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Magnesium in PDB 9m7m: Crystal Structure of Human Pseudouridine 5'-Monophosphate Phosphatase (HHDHD1A) Complexed with Pseudouridine

Enzymatic activity of Crystal Structure of Human Pseudouridine 5'-Monophosphate Phosphatase (HHDHD1A) Complexed with Pseudouridine

All present enzymatic activity of Crystal Structure of Human Pseudouridine 5'-Monophosphate Phosphatase (HHDHD1A) Complexed with Pseudouridine:
3.1.3.96;

Protein crystallography data

The structure of Crystal Structure of Human Pseudouridine 5'-Monophosphate Phosphatase (HHDHD1A) Complexed with Pseudouridine, PDB code: 9m7m was solved by S.Seo, S.Rhee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.79 / 1.26
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.62, 61.09, 68.25, 90, 90, 90
R / Rfree (%) 18.4 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Pseudouridine 5'-Monophosphate Phosphatase (HHDHD1A) Complexed with Pseudouridine (pdb code 9m7m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of Human Pseudouridine 5'-Monophosphate Phosphatase (HHDHD1A) Complexed with Pseudouridine, PDB code: 9m7m:

Magnesium binding site 1 out of 1 in 9m7m

Go back to Magnesium Binding Sites List in 9m7m
Magnesium binding site 1 out of 1 in the Crystal Structure of Human Pseudouridine 5'-Monophosphate Phosphatase (HHDHD1A) Complexed with Pseudouridine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Pseudouridine 5'-Monophosphate Phosphatase (HHDHD1A) Complexed with Pseudouridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:7.7
occ:1.00
 OD2 A:ASP14 2.0 10.9 1.0
O A:HOH511 2.1 12.5 1.0
OD1 A:ASP176 2.1 9.5 1.0
O A:ASP16 2.1 8.0 1.0
O A:HOH426 2.1 9.8 1.0
O A:HOH429 2.2 8.8 1.0
CG A:ASP14 3.0 8.6 1.0
CG A:ASP176 3.1 8.4 1.0
C A:ASP16 3.3 7.8 1.0
OD2 A:ASP176 3.4 9.4 1.0
OD1 A:ASP14 3.4 10.5 1.0
HB2 A:ASP16 3.6 11.0 1.0
HB2 A:ALA177 3.7 10.0 1.0
H A:ASP176 3.8 6.9 1.0
OE2 A:GLU175 3.9 7.7 1.0
HA3 A:GLY17 4.0 9.2 1.0
CA A:ASP16 4.0 9.8 1.0
H A:ASP16 4.1 7.8 1.0
HB2 A:LEU18 4.1 9.3 1.0
N A:ASP16 4.1 7.5 1.0
CB A:ASP16 4.2 10.7 1.0
CB A:ASP14 4.3 9.0 1.0
N A:GLY17 4.3 8.7 1.0
OE2 A:GLU23 4.3 13.4 1.0
HB3 A:ALA177 4.3 10.0 1.0
O13 A:FJF302 4.3 18.6 1.0
HB3 A:ASP14 4.3 9.4 1.0
CB A:ASP176 4.4 7.4 1.0
HB3 A:MET50 4.4 10.3 1.0
O A:HOH467 4.4 14.5 1.0
CB A:ALA177 4.5 9.4 1.0
H A:LEU18 4.5 10.5 1.0
HB3 A:ASP16 4.5 11.0 1.0
H A:ALA177 4.5 8.3 1.0
CA A:GLY17 4.5 8.8 1.0
N A:ASP176 4.6 6.1 1.0
HB3 A:ASP176 4.6 8.2 1.0
HB2 A:ASP14 4.6 9.4 1.0
N A:LEU18 4.7 10.1 1.0
O A:HOH578 4.7 4.1 1.0
HB3 A:LEU18 4.7 9.3 1.0
N A:ALA177 4.7 7.7 1.0
CD A:GLU175 4.8 6.3 1.0
C A:MET15 4.8 7.4 1.0
HG3 A:GLU23 4.8 12.4 1.0
HG2 A:GLU23 4.8 12.4 1.0
H A:MET15 4.8 8.7 1.0
C A:GLY17 4.8 9.3 1.0
CB A:LEU18 4.8 8.9 1.0
OE1 A:GLU175 4.9 9.6 1.0
CA A:ASP176 4.9 7.0 1.0
HA A:ASP16 4.9 10.1 1.0
HZ2 A:LYS149 4.9 9.7 1.0
HA2 A:GLY51 5.0 12.0 1.0

Reference:

S.Seo, M.Kim, S.Rhee. Structural and Functional Insights in the Substrate Specificity of the Pseudouridine Monophosphate Phosphatase HDHD1A. J.Biol.Chem. 10257 2025.
ISSN: ESSN 1083-351X
PubMed: 40409548
DOI: 10.1016/J.JBC.2025.110257
Page generated: Sat Aug 16 05:35:33 2025

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