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Magnesium in PDB 2hqu: Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion

Enzymatic activity of Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion

All present enzymatic activity of Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion:
3.6.1.23;

Protein crystallography data

The structure of Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion, PDB code: 2hqu was solved by O.Barabas, B.Varga, B.G.Vertessy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.409, 71.773, 76.475, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25.1

Other elements in 2hqu:

The structure of Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion (pdb code 2hqu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion, PDB code: 2hqu:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 2hqu

Go back to Magnesium Binding Sites List in 2hqu
Magnesium binding site 1 out of 4 in the Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


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-Iminodutp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg997

b:23.3
occ:1.00
 O A:HOH1042 2.1 15.5 1.0
O2G A:DUP777 2.1 19.4 1.0
O1A A:DUP777 2.1 19.9 1.0
O1B A:DUP777 2.2 17.5 1.0
O A:HOH1012 2.3 20.0 1.0
PG A:DUP777 3.2 17.7 1.0
PB A:DUP777 3.3 17.8 1.0
O1G A:DUP777 3.5 16.9 1.0
PA A:DUP777 3.5 16.6 1.0
O3B A:DUP777 3.6 17.4 1.0
N3A A:DUP777 3.8 17.4 1.0
OD1 A:ASP49 4.1 21.1 1.0
NE A:ARG85 4.2 15.8 1.0
O A:HOH1005 4.3 12.2 1.0
NH1 A:ARG85 4.3 14.9 1.0
OD2 A:ASP49 4.3 22.1 1.0
O A:HOH1046 4.4 12.7 1.0
OE1 A:GLN131 4.4 17.2 1.0
O3G A:DUP777 4.4 19.0 1.0
C5' A:DUP777 4.5 15.5 1.0
O5' A:DUP777 4.5 16.8 1.0
O2A A:DUP777 4.5 17.1 1.0
CG A:ASP49 4.6 20.9 1.0
O2B A:DUP777 4.7 17.5 1.0
CZ A:ARG85 4.7 15.4 1.0

Magnesium binding site 2 out of 4 in 2hqu

Go back to Magnesium Binding Sites List in 2hqu
Magnesium binding site 2 out of 4 in the Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


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-Iminodutp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg998

b:49.5
occ:1.00
 O C:HOH1031 2.1 41.5 1.0
O A:HOH1009 2.6 33.2 1.0
OD1 A:ASP95 3.4 27.4 1.0
OD1 C:ASP95 3.5 25.2 1.0
O B:HOH1051 3.7 44.9 1.0
OD1 B:ASP95 3.9 26.9 1.0
OD2 C:ASP95 4.0 21.8 1.0
O A:HOH1036 4.0 30.9 1.0
O A:VAL96 4.1 20.9 1.0
CG C:ASP95 4.2 22.4 1.0
CG A:ASP95 4.3 25.8 1.0
OD2 A:ASP95 4.4 27.8 1.0
O C:VAL96 4.5 22.0 1.0
O B:HOH1050 4.6 30.4 1.0
O C:HOH1038 4.6 31.6 1.0
CG B:ASP95 4.8 23.0 1.0
O B:VAL96 4.8 21.2 1.0
OD2 B:ASP95 4.9 26.2 1.0

Magnesium binding site 3 out of 4 in 2hqu

Go back to Magnesium Binding Sites List in 2hqu
Magnesium binding site 3 out of 4 in the Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


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-Iminodutp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg999

b:11.7
occ:1.00
 O C:HOH1029 1.8 11.5 1.0
O B:HOH1030 2.0 12.4 1.0
O2G C:DUP777 2.0 14.3 1.0
O B:HOH1019 2.1 12.1 1.0
O1B C:DUP777 2.1 12.0 1.0
O1A C:DUP777 2.3 13.8 1.0
PG C:DUP777 3.1 13.7 1.0
PB C:DUP777 3.2 12.7 1.0
O3B C:DUP777 3.4 14.0 1.0
O B:HOH1022 3.5 11.2 1.0
PA C:DUP777 3.5 13.1 1.0
O1G C:DUP777 3.7 11.6 1.0
N3A C:DUP777 3.8 12.5 1.0
NE B:ARG85 4.0 15.4 1.0
NH2 A:ARG153 4.1 18.6 1.0
OG1 A:THR161 4.1 20.8 1.0
OD1 B:ASP49 4.2 15.5 1.0
NH1 B:ARG85 4.3 12.6 1.0
OD2 B:ASP49 4.4 18.6 1.0
O3G C:DUP777 4.4 14.5 1.0
C5' C:DUP777 4.5 11.4 1.0
O C:HOH1009 4.5 15.5 1.0
OE1 B:GLN131 4.5 20.2 1.0
O5' C:DUP777 4.5 13.1 1.0
O2B C:DUP777 4.6 13.2 1.0
O2A C:DUP777 4.6 9.4 1.0
CZ B:ARG85 4.6 15.1 1.0
CG B:ASP49 4.7 17.0 1.0
CG2 A:THR161 4.8 25.4 1.0
O C:HOH1002 4.8 22.4 1.0
CG B:ARG85 4.9 17.2 1.0
CA B:GLY41 4.9 24.0 1.0
CD B:ARG85 4.9 15.1 1.0
NE2 B:GLN131 5.0 12.0 1.0
CD B:GLN131 5.0 18.2 1.0

Magnesium binding site 4 out of 4 in 2hqu

Go back to Magnesium Binding Sites List in 2hqu
Magnesium binding site 4 out of 4 in the Human Dutpase in Complex with Alpha,Beta-Iminodutp and Magnesium Ion


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-Iminodutp and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg998

b:18.1
occ:1.00
 O C:HOH1022 2.1 12.7 1.0
O C:HOH1021 2.1 16.2 1.0
O1A B:DUP777 2.1 15.1 1.0
O1B B:DUP777 2.2 15.1 1.0
O2G B:DUP777 2.3 19.2 1.0
PB B:DUP777 3.5 16.6 1.0
PG B:DUP777 3.5 19.5 1.0
PA B:DUP777 3.5 14.3 1.0
NH2 B:ARG153 3.7 31.8 1.0
O A:HOH1013 3.8 16.1 1.0
O3B B:DUP777 3.8 17.2 1.0
O1G B:DUP777 4.0 16.8 1.0
N3A B:DUP777 4.0 13.6 1.0
OD1 C:ASP49 4.1 13.5 1.0
O C:HOH1032 4.1 30.8 1.0
NH2 C:ARG85 4.2 19.2 1.0
OE1 C:GLN131 4.3 21.2 1.0
O5' B:DUP777 4.4 14.2 1.0
CD C:ARG85 4.4 22.4 1.0
O2A B:DUP777 4.4 13.3 1.0
C5' B:DUP777 4.5 13.2 1.0
OG1 B:THR161 4.6 29.7 1.0
OD2 C:ASP49 4.6 16.9 1.0
CZ B:ARG153 4.7 30.6 1.0
O A:HOH999 4.7 15.8 1.0
O3G B:DUP777 4.7 20.3 1.0
O2B B:DUP777 4.8 14.1 1.0
CG C:ASP49 4.8 19.5 1.0
CD C:GLN131 4.9 16.9 1.0
NH1 B:ARG153 4.9 32.7 1.0

Reference:

B.Varga, O.Barabas, J.Kovari, J.Toth, E.Hunyadi-Gulyas, E.Klement, K.F.Medzihradszky, F.Tolgyesi, J.Fidy, B.G.Vertessy. Active Site Closure Facilitates Juxtaposition of Reactant Atoms For Initiation of Catalysis By Human Dutpase. Febs Lett. V. 581 4783 2007.
ISSN: ISSN 0014-5793
PubMed: 17880943
DOI: 10.1016/J.FEBSLET.2007.09.005
Page generated: Mon Dec 14 07:26:19 2020

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