Manganese in PDB 4gik: Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear R5P Adduct

The structure of Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear R5P Adduct, PDB code: 4gik 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)	41.20 / 2.19
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	61.347, 116.496, 132.153, 90.00, 90.00, 90.00
R / Rfree (%)	17.9 / 23.1

The binding sites of Manganese atom in the Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear R5P Adduct (pdb code 4gik). 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 R5P Adduct, PDB code: 4gik:
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 R5P 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 R5P Adduct within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn402 b:26.9 occ:1.00 OD1 A:ASP145 2.1 20.4 1.0 O A:HOH622 2.2 16.6 1.0 O C:HOH553 2.2 34.3 1.0 O A:HOH620 2.2 22.0 1.0 O A:HOH623 2.3 19.8 1.0 O A:HOH645 2.5 30.0 1.0 CG A:ASP145 3.2 31.8 1.0 OD2 A:ASP145 3.5 32.9 1.0 NE2 A:HIS137 4.0 30.7 1.0 O A:GLY266 4.0 41.4 1.0 O C:HOH503 4.0 26.3 1.0 OE1 C:GLU179 4.0 36.5 1.0 OE2 C:GLU179 4.0 33.5 1.0 O3P A:R5P401 4.1 24.8 1.0 OE1 C:GLU176 4.2 37.0 1.0 CD C:GLU179 4.2 35.2 1.0 O A:HOH535 4.3 26.6 1.0 C A:GLY266 4.3 38.8 1.0 O A:HOH529 4.3 26.4 1.0 CD2 A:HIS137 4.4 26.4 1.0 O1P A:R5P401 4.4 36.0 1.0 CB A:ASP145 4.5 32.8 1.0 N A:ILE146 4.6 28.7 1.0 CE1 A:HIS137 4.6 28.7 1.0 CA A:GLY266 4.6 36.4 1.0 CA A:ASP145 4.7 29.7 1.0 O A:ILE146 4.7 29.3 1.0 C A:ASP145 4.8 31.2 1.0 C A:ILE146 4.8 30.0 1.0 P A:R5P401 4.8 30.5 1.0 N A:LYS267 4.9 39.2 1.0 N A:SER147 5.0 26.4 1.0 O C:HOH504 5.0 30.3 1.0

Manganese binding site 2 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear R5P 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 R5P Adduct within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn402 b:24.8 occ:1.00 OD1 B:ASP145 2.2 19.2 1.0 O B:HOH618 2.2 30.0 1.0 O A:HOH625 2.2 24.1 1.0 O A:HOH624 2.3 19.0 1.0 O B:HOH601 2.3 19.0 1.0 O B:HOH599 2.3 20.8 1.0 CG B:ASP145 3.2 25.4 1.0 OD2 B:ASP145 3.6 23.7 1.0 OE2 A:GLU179 3.9 30.9 1.0 OE1 A:GLU179 4.0 31.9 1.0 O B:GLY266 4.0 31.1 1.0 O A:HOH503 4.1 17.7 1.0 NE2 B:HIS137 4.1 24.7 1.0 CD A:GLU179 4.2 28.6 1.0 O3P B:R5P401 4.2 25.6 1.0 OE1 A:GLU176 4.2 34.5 1.0 O B:HOH534 4.2 31.2 1.0 O B:HOH508 4.2 21.5 1.0 C B:GLY266 4.3 27.9 1.0 CD2 B:HIS137 4.3 25.8 1.0 O1P B:R5P401 4.4 28.5 1.0 CA B:GLY266 4.5 29.9 1.0 CB B:ASP145 4.5 23.5 1.0 N B:ILE146 4.6 21.3 1.0 O B:HOH502 4.7 24.6 1.0 CA B:ASP145 4.8 21.0 1.0 C B:ILE146 4.8 20.2 1.0 P B:R5P401 4.8 30.0 1.0 C B:ASP145 4.8 24.2 1.0 O B:ILE146 4.8 22.8 1.0 N B:SER147 4.8 20.9 1.0 N B:LYS267 4.9 29.2 1.0 CE1 B:HIS137 4.9 27.4 1.0 CA B:SER147 4.9 24.5 1.0

Manganese binding site 3 out of 3 in the Crystal Structure of Pseudouridine Monophosphate Glycosidase/Linear R5P 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 R5P Adduct within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:37.1 occ:1.00 O C:HOH550 2.2 29.3 1.0 OD1 C:ASP145 2.2 34.1 1.0 O B:HOH598 2.3 31.9 1.0 O C:HOH552 2.3 31.4 1.0 O C:HOH549 2.4 35.9 1.0 O C:HOH551 2.5 36.9 1.0 CG C:ASP145 3.2 42.4 1.0 OD2 C:ASP145 3.6 48.7 1.0 OE2 B:GLU179 4.0 41.6 1.0 O B:HOH509 4.0 32.6 1.0 OE1 B:GLU179 4.0 42.5 1.0 NE2 C:HIS137 4.0 43.0 1.0 O3P C:R5P401 4.1 34.8 1.0 O C:HOH505 4.1 28.0 1.0 O C:GLY266 4.2 39.9 1.0 O C:HOH556 4.2 37.1 1.0 CD B:GLU179 4.2 37.9 1.0 OE1 B:GLU176 4.2 37.4 1.0 C C:GLY266 4.4 36.0 1.0 O1P C:R5P401 4.4 38.6 1.0 CD2 C:HIS137 4.5 40.5 1.0 N C:ILE146 4.5 39.3 1.0 CB C:ASP145 4.5 35.5 1.0 CE1 C:HIS137 4.6 48.1 1.0 CA C:GLY266 4.7 41.5 1.0 C C:ILE146 4.7 31.2 1.0 P C:R5P401 4.7 42.5 1.0 O C:ILE146 4.7 29.5 1.0 CA C:ASP145 4.7 34.0 1.0 C C:ASP145 4.8 37.5 1.0 N C:SER147 4.9 31.4 1.0 N C:LYS267 4.9 36.1 1.0 CA C:SER147 4.9 32.3 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