Manganese in PDB 4gij: Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate

The structure of Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate, PDB code: 4gij was solved by S.Huang, N.Mahanta, T.P.Begley, S.E.Ealick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.44 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	62.102, 115.403, 132.017, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 22

The binding sites of Manganese atom in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate (pdb code 4gij). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate, PDB code: 4gij:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:34.0 occ:1.00 O C:HOH526 2.3 26.5 1.0 OD1 A:ASP145 2.3 22.3 1.0 O A:HOH529 2.3 27.5 1.0 O A:HOH516 2.3 22.0 1.0 O C:HOH510 2.3 27.4 1.0 O A:HOH566 2.4 26.0 1.0 CG A:ASP145 3.3 26.7 1.0 O A:GLY266 3.6 78.3 1.0 OD2 A:ASP145 3.6 24.9 1.0 O A:HOH524 4.1 20.4 1.0 OE2 C:GLU179 4.1 29.3 1.0 OE1 C:GLU179 4.1 27.2 1.0 NE2 A:HIS137 4.1 23.9 1.0 O C:HOH503 4.1 19.0 1.0 C A:GLY266 4.1 78.7 1.0 OE1 C:GLU176 4.2 24.0 1.0 CD C:GLU179 4.3 31.3 1.0 O A:HOH658 4.3 45.1 1.0 O4 A:SO4400 4.4 47.7 1.0 O1 A:SO4400 4.4 57.7 1.0 CD2 A:HIS137 4.4 23.7 1.0 CB A:ASP145 4.6 24.2 1.0 O A:HOH659 4.6 54.4 1.0 N A:ILE146 4.7 17.1 1.0 N A:LYS267 4.7 78.5 1.0 CA A:GLY266 4.7 82.5 1.0 CE1 A:HIS137 4.8 28.3 1.0 O A:ILE146 4.8 18.2 1.0 C A:ILE146 4.8 15.2 1.0 CA A:ASP145 4.9 23.2 1.0 C A:ASP145 4.9 17.6 1.0 S A:SO4400 4.9 55.1 1.0 N A:SER147 5.0 16.7 1.0 CA A:LYS267 5.0 79.6 1.0 CA A:SER147 5.0 17.4 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:22.8 occ:1.00 OD1 B:ASP145 2.2 18.4 1.0 O B:HOH509 2.2 18.5 1.0 O A:HOH521 2.3 21.4 1.0 O B:HOH511 2.3 22.8 1.0 O B:HOH503 2.3 18.8 1.0 O A:HOH515 2.4 20.6 1.0 CG B:ASP145 3.2 23.4 1.0 OD2 B:ASP145 3.5 23.1 1.0 OE2 A:GLU179 4.0 25.2 1.0 O A:HOH502 4.1 17.7 1.0 NE2 B:HIS137 4.1 21.5 1.0 O B:HOH506 4.1 14.5 1.0 OE1 A:GLU179 4.2 19.6 1.0 O B:GLY266 4.2 32.2 1.0 OE1 A:GLU176 4.2 22.0 1.0 CD A:GLU179 4.2 20.1 1.0 C B:GLY266 4.3 31.9 1.0 CA B:GLY266 4.3 31.6 1.0 O1 B:SO4400 4.4 36.6 1.0 O2 B:SO4400 4.4 36.9 1.0 CD2 B:HIS137 4.4 23.5 1.0 O B:HOH568 4.4 37.0 1.0 CB B:ASP145 4.5 21.6 1.0 CE1 B:HIS137 4.6 27.9 1.0 N B:ILE146 4.6 16.4 1.0 O B:ILE146 4.7 18.4 1.0 O A:HOH525 4.7 24.0 1.0 C B:ILE146 4.8 18.6 1.0 CA B:ASP145 4.8 20.7 1.0 C B:ASP145 4.8 17.1 1.0 N B:SER147 4.8 18.3 1.0 N B:LYS267 4.9 27.9 1.0 N B:GLY266 4.9 29.5 1.0 CA B:SER147 4.9 17.3 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Sulfate within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:48.3 occ:1.00 O B:HOH535 2.3 38.0 1.0 OD1 C:ASP145 2.3 31.8 1.0 O B:HOH557 2.3 35.3 1.0 O C:HOH580 2.4 42.2 1.0 O C:HOH534 2.4 29.1 1.0 O C:HOH514 2.4 29.5 1.0 CG C:ASP145 3.3 34.4 1.0 OD2 C:ASP145 3.7 39.8 1.0 O B:HOH507 4.0 21.5 1.0 OE1 B:GLU179 4.0 33.2 1.0 OE2 B:GLU179 4.1 35.3 1.0 OE1 B:GLU176 4.2 28.5 1.0 O C:HOH516 4.2 28.8 1.0 CD B:GLU179 4.2 30.3 1.0 NE2 C:HIS137 4.2 31.3 1.0 O1 C:SO4400 4.3 92.0 1.0 O4 C:SO4400 4.4 93.5 1.0 CD2 C:HIS137 4.6 29.4 1.0 CB C:ASP145 4.6 28.4 1.0 N C:ILE146 4.7 26.2 1.0 O3 C:SO4400 4.7 92.3 1.0 S C:SO4400 4.7 91.8 1.0 O B:HOH585 4.8 49.5 1.0 CA C:ASP145 4.8 27.0 1.0 O C:ILE146 4.8 19.7 1.0 C C:ASP145 4.9 30.3 1.0 C C:ILE146 4.9 22.7 1.0 CE1 C:HIS137 4.9 35.7 1.0

S.Huang, N.Mahanta, T.P.Begley, S.E.Ealick. Pseudouridine Monophosphate Glycosidase: A New Glycosidase Mechanism. Biochemistry V. 51 9245 2012.
ISSN: ISSN 0006-2960
PubMed: 23066817
DOI: 10.1021/BI3006829