Manganese in PDB 8k06: Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant

All present enzymatic activity of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant:
4.2.1.70;

The structure of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant, PDB code: 8k06 was solved by J.Y.Lee, S.H.Kim, S.K.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.92 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.56, 105.838, 73.555, 90, 118.87, 90
R / Rfree (%)	18.3 / 20.8

The binding sites of Manganese atom in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant (pdb code 8k06). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant, PDB code: 8k06:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn400 b:32.2 occ:1.00 O C:HOH562 2.1 30.6 1.0 OD1 A:ASP164 2.1 25.8 1.0 O A:HOH561 2.2 28.4 1.0 O A:HOH647 2.3 24.6 1.0 O A:HOH525 2.4 31.1 1.0 O C:HOH530 2.4 30.2 1.0 CG A:ASP164 3.1 29.6 1.0 OD2 A:ASP164 3.5 28.4 1.0 OE2 C:GLU198 3.9 36.0 1.0 NE2 A:HIS156 3.9 30.8 1.0 OP2 A:PSU401 4.1 41.9 1.0 O C:HOH571 4.1 23.1 1.0 OE1 C:GLU198 4.1 31.9 1.0 OE1 C:GLU195 4.2 32.5 1.0 O A:GLY285 4.2 31.9 1.0 CD C:GLU198 4.2 33.0 1.0 CD2 A:HIS156 4.3 27.9 1.0 C A:GLY285 4.4 33.9 1.0 OP3 A:PSU401 4.5 34.8 1.0 O A:HOH627 4.5 28.3 1.0 O A:HOH542 4.5 36.4 1.0 CB A:ASP164 4.5 25.1 1.0 N A:ILE165 4.6 24.0 1.0 CA A:GLY285 4.7 35.5 1.0 O A:ILE165 4.7 23.3 1.0 CE1 A:HIS156 4.7 31.8 1.0 C A:ILE165 4.8 23.0 1.0 C A:ASP164 4.8 24.7 1.0 CA A:ASP164 4.8 24.0 1.0 O C:HOH584 4.9 35.5 1.0 P A:PSU401 4.9 40.3 1.0 N A:ASN286 4.9 34.1 1.0 N A:SER166 5.0 23.1 1.0 CA A:SER166 5.0 23.0 1.0

Manganese binding site 2 out of 3 in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn400 b:55.0 occ:1.00 OD1 B:ASP164 2.2 30.1 1.0 O B:HOH518 2.2 41.8 1.0 O A:HOH564 2.3 41.6 1.0 O B:HOH662 2.5 35.1 1.0 O B:HOH568 2.5 40.4 1.0 H51 B:RP5401 2.7 56.7 1.0 H52 B:RP5401 3.2 56.7 1.0 CG B:ASP164 3.2 34.5 1.0 C5 B:RP5401 3.4 47.2 1.0 OD2 B:ASP164 3.6 36.3 1.0 NE2 B:HIS156 3.8 30.4 1.0 OE2 A:GLU198 3.9 34.4 1.0 O2X B:RP5401 3.9 41.8 1.0 O A:HOH576 4.0 24.6 1.0 OE1 A:GLU195 4.1 31.0 1.0 O5 B:RP5401 4.2 39.4 1.0 CD2 B:HIS156 4.3 30.9 1.0 H3 B:RP5401 4.4 61.0 1.0 CE1 B:HIS156 4.5 34.4 1.0 C4 B:RP5401 4.5 48.0 1.0 P' B:RP5401 4.5 33.6 1.0 CB B:ASP164 4.6 27.0 1.0 N B:ILE165 4.6 22.8 1.0 O3 B:RP5401 4.7 52.8 1.0 H4 B:RP5401 4.7 57.6 1.0 O B:ILE165 4.7 24.8 1.0 C3 B:RP5401 4.8 50.8 1.0 C B:ASP164 4.8 24.7 1.0 C B:ILE165 4.8 23.4 1.0 CA B:ASP164 4.8 26.7 1.0 O3X B:RP5401 4.8 33.1 1.0 N B:SER166 5.0 23.4 1.0

Manganese binding site 3 out of 3 in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Psu, R5P Bound K185A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn400 b:33.6 occ:1.00 O B:HOH524 2.2 27.5 1.0 O C:HOH552 2.2 30.5 1.0 O B:HOH530 2.2 28.0 1.0 OD1 C:ASP164 2.2 27.3 1.0 O C:HOH531 2.3 28.6 1.0 O C:HOH608 2.4 26.2 1.0 CG C:ASP164 3.3 31.5 1.0 OD2 C:ASP164 3.7 34.8 1.0 NE2 C:HIS156 3.9 31.8 1.0 OE2 B:GLU198 4.0 35.3 1.0 O B:HOH578 4.1 24.0 1.0 OE1 B:GLU198 4.1 29.9 1.0 OE1 B:GLU195 4.1 26.2 1.0 CD B:GLU198 4.1 31.3 1.0 O C:GLY285 4.2 32.1 1.0 OP1 C:PSU401 4.3 35.1 1.0 C C:GLY285 4.3 32.7 1.0 CD2 C:HIS156 4.4 29.2 1.0 CA C:GLY285 4.5 32.4 1.0 OP2 C:PSU401 4.5 40.3 1.0 O C:HOH625 4.6 29.0 1.0 CB C:ASP164 4.6 28.4 1.0 O C:ILE165 4.7 22.5 1.0 CE1 C:HIS156 4.7 35.2 1.0 N C:ILE165 4.7 22.3 1.0 O C:HOH549 4.8 34.2 1.0 C C:ILE165 4.8 23.1 1.0 CA C:ASP164 4.8 25.8 1.0 C C:ASP164 4.8 23.8 1.0 P C:PSU401 4.9 33.9 1.0 OE1 C:GLU288 4.9 50.2 1.0 O B:HOH514 4.9 38.2 1.0

J.Lee, S.H.Kim, S.Rhee. Structure and Function of the Pseudouridine 5'-Monophosphate Glycosylase Pumy From Arabidopsis Thaliana. Rna Biol. V. 21 1 2024.
ISSN: ESSN 1555-8584
PubMed: 38117089
DOI: 10.1080/15476286.2023.2293340