Manganese in PDB 8k07: Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Citrate Bound K185A Mutant

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

The structure of Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Citrate Bound K185A Mutant, PDB code: 8k07 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)	24.80 / 1.12
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	57.299, 68.518, 73.095, 117.88, 94.31, 109.38
R / Rfree (%)	20.5 / 21.9

The binding sites of Manganese atom in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Citrate Bound K185A Mutant (pdb code 8k07). 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 - - Citrate Bound K185A Mutant, PDB code: 8k07:
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 - - Citrate 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 - - Citrate Bound K185A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn401 b:14.2 occ:1.00 O A:HOH595 2.1 14.4 1.0 OD1 A:ASP164 2.1 14.8 1.0 O A:HOH528 2.2 17.1 1.0 O5 A:CIT402 2.2 14.2 1.0 O C:HOH555 2.2 15.7 1.0 O7 A:CIT402 2.3 14.3 1.0 C6 A:CIT402 3.0 12.8 1.0 CG A:ASP164 3.1 16.1 1.0 C3 A:CIT402 3.2 13.1 1.0 OD2 A:ASP164 3.5 16.6 1.0 NE2 A:HIS156 3.7 16.8 1.0 O4 A:CIT402 3.9 13.0 1.0 O C:HOH587 4.0 13.4 1.0 O1 A:CIT402 4.0 21.8 1.0 C1 A:CIT402 4.1 17.8 1.0 OE1 C:GLU195 4.1 15.9 1.0 OE1 C:GLU198 4.1 14.6 1.0 C2 A:CIT402 4.2 14.9 1.0 O6 A:CIT402 4.2 13.5 1.0 CD2 A:HIS156 4.2 15.9 1.0 OE2 C:GLU198 4.3 17.4 1.0 CD C:GLU198 4.3 14.6 1.0 C4 A:CIT402 4.4 14.6 1.0 CE1 A:HIS156 4.4 15.9 1.0 CB A:ASP164 4.5 15.6 1.0 C5 A:CIT402 4.5 12.9 1.0 O C:HOH595 4.6 22.3 1.0 O2 A:CIT402 4.6 22.5 1.0 N A:ILE165 4.6 13.3 1.0 C A:ASP164 4.8 14.4 1.0 CA A:ASP164 4.8 14.6 1.0 C A:ILE165 4.8 13.4 1.0 O A:ILE165 4.8 13.2 1.0 N A:SER166 4.9 12.5 1.0 CA A:SER166 4.9 12.2 1.0

Manganese binding site 2 out of 3 in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Citrate 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 - - Citrate Bound K185A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn401 b:13.5 occ:1.00 O B:HOH591 2.1 14.3 1.0 OD1 B:ASP165 2.1 13.1 1.0 O B:HOH520 2.2 14.3 1.0 O6 B:CIT402 2.2 13.9 1.0 O A:HOH563 2.2 13.8 1.0 O7 B:CIT402 2.2 14.2 1.0 C6 B:CIT402 3.0 13.8 1.0 CG B:ASP165 3.2 13.6 1.0 C3 B:CIT402 3.2 13.5 1.0 OD2 B:ASP165 3.5 16.3 1.0 O B:HOH732 3.6 13.5 1.0 NE2 B:HIS157 3.7 15.9 1.0 O3 B:CIT402 3.9 12.8 1.0 O A:HOH617 4.0 12.4 1.0 OE1 A:GLU195 4.1 13.8 1.0 OE1 A:GLU198 4.1 13.2 1.0 C1 B:CIT402 4.1 20.7 1.0 O2 B:CIT402 4.1 22.6 1.0 C2 B:CIT402 4.1 16.8 1.0 O5 B:CIT402 4.2 14.8 1.0 CD2 B:HIS157 4.2 14.8 1.0 OE2 A:GLU198 4.2 15.2 1.0 CD A:GLU198 4.3 12.2 1.0 O B:HOH660 4.3 23.0 1.0 C4 B:CIT402 4.3 13.9 1.0 CE1 B:HIS157 4.4 15.9 1.0 CB B:ASP165 4.5 14.5 1.0 O A:HOH629 4.6 21.1 1.0 C5 B:CIT402 4.6 11.8 1.0 N B:ILE166 4.7 12.8 1.0 O1 B:CIT402 4.7 25.0 1.0 C B:ASP165 4.8 13.1 1.0 CA B:ASP165 4.8 14.0 1.0 C B:ILE166 4.8 12.6 1.0 O B:ILE166 4.9 12.4 1.0 O A:HOH557 4.9 21.7 1.0 N B:SER167 4.9 12.1 1.0 CA B:SER167 5.0 11.2 1.0

Manganese binding site 3 out of 3 in the Pseudouridine 5'-Monophosphate Glycosylase From Arabidopsis Thaliana - - Citrate 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 - - Citrate Bound K185A Mutant within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:15.2 occ:1.00 O C:HOH518 2.1 18.5 1.0 O C:HOH554 2.1 14.6 1.0 OD1 C:ASP164 2.1 15.3 1.0 O6 C:CIT402 2.2 15.8 1.0 O B:HOH548 2.3 16.0 1.0 O7 C:CIT402 2.3 15.8 1.0 C6 C:CIT402 3.0 15.9 1.0 CG C:ASP164 3.1 16.5 1.0 C3 C:CIT402 3.2 16.0 1.0 OD2 C:ASP164 3.5 18.2 1.0 NE2 C:HIS156 3.8 19.0 1.0 O4 C:CIT402 3.9 14.1 1.0 O2 C:CIT402 4.0 23.4 1.0 C1 C:CIT402 4.0 21.8 1.0 O B:HOH602 4.0 13.7 1.0 OE1 B:GLU196 4.1 14.9 1.0 OE1 B:GLU199 4.1 15.5 1.0 C2 C:CIT402 4.2 19.3 1.0 O5 C:CIT402 4.2 14.8 1.0 OE2 B:GLU199 4.3 17.1 1.0 CD2 C:HIS156 4.3 16.2 1.0 CD B:GLU199 4.3 15.6 1.0 C4 C:CIT402 4.4 15.8 1.0 CE1 C:HIS156 4.5 18.3 1.0 CB C:ASP164 4.5 15.3 1.0 O1 C:CIT402 4.5 26.0 1.0 C5 C:CIT402 4.6 13.9 1.0 N C:ILE165 4.6 13.5 1.0 C C:ASP164 4.8 13.8 1.0 CA C:ASP164 4.8 14.8 1.0 C C:ILE165 4.8 13.6 1.0 O C:ILE165 4.9 13.8 1.0 N C:SER166 4.9 12.9 1.0 CA C:SER166 5.0 12.8 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