Magnesium in PDB 3tpw: Crystal Structure of M-Pmv Dutpase - Dupnpp Complex Revealing Distorted Ligand Geometry (Approach Intermediate)

Enzymatic activity of Crystal Structure of M-Pmv Dutpase - Dupnpp Complex Revealing Distorted Ligand Geometry (Approach Intermediate)

All present enzymatic activity of Crystal Structure of M-Pmv Dutpase - Dupnpp Complex Revealing Distorted Ligand Geometry (Approach Intermediate):
3.6.1.23;

Protein crystallography data

The structure of Crystal Structure of M-Pmv Dutpase - Dupnpp Complex Revealing Distorted Ligand Geometry (Approach Intermediate), PDB code: 3tpw 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 / 1.65
*Space group*	P 6₃
*Cell size a, b, c (Å), α, β, γ (°)*	60.619, 60.619, 63.731, 90.00, 90.00, 120.00
*R / R_free (%)*	16.7 / 19.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of M-Pmv Dutpase - Dupnpp Complex Revealing Distorted Ligand Geometry (Approach Intermediate) (pdb code 3tpw). 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 - Dupnpp Complex Revealing Distorted Ligand Geometry (Approach Intermediate), PDB code: 3tpw:

Magnesium binding site 1 out of 1 in 3tpw

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Magnesium Binding Sites List in 3tpw

Magnesium binding site 1 out of 1 in the Crystal Structure of M-Pmv Dutpase - Dupnpp Complex Revealing Distorted Ligand Geometry (Approach Intermediate)

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 - Dupnpp Complex Revealing Distorted Ligand Geometry (Approach Intermediate) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg153 b:28.4 occ:1.00	O2G	A:DUP777	2.0	34.7	1.0
	O	A:HOH250	2.0	25.1	1.0
	O1B	A:DUP777	2.0	31.0	1.0
	O1A	A:DUP777	2.1	24.6	1.0
	O	A:HOH265	2.2	29.2	1.0
	O	A:HOH258	2.2	28.2	1.0
	PG	A:DUP777	3.0	45.1	1.0
	PB	A:DUP777	3.1	31.1	1.0
	O1G	A:DUP777	3.4	41.8	1.0
	N3A	A:DUP777	3.4	25.4	1.0
	PA	A:DUP777	3.5	22.7	1.0
	O3B	A:DUP777	3.5	40.6	1.0
	O	A:HOH200	3.7	30.9	1.0
	O	A:HOH156	4.1	20.0	1.0
	O	A:HOH241	4.2	42.0	1.0
	O3G	A:DUP777	4.4	46.3	1.0
	O2A	A:DUP777	4.4	22.3	1.0
	O2B	A:DUP777	4.4	31.2	1.0
	O5'	A:DUP777	4.5	24.7	1.0
	C5'	A:DUP777	4.6	19.0	1.0
	OD2	A:ASP95	5.0	28.3	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 03:58:35 2025

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