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Magnesium in PDB 9m7l: Crystal Structure of Pseudouridine 5'-Monophosphate Phosphatase From Human (HHDHD1A) in the Unliganded State

Enzymatic activity of Crystal Structure of Pseudouridine 5'-Monophosphate Phosphatase From Human (HHDHD1A) in the Unliganded State

All present enzymatic activity of Crystal Structure of Pseudouridine 5'-Monophosphate Phosphatase From Human (HHDHD1A) in the Unliganded State:
3.1.3.96;

Protein crystallography data

The structure of Crystal Structure of Pseudouridine 5'-Monophosphate Phosphatase From Human (HHDHD1A) in the Unliganded State, PDB code: 9m7l 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) 28.38 / 1.36
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.56, 60.96, 68, 90, 90, 90
R / Rfree (%) 14.9 / 15.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Pseudouridine 5'-Monophosphate Phosphatase From Human (HHDHD1A) in the Unliganded State (pdb code 9m7l). 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 Pseudouridine 5'-Monophosphate Phosphatase From Human (HHDHD1A) in the Unliganded State, PDB code: 9m7l:

Magnesium binding site 1 out of 1 in 9m7l

Go back to Magnesium Binding Sites List in 9m7l
Magnesium binding site 1 out of 1 in the Crystal Structure of Pseudouridine 5'-Monophosphate Phosphatase From Human (HHDHD1A) in the Unliganded State


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 Pseudouridine 5'-Monophosphate Phosphatase From Human (HHDHD1A) in the Unliganded State within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:10.0
occ:1.00
 OD2 A:ASP14 2.0 12.6 1.0
O A:HOH427 2.1 11.5 1.0
OD1 A:ASP176 2.1 10.7 1.0
O A:ASP16 2.1 10.3 1.0
O A:HOH590 2.1 12.6 1.0
O A:HOH428 2.1 11.4 1.0
CG A:ASP14 3.0 11.1 1.0
CG A:ASP176 3.1 11.1 1.0
C A:ASP16 3.3 9.8 1.0
OD2 A:ASP176 3.4 12.8 1.0
OD1 A:ASP14 3.5 11.9 1.0
HB2 A:ASP16 3.5 11.2 1.0
HB2 A:ALA177 3.8 12.6 1.0
H A:ASP176 3.8 9.7 1.0
OE2 A:GLU175 3.9 10.3 1.0
HA3 A:GLY17 4.0 10.9 1.0
CA A:ASP16 4.0 10.3 1.0
H A:ASP16 4.1 10.2 1.0
N A:ASP16 4.1 9.6 1.0
HB2 A:LEU18 4.1 11.5 1.0
CB A:ASP16 4.2 10.7 1.0
HB3 A:ALA177 4.2 12.6 1.0
OE2 A:GLU23 4.3 16.0 1.0
CB A:ASP14 4.3 11.2 1.0
O A:HOH487 4.3 16.5 1.0
N A:GLY17 4.3 9.9 1.0
HB3 A:ASP14 4.3 11.7 1.0
HB3 A:MET50 4.4 11.9 1.0
O A:HOH432 4.4 13.8 1.0
CB A:ASP176 4.4 10.1 1.0
H A:LEU18 4.4 11.9 1.0
H A:ALA177 4.4 9.7 1.0
CB A:ALA177 4.4 12.2 1.0
HB3 A:ASP16 4.5 11.2 1.0
CA A:GLY17 4.5 10.2 1.0
HB3 A:ASP176 4.6 10.4 1.0
N A:ASP176 4.6 9.2 1.0
O A:HOH589 4.6 4.4 1.0
HB2 A:ASP14 4.7 11.7 1.0
N A:LEU18 4.7 11.4 1.0
N A:ALA177 4.7 9.2 1.0
CD A:GLU175 4.8 9.8 1.0
C A:GLY17 4.8 10.6 1.0
C A:MET15 4.8 9.2 1.0
HA2 A:GLY51 4.8 11.9 1.0
H A:GLY51 4.8 11.6 1.0
HZ2 A:LYS149 4.9 11.3 1.0
OE1 A:GLU175 4.9 11.4 1.0
HG2 A:GLU23 4.9 16.9 1.0
HB3 A:LEU18 4.9 11.5 1.0
H A:MET15 4.9 10.7 1.0
HG3 A:GLU23 4.9 16.9 1.0
CA A:ASP176 4.9 9.5 1.0
CB A:LEU18 4.9 10.8 1.0
HA A:ASP16 5.0 10.9 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 05:35:11 2025

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