42 O1 A:PO41239 1.8 19.6 0.2 O A:HOH2488 1.8 17.9 0.8 O A:HOH2288 2.0 26.9 1.0 O A:HOH2493 2.0 51.4 1.0 O A:HOH2411 2.1 18.4 0.4 OD2 A:ASP185 2.1 16.9 0.6 O A:HOH2287 2.2 18.9 1.0 OD2 A:ASP185 2.8 16.0 0.4 CG A:ASP185 3.1 15.5 0.6 P A:PO41239 3.2 18.0 0.2 CG A:ASP185 3.4 14.5 0.4 O A:HOH2412 3.4 30.7 0.6 OD1 A:ASP185 3.5 20.9 0.4 OD1 A:ASP185 3.6 13.2 0.6 OD2 A:ASP111 3.6 26.7 1.0 MN A:MN1235 3.6 13.8 0.6 O4 A:PO41239 3.8 19.4 0.2 O2 A:PO41239 3.9 24.8 0.2 O A:HOH2489 4.0 22.5 0.8 O A:HOH2487 4.1 14.6 0.8 O A:HOH2492 4.1 53.9 1.0 OD2 A:ASP35 4.1 14.1 1.0 OD1 A:ASP111 4.1 16.5 1.0 MG A:MG1237 4.2 13.8 0.2 CG A:ASP111 4.2 18.1 1.0 O A:HOH2490 4.2 16.8 1.0 O A:HOH2363 4.3 46.1 1.0 O3 A:PO41239 4.3 20.9 0.2 CB A:ASP185 4.4 15.4 0.6 CB A:ASP185 4.5 14.4 0.4 O A:HOH2410 4.5 29.1 1.0 OD2 A:ASP223 4.6 15.6 1.0 O A:HOH2486 4.6 14.6 0.8 O A:HIS153 4.7 29.2 1.0 O A:HOH2289 4.7 14.7 1.0 CA A:HIS153 4.9 20.4 1.0 CG A:ASP35 4.9 13.2 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution


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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1237 b:13.8 occ:0.17 O A:HOH2412 1.9 30.7 0.6 O A:HOH2365 1.9 32.8 1.0 O A:HOH2410 2.0 29.1 1.0 OD2 A:ASP185 2.1 16.0 0.4 O A:HOH2363 2.2 46.1 1.0 O A:HOH2361 2.4 43.8 1.0 O A:HOH2411 2.9 18.4 0.4 OD2 A:ASP185 3.2 16.9 0.6 CG A:ASP185 3.2 14.5 0.4 CG A:ASP185 3.5 15.5 0.6 CD A:ARG152 3.8 32.3 0.6 CB A:ASP185 3.8 14.4 0.4 O A:HOH2357 3.9 38.6 1.0 CB A:ASP185 3.9 15.4 0.6 NH2 A:ARG152 4.1 34.9 0.6 NE A:ARG152 4.1 41.6 0.6 O A:HOH2473 4.1 30.4 1.0 OD1 A:ASP185 4.1 13.2 0.6 O A:ASP185 4.1 18.0 1.0 OD1 A:ASP185 4.1 20.9 0.4 CZ A:ARG152 4.2 42.3 0.6 MG A:MG1236 4.2 15.6 0.4 CG A:ARG152 4.2 33.9 0.6 O A:HOH2358 4.3 22.8 0.3 OD2 A:ASP223 4.4 15.6 1.0 O A:HOH2288 4.5 26.9 1.0 O A:HOH2364 4.5 39.2 0.5 C A:ASP185 4.5 15.0 1.0 O A:HOH2360 4.6 50.4 1.0 O A:HOH2488 4.6 17.9 0.8 NE A:ARG152 4.8 22.2 0.4 O1 A:PO41239 4.8 19.6 0.2 CA A:ASP185 4.8 14.7 0.6 O A:HOH2492 4.9 53.9 1.0 CA A:ASP185 4.9 14.7 0.4 NH1 A:ARG152 5.0 60.4 0.6

Magnesium binding site 4 out of 4 in the Crystal Structure of the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution


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 the Ppm Ser-Thr Phosphatase Mspp From Mycobacterium Smegmatis in Complex with Phosphate at 0.83 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1240 b:17.3 occ:0.45 O A:HOH2056 1.9 36.7 1.0 O A:HOH2025 2.0 35.0 1.0 O A:HOH2026 2.1 35.4 1.0 O A:HOH2052 2.1 30.3 1.0 O A:HOH2054 2.1 20.5 1.0 O A:HOH2057 3.9 42.2 0.5 O A:PRO15 4.2 25.9 1.0 O A:HOH2060 4.3 45.4 0.5 O A:ARG17 4.4 17.2 1.0 NE2 A:GLN13 4.4 19.2 1.0 O A:GLY14 4.4 18.8 1.0 C A:PRO15 4.5 21.6 1.0 CA A:PRO15 4.6 22.1 1.0

M.Bellinzoni, A.Wehenkel, W.Shepard, P.M.Alzari. Insights Into the Mechanism of Ppm Ser/Thr Phosphatases From the Atomic Resolution Structures of A Mycobacterial Enzyme Structure V. 15 863 2007.
ISSN: ISSN 0969-2126
PubMed: 17637345
DOI: 10.1016/J.STR.2007.06.002