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Magnesium in PDB 3v93: Unliganded Structure of TCRPDEC1 Catalytic Domain

Enzymatic activity of Unliganded Structure of TCRPDEC1 Catalytic Domain

All present enzymatic activity of Unliganded Structure of TCRPDEC1 Catalytic Domain:
3.1.4.17;

Protein crystallography data

The structure of Unliganded Structure of TCRPDEC1 Catalytic Domain, PDB code: 3v93 was solved by H.Wang, S.Kunz, G.Chen, T.Seebeck, Y.Wan, H.Robinson, S.Martinelli, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 130.342, 130.342, 388.853, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 22.6

Other elements in 3v93:

The structure of Unliganded Structure of TCRPDEC1 Catalytic Domain also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Unliganded Structure of TCRPDEC1 Catalytic Domain (pdb code 3v93). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Unliganded Structure of TCRPDEC1 Catalytic Domain, PDB code: 3v93:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3v93

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Magnesium binding site 1 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg702

b:18.7
occ:1.00
 OD1 A:ASP410 2.1 12.2 1.0
O A:HOH801 2.2 15.0 1.0
O A:HOH805 2.2 9.7 1.0
O A:HOH804 2.3 10.5 1.0
O A:HOH803 2.3 13.9 1.0
O A:HOH806 2.4 15.8 1.0
CG A:ASP410 3.1 12.0 1.0
OD2 A:ASP410 3.4 12.6 1.0
ZN A:ZN701 3.7 18.6 1.0
OE2 A:GLU439 4.0 17.2 1.0
CD2 A:HIS409 4.0 12.9 1.0
O A:HOH802 4.1 18.9 1.0
O A:HIS409 4.2 11.8 1.0
OG1 A:THR480 4.2 14.0 1.0
NE2 A:HIS442 4.2 13.9 1.0
CD2 A:HIS442 4.4 15.3 1.0
CD2 A:HIS413 4.4 13.0 1.0
O A:HOH966 4.4 33.9 1.0
CB A:ASP410 4.4 11.7 1.0
OD2 A:ASP521 4.4 16.5 1.0
NE2 A:HIS409 4.5 12.6 1.0
O A:HOH809 4.6 24.3 1.0
CB A:THR480 4.7 15.4 1.0
CA A:ASP410 4.7 13.6 1.0
O A:THR480 4.8 20.6 1.0
NE2 A:HIS413 4.8 15.0 1.0
CD2 A:HIS368 4.9 14.0 1.0
CD A:GLU439 4.9 16.2 1.0
C A:HIS409 4.9 12.8 1.0
CG A:GLU439 5.0 13.8 1.0

Magnesium binding site 2 out of 8 in 3v93

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Magnesium binding site 2 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg702

b:21.8
occ:1.00
 OD1 B:ASP410 2.1 16.9 1.0
O B:HOH801 2.2 17.3 1.0
O B:HOH803 2.3 13.3 1.0
O B:HOH804 2.3 14.2 1.0
O B:HOH805 2.3 12.9 1.0
O B:HOH806 2.4 17.1 1.0
CG B:ASP410 3.1 17.8 1.0
OD2 B:ASP410 3.5 18.1 1.0
ZN B:ZN701 3.7 21.4 1.0
CD2 B:HIS409 4.0 14.7 1.0
OE2 B:GLU439 4.0 21.8 1.0
O B:HOH802 4.1 16.9 1.0
NE2 B:HIS442 4.1 16.7 1.0
O B:HIS409 4.2 19.5 1.0
OG1 B:THR480 4.2 16.4 1.0
CD2 B:HIS442 4.3 15.8 1.0
CD2 B:HIS413 4.4 20.7 1.0
NE2 B:HIS409 4.4 13.1 1.0
CB B:ASP410 4.5 16.3 1.0
O B:HOH810 4.5 21.9 1.0
OD2 B:ASP521 4.5 23.6 1.0
CA B:ASP410 4.7 16.1 1.0
CB B:THR480 4.7 19.6 1.0
O B:THR480 4.8 19.5 1.0
CD B:GLU439 4.8 20.5 1.0
NE2 B:HIS413 4.9 21.3 1.0
CD2 B:HIS368 4.9 19.1 1.0
CG B:GLU439 4.9 18.8 1.0
C B:HIS409 5.0 16.1 1.0
O B:HOH808 5.0 19.6 1.0

Magnesium binding site 3 out of 8 in 3v93

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Magnesium binding site 3 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg702

b:15.4
occ:1.00
 OD1 C:ASP410 2.1 13.4 1.0
O C:HOH801 2.2 16.4 1.0
O C:HOH805 2.2 14.3 1.0
O C:HOH803 2.3 15.8 1.0
O C:HOH804 2.3 14.8 1.0
O C:HOH806 2.4 15.0 1.0
CG C:ASP410 3.1 13.9 1.0
OD2 C:ASP410 3.4 16.2 1.0
ZN C:ZN701 3.6 19.3 1.0
OE2 C:GLU439 4.0 17.1 1.0
CD2 C:HIS409 4.0 15.4 1.0
O C:HIS409 4.1 14.3 1.0
NE2 C:HIS442 4.1 12.8 1.0
O C:HOH802 4.2 19.2 1.0
OG1 C:THR480 4.3 15.9 1.0
CD2 C:HIS413 4.3 16.4 1.0
CD2 C:HIS442 4.3 10.7 1.0
OD2 C:ASP521 4.4 19.3 1.0
CB C:ASP410 4.4 14.8 1.0
NE2 C:HIS409 4.4 17.1 1.0
O C:HOH810 4.6 24.8 1.0
O C:HOH884 4.6 35.6 1.0
CA C:ASP410 4.7 14.4 1.0
O C:THR480 4.8 17.0 1.0
NE2 C:HIS413 4.8 15.6 1.0
CB C:THR480 4.8 17.7 1.0
O C:HOH808 4.8 20.1 1.0
CD C:GLU439 4.9 17.7 1.0
C C:HIS409 4.9 13.6 1.0
CD2 C:HIS368 4.9 16.6 1.0
OD1 C:ASP521 5.0 15.5 1.0

Magnesium binding site 4 out of 8 in 3v93

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Magnesium binding site 4 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg702

b:31.2
occ:1.00
 OD1 D:ASP410 2.1 24.6 1.0
O D:HOH803 2.3 23.6 1.0
O D:HOH801 2.3 25.4 1.0
O D:HOH806 2.3 23.6 1.0
O D:HOH804 2.3 23.4 1.0
O D:HOH805 2.4 22.8 1.0
CG D:ASP410 3.1 26.9 1.0
OD2 D:ASP410 3.5 28.8 1.0
ZN D:ZN701 3.8 34.5 1.0
OE2 D:GLU439 3.8 25.6 1.0
NE2 D:HIS442 4.0 28.9 1.0
CD2 D:HIS409 4.2 26.3 1.0
OG1 D:THR480 4.3 25.9 1.0
O D:HIS409 4.3 25.5 1.0
CD2 D:HIS442 4.3 27.3 1.0
O D:HOH808 4.4 35.0 1.0
CD2 D:HIS413 4.4 38.0 1.0
O D:HOH802 4.4 32.0 1.0
CB D:ASP410 4.5 27.8 1.0
NE2 D:HIS409 4.7 28.9 1.0
OD2 D:ASP521 4.7 30.5 1.0
CA D:ASP410 4.7 27.4 1.0
CD D:GLU439 4.8 24.0 1.0
CB D:THR480 4.8 28.0 1.0
O D:THR480 4.8 28.6 1.0
CD2 D:HIS368 4.9 34.5 1.0
NE2 D:HIS413 4.9 39.9 1.0
CG D:GLU439 5.0 23.8 1.0

Magnesium binding site 5 out of 8 in 3v93

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Magnesium binding site 5 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg702

b:26.2
occ:1.00
 OD1 E:ASP410 2.1 21.9 1.0
O E:HOH801 2.2 18.4 1.0
O E:HOH805 2.3 16.5 1.0
O E:HOH803 2.3 18.9 1.0
O E:HOH806 2.4 16.6 1.0
O E:HOH804 2.4 27.2 1.0
CG E:ASP410 3.0 20.2 1.0
OD2 E:ASP410 3.3 20.1 1.0
ZN E:ZN701 3.7 25.1 1.0
CD2 E:HIS409 4.0 14.7 1.0
OE2 E:GLU439 4.0 24.1 1.0
NE2 E:HIS442 4.1 18.0 1.0
O E:HIS409 4.1 16.8 1.0
O E:HOH802 4.2 22.1 1.0
OG1 E:THR480 4.2 21.8 1.0
CD2 E:HIS442 4.3 17.3 1.0
NE2 E:HIS409 4.4 17.1 1.0
CB E:ASP410 4.4 20.1 1.0
O E:HOH810 4.4 24.6 1.0
OD2 E:ASP521 4.4 20.7 1.0
CD2 E:HIS413 4.5 22.2 1.0
CA E:ASP410 4.7 18.9 1.0
O E:HOH808 4.7 30.8 1.0
CB E:THR480 4.8 20.2 1.0
CD2 E:HIS368 4.8 22.1 1.0
O E:THR480 4.8 23.7 1.0
NE2 E:HIS413 4.9 25.0 1.0
CD E:GLU439 4.9 22.5 1.0
C E:HIS409 4.9 17.5 1.0
CG E:GLU439 5.0 19.1 1.0

Magnesium binding site 6 out of 8 in 3v93

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Magnesium binding site 6 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg702

b:19.0
occ:1.00
 OD1 F:ASP410 2.1 15.1 1.0
O F:HOH801 2.1 20.5 1.0
O F:HOH805 2.2 12.4 1.0
O F:HOH804 2.2 13.3 1.0
O F:HOH806 2.3 10.2 1.0
O F:HOH803 2.3 12.2 1.0
CG F:ASP410 3.0 15.7 1.0
OD2 F:ASP410 3.3 16.3 1.0
ZN F:ZN701 3.6 20.2 1.0
CD2 F:HIS409 4.0 14.9 1.0
O F:HOH802 4.1 21.1 1.0
NE2 F:HIS442 4.1 13.8 1.0
O F:HIS409 4.2 14.4 1.0
OE2 F:GLU439 4.2 19.1 1.0
OG1 F:THR480 4.2 18.1 1.0
CD2 F:HIS442 4.3 11.7 1.0
CD2 F:HIS413 4.3 14.3 1.0
NE2 F:HIS409 4.4 15.8 1.0
CB F:ASP410 4.4 16.3 1.0
OD2 F:ASP521 4.4 15.5 1.0
O F:HOH810 4.4 20.6 1.0
CB F:THR480 4.7 17.4 1.0
CA F:ASP410 4.7 14.8 1.0
NE2 F:HIS413 4.8 15.0 1.0
O F:THR480 4.8 15.8 1.0
CD2 F:HIS368 4.8 15.1 1.0
C F:HIS409 4.9 14.7 1.0
OD1 F:ASP521 4.9 16.9 1.0
CD F:GLU439 4.9 20.4 1.0
CG F:GLU439 5.0 18.9 1.0

Magnesium binding site 7 out of 8 in 3v93

Go back to Magnesium Binding Sites List in 3v93
Magnesium binding site 7 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg702

b:18.4
occ:1.00
 OD1 G:ASP410 2.1 17.3 1.0
O G:HOH801 2.1 13.0 1.0
O G:HOH805 2.2 12.7 1.0
O G:HOH804 2.3 14.3 1.0
O G:HOH803 2.3 13.2 1.0
O G:HOH806 2.3 15.6 1.0
CG G:ASP410 3.1 17.0 1.0
OD2 G:ASP410 3.4 18.5 1.0
ZN G:ZN701 3.7 22.1 1.0
CD2 G:HIS409 4.0 17.5 1.0
O G:HOH802 4.0 19.1 1.0
OE2 G:GLU439 4.1 20.2 1.0
NE2 G:HIS442 4.1 14.7 1.0
O G:HIS409 4.2 15.2 1.0
OG1 G:THR480 4.2 16.0 1.0
CD2 G:HIS442 4.3 14.5 1.0
CD2 G:HIS413 4.4 16.8 1.0
NE2 G:HIS409 4.4 17.3 1.0
CB G:ASP410 4.4 16.7 1.0
OD2 G:ASP521 4.5 21.6 1.0
O G:HOH810 4.6 25.1 1.0
CB G:THR480 4.6 19.4 1.0
CA G:ASP410 4.7 17.5 1.0
O G:THR480 4.7 18.5 1.0
NE2 G:HIS413 4.8 18.5 1.0
CD G:GLU439 4.9 18.4 1.0
CG G:GLU439 4.9 16.6 1.0
O G:HOH808 4.9 19.8 1.0
C G:HIS409 4.9 16.0 1.0
CD2 G:HIS368 5.0 15.3 1.0

Magnesium binding site 8 out of 8 in 3v93

Go back to Magnesium Binding Sites List in 3v93
Magnesium binding site 8 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg702

b:25.8
occ:1.00
 OD1 H:ASP410 2.1 22.9 1.0
O H:HOH801 2.2 23.2 1.0
O H:HOH804 2.3 20.4 1.0
O H:HOH803 2.3 21.6 1.0
O H:HOH805 2.3 18.6 1.0
O H:HOH806 2.3 15.3 1.0
CG H:ASP410 3.1 18.0 1.0
OD2 H:ASP410 3.3 19.5 1.0
ZN H:ZN701 3.7 25.1 1.0
OE2 H:GLU439 3.9 21.1 1.0
CD2 H:HIS409 4.1 21.6 1.0
O H:HIS409 4.2 21.2 1.0
NE2 H:HIS442 4.2 21.8 1.0
OG1 H:THR480 4.3 16.9 1.0
CD2 H:HIS413 4.3 24.8 1.0
CD2 H:HIS442 4.4 18.2 1.0
O H:HOH809 4.4 27.3 1.0
CB H:ASP410 4.4 17.7 1.0
NE2 H:HIS409 4.4 22.2 1.0
OD2 H:ASP521 4.5 21.9 1.0
O H:HOH802 4.5 31.8 1.0
NE2 H:HIS413 4.8 26.2 1.0
CA H:ASP410 4.8 17.8 1.0
O H:THR480 4.8 19.7 1.0
CB H:THR480 4.8 19.5 1.0
CD H:GLU439 4.8 20.7 1.0
CD2 H:HIS368 4.9 18.6 1.0
C H:HIS409 5.0 20.1 1.0
CG H:GLU439 5.0 19.7 1.0

Reference:

H.Wang, S.Kunz, G.Chen, T.Seebeck, Y.Wan, H.Robinson, S.Martinelli, H.Ke. Biological and Structural Characterization of Trypanosoma Cruzi Phosphodiesterase C and Implications For Design of Parasite Selective Inhibitors. J.Biol.Chem. V. 287 11788 2012.
ISSN: ISSN 0021-9258
PubMed: 22356915
DOI: 10.1074/JBC.M111.326777
Page generated: Thu Aug 15 12:46:53 2024

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