Manganese in PDB 4gil: Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear Pseudouridine 5'-Phosphate Adduct

The structure of Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear Pseudouridine 5'-Phosphate Adduct, PDB code: 4gil 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)	48.07 / 2.54
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.472, 77.116, 200.219, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 26

The binding sites of Manganese atom in the Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear Pseudouridine 5'-Phosphate Adduct (pdb code 4gil). 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/Linear Pseudouridine 5'-Phosphate Adduct, PDB code: 4gil:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear Pseudouridine 5'-Phosphate Adduct


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/Linear Pseudouridine 5'-Phosphate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn400 b:38.0 occ:1.00 O A:HOH570 2.2 24.2 1.0 O C:HOH502 2.2 28.8 1.0 O A:HOH502 2.2 21.9 1.0 O C:HOH538 2.3 43.1 1.0 OD1 A:ASP145 2.3 32.2 1.0 O A:HOH600 2.3 40.6 1.0 CG A:ASP145 3.3 32.4 1.0 OD2 A:ASP145 3.8 36.1 1.0 OE2 C:GLU179 3.9 42.6 1.0 OE1 C:GLU179 3.9 49.4 1.0 NE2 A:HIS137 4.0 30.4 1.0 O A:HOH514 4.0 37.4 1.0 OE1 C:GLU176 4.0 53.6 1.0 CD C:GLU179 4.1 47.0 1.0 O3T A:KPS401 4.1 43.0 1.0 O A:HOH530 4.2 34.2 1.0 CD2 A:HIS137 4.3 35.4 1.0 O A:GLY266 4.4 40.8 1.0 C A:GLY266 4.4 38.2 1.0 N A:ILE146 4.4 36.6 1.0 O1P A:KPS401 4.5 28.7 1.0 CA A:GLY266 4.5 36.5 1.0 CB A:ASP145 4.6 25.4 1.0 O A:ILE146 4.6 30.3 1.0 C A:ILE146 4.6 34.9 1.0 C A:ASP145 4.7 32.7 1.0 CE1 A:HIS137 4.7 32.6 1.0 CA A:ASP145 4.8 24.7 1.0 N A:SER147 4.8 33.8 1.0 P A:KPS401 4.8 37.6 1.0 O A:HOH524 4.9 31.4 1.0 CA A:SER147 4.9 39.7 1.0 N A:LYS267 4.9 38.7 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear Pseudouridine 5'-Phosphate Adduct


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/Linear Pseudouridine 5'-Phosphate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:29.2 occ:1.00 O B:HOH548 2.2 23.2 1.0 O B:HOH513 2.2 32.9 1.0 O A:HOH503 2.3 30.2 1.0 O A:HOH571 2.3 28.8 1.0 OD1 B:ASP145 2.4 32.4 1.0 O A:HOH589 2.5 27.7 1.0 CG B:ASP145 3.3 36.9 1.0 OD2 B:ASP145 3.7 32.3 1.0 OE2 A:GLU179 3.8 31.6 1.0 NE2 B:HIS137 3.9 36.4 1.0 O A:HOH510 4.0 26.1 1.0 O1P B:KPS401 4.0 49.8 1.0 OE1 A:GLU179 4.1 33.5 1.0 CD A:GLU179 4.1 31.2 1.0 O B:HOH519 4.2 31.9 1.0 O B:GLY266 4.2 39.8 1.0 OE1 A:GLU176 4.2 32.1 1.0 CD2 B:HIS137 4.3 35.1 1.0 C B:GLY266 4.3 39.3 1.0 O B:HOH531 4.4 49.2 1.0 CA B:GLY266 4.5 35.9 1.0 N B:ILE146 4.6 25.7 1.0 CE1 B:HIS137 4.6 39.3 1.0 CB B:ASP145 4.7 31.8 1.0 O B:ILE146 4.8 28.6 1.0 C B:ASP145 4.8 29.2 1.0 P B:KPS401 4.8 39.8 1.0 C B:ILE146 4.8 34.7 1.0 O B:HOH510 4.9 26.7 1.0 CA B:ASP145 4.9 33.0 1.0 N B:LYS267 4.9 31.5 1.0 O3T B:KPS401 5.0 39.8 1.0 N B:SER147 5.0 35.5 1.0 CA B:SER147 5.0 32.2 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear Pseudouridine 5'-Phosphate Adduct


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/Linear Pseudouridine 5'-Phosphate Adduct within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:43.6 occ:1.00 O B:HOH515 1.9 40.7 1.0 O C:HOH501 2.1 24.5 1.0 O B:HOH501 2.2 32.3 1.0 O C:HOH541 2.2 51.8 1.0 OD1 C:ASP145 2.3 35.4 1.0 O C:HOH542 2.7 48.1 1.0 CG C:ASP145 3.4 42.0 1.0 OE2 B:GLU179 3.6 43.5 1.0 OD2 C:ASP145 3.7 43.8 1.0 O B:HOH504 3.8 37.3 1.0 OE1 B:GLU179 3.9 54.1 1.0 O3T C:KPS401 4.0 41.9 1.0 NE2 C:HIS137 4.0 44.9 1.0 CD B:GLU179 4.0 51.8 1.0 O C:HOH524 4.0 44.5 1.0 O C:GLY266 4.2 49.4 1.0 OE1 B:GLU176 4.2 37.5 1.0 C C:GLY266 4.2 42.4 1.0 CD2 C:HIS137 4.3 48.4 1.0 O1P C:KPS401 4.3 53.6 1.0 CA C:GLY266 4.4 41.7 1.0 O C:HOH516 4.5 37.0 1.0 N C:ILE146 4.6 43.8 1.0 P C:KPS401 4.6 53.5 1.0 C C:ILE146 4.7 43.6 1.0 CB C:ASP145 4.7 37.5 1.0 N C:SER147 4.7 41.9 1.0 N C:LYS267 4.8 38.2 1.0 O C:ILE146 4.8 37.5 1.0 C C:ASP145 4.8 40.1 1.0 CA C:SER147 4.9 45.5 1.0 CE1 C:HIS137 4.9 46.0 1.0 CA C:ASP145 4.9 42.2 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