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Magnesium in PDB 3ehw: Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site

Enzymatic activity of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site

All present enzymatic activity of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site:
3.6.1.23;

Protein crystallography data

The structure of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site, PDB code: 3ehw was solved by E.Takacs, O.Barabas, B.G.Vertessy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.446, 87.160, 70.608, 90.00, 90.09, 90.00
R / Rfree (%) 15.8 / 19.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site (pdb code 3ehw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site, PDB code: 3ehw:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3ehw

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Magnesium binding site 1 out of 8 in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg165

b:22.3
occ:1.00
 O C:HOH857 2.0 19.0 1.0
O1B C:DUP777 2.0 16.1 1.0
O1A C:DUP777 2.1 16.7 1.0
O A:HOH854 2.1 17.0 1.0
O3G C:DUP777 2.2 19.7 1.0
O A:HOH850 2.2 16.9 1.0
PB C:DUP777 3.2 20.5 1.0
PG C:DUP777 3.2 19.8 1.0
PA C:DUP777 3.4 21.1 1.0
O3B C:DUP777 3.4 20.6 1.0
N3A C:DUP777 3.6 20.0 1.0
O2G C:DUP777 3.9 22.3 1.0
NH2 C:ARG153 4.0 21.1 1.0
O X:HOH844 4.0 17.8 1.0
OD1 A:ASP49 4.1 19.0 1.0
NE A:ARG85 4.1 17.2 1.0
O A:HOH821 4.1 33.8 1.0
OG1 C:THR161 4.2 18.2 1.0
OD2 A:ASP49 4.3 20.9 1.0
NH2 A:ARG85 4.4 17.1 1.0
O5' C:DUP777 4.4 20.1 1.0
O2A C:DUP777 4.4 19.1 1.0
C5' C:DUP777 4.5 16.2 1.0
O1G C:DUP777 4.5 20.6 1.0
OE1 A:GLN131 4.5 21.0 1.0
O2B C:DUP777 4.5 18.1 1.0
CG A:ASP49 4.6 20.9 1.0
CZ A:ARG85 4.7 24.0 1.0
O B:HOH778 4.8 13.1 1.0
CA A:GLY41 4.9 24.4 1.0
CZ C:ARG153 4.9 24.9 1.0
CG2 C:THR161 5.0 19.9 1.0

Magnesium binding site 2 out of 8 in 3ehw

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Magnesium binding site 2 out of 8 in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg778

b:32.7
occ:1.00
 O B:HOH883 2.4 46.3 1.0
O B:HOH803 2.5 28.4 1.0
OD1 A:ASP95 2.5 32.0 1.0
OD1 C:ASP95 2.6 29.0 1.0
OD1 B:ASP95 2.6 26.2 1.0
O A:HOH852 2.6 42.9 1.0
O A:HOH839 2.8 31.8 1.0
CG A:ASP95 3.7 24.9 1.0
CG C:ASP95 3.7 23.1 1.0
CG B:ASP95 3.7 22.2 1.0
O B:HOH815 4.0 36.0 1.0
O C:HOH812 4.0 42.6 1.0
O A:HOH823 4.0 36.4 1.0
OD2 C:ASP95 4.2 23.6 1.0
OD2 A:ASP95 4.3 24.9 1.0
OD2 B:ASP95 4.3 25.6 1.0
CE2 B:PHE116 4.7 18.5 1.0
CB A:ASP95 4.8 22.6 1.0
CE2 A:PHE116 4.8 24.4 1.0
CB B:ASP95 4.9 18.6 1.0
CZ B:PHE116 4.9 22.8 1.0
CB C:ASP95 4.9 20.2 1.0
O C:VAL96 4.9 21.2 1.0
O A:VAL96 5.0 22.4 1.0

Magnesium binding site 3 out of 8 in 3ehw

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Magnesium binding site 3 out of 8 in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg165

b:21.3
occ:1.00
 O1A A:DUP777 2.0 17.2 1.0
O2G A:DUP777 2.0 25.5 1.0
O1B A:DUP777 2.1 20.5 1.0
O B:HOH856 2.1 18.0 1.0
O B:HOH796 2.2 21.8 1.0
O X:HOH888 2.2 20.6 1.0
PB A:DUP777 3.1 19.3 1.0
PG A:DUP777 3.1 19.4 1.0
PA A:DUP777 3.3 19.6 1.0
O3B A:DUP777 3.4 22.0 1.0
N3A A:DUP777 3.6 18.6 1.0
O1G A:DUP777 3.8 17.3 1.0
NH2 A:ARG153 3.8 20.2 1.0
O X:HOH810 4.1 21.0 1.0
O B:HOH795 4.1 23.1 1.0
OD1 B:ASP49 4.2 19.0 1.0
NE B:ARG85 4.2 18.6 1.0
C5' A:DUP777 4.3 18.1 1.0
O5' A:DUP777 4.3 19.8 1.0
OG1 A:THR161 4.3 19.1 1.0
O2A A:DUP777 4.3 20.8 1.0
O3G A:DUP777 4.4 17.2 1.0
NH1 B:ARG85 4.4 21.8 1.0
OE1 B:GLN131 4.4 20.8 1.0
O2B A:DUP777 4.5 19.8 1.0
OD2 B:ASP49 4.5 23.6 1.0
O X:HOH800 4.6 15.1 1.0
CZ B:ARG85 4.8 21.3 1.0
CZ A:ARG153 4.8 19.4 1.0
CG B:ASP49 4.8 20.8 1.0
NH1 A:ARG153 5.0 21.6 1.0

Magnesium binding site 4 out of 8 in 3ehw

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Magnesium binding site 4 out of 8 in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg778

b:19.1
occ:1.00
 O1A B:DUP777 2.0 19.6 1.0
O1B B:DUP777 2.0 19.0 1.0
O B:HOH849 2.0 17.1 1.0
O2G B:DUP777 2.1 19.9 1.0
O C:HOH855 2.1 20.8 1.0
O X:HOH874 2.1 15.6 1.0
PB B:DUP777 3.1 19.5 1.0
PG B:DUP777 3.1 20.2 1.0
PA B:DUP777 3.3 23.8 1.0
O3B B:DUP777 3.4 20.8 1.0
N3A B:DUP777 3.5 20.1 1.0
O1G B:DUP777 3.8 19.8 1.0
NH1 B:ARG153 3.9 23.8 1.0
O X:HOH782 4.1 16.9 1.0
O A:HOH780 4.2 19.2 1.0
NE C:ARG85 4.2 19.2 1.0
O5' B:DUP777 4.2 21.1 1.0
OD1 C:ASP49 4.2 21.1 1.0
C5' B:DUP777 4.3 18.5 1.0
O2A B:DUP777 4.3 24.4 1.0
OG1 B:THR161 4.3 21.7 1.0
OE1 C:GLN131 4.3 20.7 1.0
O3G B:DUP777 4.4 16.1 1.0
NH2 C:ARG85 4.4 17.7 1.0
O2B B:DUP777 4.5 18.7 1.0
OD2 C:ASP49 4.6 23.2 1.0
O A:HOH779 4.6 13.8 1.0
CZ C:ARG85 4.8 20.7 1.0
CG C:ASP49 4.8 20.2 1.0
CG2 B:THR161 4.9 22.0 1.0
CZ B:ARG153 4.9 22.0 1.0
CD C:GLN131 5.0 20.4 1.0

Magnesium binding site 5 out of 8 in 3ehw

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Magnesium binding site 5 out of 8 in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg165

b:21.2
occ:1.00
 O2A Z:DUP777 2.0 23.7 1.0
O X:HOH990 2.1 17.6 1.0
O2B Z:DUP777 2.1 24.2 1.0
O Z:HOH839 2.2 17.2 1.0
O3G Z:DUP777 2.2 22.8 1.0
O X:HOH828 2.2 21.6 1.0
PB Z:DUP777 3.1 22.9 1.0
PG Z:DUP777 3.1 24.4 1.0
O3B Z:DUP777 3.3 18.7 1.0
PA Z:DUP777 3.3 21.6 1.0
N3A Z:DUP777 3.6 24.6 1.0
O1G Z:DUP777 3.7 27.8 1.0
NH2 Z:ARG153 3.9 21.4 1.0
O X:HOH899 4.0 23.0 1.0
OD1 X:ASP49 4.1 19.4 1.0
OG1 Z:THR161 4.2 23.9 1.0
NH1 X:ARG85 4.2 19.5 1.0
NE X:ARG85 4.2 19.9 1.0
O1A Z:DUP777 4.3 25.8 1.0
O X:HOH933 4.3 29.8 1.0
O5' Z:DUP777 4.3 21.3 1.0
C5' Z:DUP777 4.4 20.8 1.0
OD2 X:ASP49 4.4 22.9 1.0
O2G Z:DUP777 4.4 21.0 1.0
O1B Z:DUP777 4.5 21.4 1.0
OE1 X:GLN131 4.5 24.1 1.0
CG X:ASP49 4.7 22.4 1.0
CZ X:ARG85 4.7 22.3 1.0
O Y:HOH778 4.8 14.8 1.0
CZ Z:ARG153 4.9 24.3 1.0
CA X:GLY41 5.0 24.3 1.0

Magnesium binding site 6 out of 8 in 3ehw

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Magnesium binding site 6 out of 8 in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Mg778

b:35.3
occ:1.00
 OD1 Y:ASP95 2.5 34.8 1.0
O X:HOH994 2.5 45.5 1.0
O Y:HOH824 2.5 41.1 1.0
OD1 X:ASP95 2.5 27.3 1.0
O X:HOH960 2.6 41.0 1.0
OD1 Z:ASP95 2.6 29.4 1.0
O X:HOH953 2.8 26.1 1.0
CG Y:ASP95 3.7 25.7 1.0
CG X:ASP95 3.7 24.1 1.0
CG Z:ASP95 3.8 24.0 1.0
O Y:HOH821 4.0 36.8 1.0
O Z:HOH843 4.2 43.2 1.0
OD2 Y:ASP95 4.3 23.6 1.0
OD2 X:ASP95 4.3 25.6 1.0
OD2 Z:ASP95 4.4 24.6 1.0
CB Y:ASP95 4.8 21.4 1.0
CE2 X:PHE116 4.8 22.6 1.0
CB X:ASP95 4.9 21.2 1.0
CE2 Y:PHE116 4.9 33.6 1.0
CB Z:ASP95 5.0 20.4 1.0
O Y:VAL96 5.0 21.7 1.0

Magnesium binding site 7 out of 8 in 3ehw

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Magnesium binding site 7 out of 8 in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Mg165

b:19.8
occ:1.00
 O1A X:DUP777 2.0 19.6 1.0
O1B X:DUP777 2.0 19.2 1.0
O Y:HOH852 2.1 18.3 1.0
O2G X:DUP777 2.1 19.0 1.0
O X:HOH920 2.2 19.8 1.0
O X:HOH993 2.2 19.2 1.0
PB X:DUP777 3.1 21.3 1.0
PG X:DUP777 3.2 23.4 1.0
PA X:DUP777 3.2 21.6 1.0
O3B X:DUP777 3.4 19.4 1.0
N3A X:DUP777 3.5 21.3 1.0
O1G X:DUP777 3.8 24.8 1.0
O X:HOH864 4.1 21.0 1.0
NH2 X:ARG153 4.1 22.8 1.0
O Y:HOH785 4.1 21.2 1.0
OD1 Y:ASP49 4.2 18.2 1.0
NE Y:ARG85 4.2 24.1 1.0
O2A X:DUP777 4.2 22.1 1.0
OG1 X:THR161 4.3 23.5 1.0
O5' X:DUP777 4.3 24.2 1.0
OE1 Y:GLN131 4.3 17.7 1.0
C5' X:DUP777 4.3 20.4 1.0
NH1 Y:ARG85 4.4 17.5 1.0
O3G X:DUP777 4.4 19.6 1.0
OD2 Y:ASP49 4.5 24.7 1.0
O2B X:DUP777 4.5 22.1 1.0
O Z:HOH778 4.7 15.2 1.0
CZ Y:ARG85 4.7 22.3 1.0
CG Y:ASP49 4.8 18.1 1.0
CD Y:GLN131 4.9 17.6 1.0
CG2 X:THR161 5.0 22.3 1.0

Magnesium binding site 8 out of 8 in 3ehw

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Magnesium binding site 8 out of 8 in the Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Mg165

b:20.2
occ:1.00
 O1A Y:DUP777 2.0 17.9 1.0
O1B Y:DUP777 2.0 18.1 1.0
O Y:HOH854 2.1 18.2 1.0
O Z:HOH779 2.1 14.9 1.0
O2G Y:DUP777 2.1 21.1 1.0
O Z:HOH836 2.2 17.6 1.0
PG Y:DUP777 3.2 20.8 1.0
PB Y:DUP777 3.2 19.4 1.0
PA Y:DUP777 3.3 21.2 1.0
O3B Y:DUP777 3.4 17.6 1.0
N3A Y:DUP777 3.6 18.5 1.0
O1G Y:DUP777 3.8 16.4 1.0
O X:HOH866 3.9 17.8 1.0
NH2 Y:ARG153 4.0 19.1 1.0
O Z:HOH784 4.0 23.4 1.0
OD1 Z:ASP49 4.1 22.4 1.0
NE Z:ARG85 4.2 21.1 1.0
OG1 Y:THR161 4.2 20.5 1.0
OE1 Z:GLN131 4.3 23.2 1.0
O5' Y:DUP777 4.3 21.0 1.0
C5' Y:DUP777 4.3 20.5 1.0
O2A Y:DUP777 4.4 24.9 1.0
NH2 Z:ARG85 4.4 17.2 1.0
OD2 Z:ASP49 4.4 20.4 1.0
O3G Y:DUP777 4.5 17.6 1.0
O2B Y:DUP777 4.5 18.9 1.0
O X:HOH796 4.7 12.9 1.0
CG Z:ASP49 4.7 21.5 1.0
CZ Z:ARG85 4.8 18.1 1.0
CD Z:GLN131 4.9 19.3 1.0
CG2 Y:THR161 4.9 18.7 1.0
CZ Y:ARG153 4.9 24.5 1.0

Reference:

E.Takacs, O.Barabas, B.G.Vertessy. Human Dutpase in Complex with Alpha,Beta-Imido-Dutp and MG2+: Visualization of the Full-Length C-Termini in All Monomers and Suggestion For An Additional Metal Ion Binding Site To Be Published.
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