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Magnesium in PDB 3tpy: Crystal Structure of M-Pmv Dutpase with A Mixed Population of Substrate (Dupnpp) and Post-Inversion Product (Dump) in the Active Sites

Enzymatic activity of Crystal Structure of M-Pmv Dutpase with A Mixed Population of Substrate (Dupnpp) and Post-Inversion Product (Dump) in the Active Sites

All present enzymatic activity of Crystal Structure of M-Pmv Dutpase with A Mixed Population of Substrate (Dupnpp) and Post-Inversion Product (Dump) in the Active Sites:
3.6.1.23;

Protein crystallography data

The structure of Crystal Structure of M-Pmv Dutpase with A Mixed Population of Substrate (Dupnpp) and Post-Inversion Product (Dump) in the Active Sites, PDB code: 3tpy was solved by O.Barabas, V.Nemeth, B.G.Vertessy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.75
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 60.559, 60.559, 63.635, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 18.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of M-Pmv Dutpase with A Mixed Population of Substrate (Dupnpp) and Post-Inversion Product (Dump) in the Active Sites (pdb code 3tpy). 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 M-Pmv Dutpase with A Mixed Population of Substrate (Dupnpp) and Post-Inversion Product (Dump) in the Active Sites, PDB code: 3tpy:

Magnesium binding site 1 out of 1 in 3tpy

Go back to Magnesium Binding Sites List in 3tpy
Magnesium binding site 1 out of 1 in the Crystal Structure of M-Pmv Dutpase with A Mixed Population of Substrate (Dupnpp) and Post-Inversion Product (Dump) in the Active Sites


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 M-Pmv Dutpase with A Mixed Population of Substrate (Dupnpp) and Post-Inversion Product (Dump) in the Active Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg999

b:28.1
occ:0.70
 O A:HOH245 1.9 32.4 1.0
O2G A:DUP777 2.1 29.2 0.7
O1A A:DUP777 2.1 24.1 0.7
O A:HOH223 2.2 33.8 1.0
O A:HOH225 2.2 33.4 1.0
O1B A:DUP777 2.3 33.2 0.7
OP1 A:UMP154 2.5 9.7 0.3
PG A:DUP777 3.1 33.9 0.7
O1G A:DUP777 3.3 39.1 0.7
PB A:DUP777 3.3 27.8 0.7
PA A:DUP777 3.4 19.6 0.7
O A:HOH213 3.6 39.2 1.0
O3B A:DUP777 3.6 37.2 0.7
P A:UMP154 3.7 11.4 0.3
N3A A:DUP777 3.8 26.7 0.7
OP2 A:UMP154 3.9 9.2 0.3
O A:HOH156 4.0 19.4 1.0
O2A A:DUP777 4.4 18.6 0.7
O3G A:DUP777 4.5 46.5 0.7
OP3 A:UMP154 4.5 12.9 0.3
O5' A:DUP777 4.6 23.4 0.7
O2B A:DUP777 4.7 23.2 0.7
C5' A:DUP777 4.8 21.2 0.7
O5' A:UMP154 4.9 15.1 0.3
OD2 A:ASP95 4.9 30.7 1.0

Reference:

O.Barabas, V.Nemeth, A.Bodor, A.Perczel, E.Rosta, Z.Kele, I.Zagyva, Z.Szabadka, V.I.Grolmusz, M.Wilmanns, B.G.Vertessy. Structural Snapshots of Enzyme-Catalysed Phosphate Ester Hydrolysis Directly Visualize in-Line Attack and Inversion To Be Published.
Page generated: Mon Aug 11 03:58:41 2025

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