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Magnesium in PDB 3v94: TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16

Enzymatic activity of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16

All present enzymatic activity of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16:
3.1.4.17;

Protein crystallography data

The structure of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16, PDB code: 3v94 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 / 2.33
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 131.147, 131.147, 394.861, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.8

Other elements in 3v94:

The structure of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 also contains other interesting chemical elements:

Zinc (Zn) 8 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 (pdb code 3v94). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16, PDB code: 3v94:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 3v94

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Magnesium binding site 1 out of 8 in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg703

b:15.1
occ:1.00
 OD1 A:ASP410 2.1 12.5 1.0
O A:HOH801 2.2 4.1 1.0
O A:HOH804 2.3 7.3 1.0
O A:HOH803 2.3 7.5 1.0
O A:HOH805 2.3 8.0 1.0
O A:HOH806 2.4 7.2 1.0
CG A:ASP410 3.1 13.9 1.0
OD2 A:ASP410 3.5 12.7 1.0
OE2 A:GLU439 3.9 21.7 1.0
NE2 A:HIS442 3.9 14.0 1.0
ZN A:ZN702 3.9 20.1 1.0
O A:HOH809 4.0 17.2 1.0
CD2 A:HIS413 4.1 16.1 1.0
CD2 A:HIS442 4.3 10.5 1.0
O A:HIS409 4.3 14.2 1.0
CD2 A:HIS409 4.3 9.9 1.0
CB A:ASP410 4.5 13.6 1.0
OD1 A:ASP521 4.5 19.1 1.0
OG1 A:THR480 4.5 12.4 1.0
NE2 A:HIS413 4.5 17.1 1.0
O A:HOH802 4.5 10.2 1.0
O A:HOH956 4.6 29.2 1.0
NE2 A:HIS409 4.7 15.5 1.0
CA A:ASP410 4.8 15.9 1.0
CD2 A:HIS368 4.8 20.3 1.0
CD A:GLU439 4.9 20.2 1.0
O A:THR480 5.0 17.4 1.0
NE2 A:HIS368 5.0 20.4 1.0

Magnesium binding site 2 out of 8 in 3v94

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Magnesium binding site 2 out of 8 in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg703

b:15.4
occ:1.00
 OD1 B:ASP410 2.1 9.7 1.0
O B:HOH803 2.2 13.1 1.0
O B:HOH801 2.2 4.8 1.0
O B:HOH805 2.3 12.8 1.0
O B:HOH804 2.4 12.0 1.0
O B:HOH806 2.4 8.5 1.0
CG B:ASP410 3.2 13.5 1.0
OD2 B:ASP410 3.6 16.4 1.0
OE2 B:GLU439 3.7 16.8 1.0
NE2 B:HIS442 3.9 14.1 1.0
O B:HOH892 4.0 20.9 1.0
CD2 B:HIS413 4.1 18.9 1.0
ZN B:ZN702 4.1 20.4 1.0
CD2 B:HIS442 4.1 12.7 1.0
O B:HIS409 4.3 15.6 1.0
CD2 B:HIS409 4.4 9.1 1.0
OG1 B:THR480 4.4 13.1 1.0
O B:HOH912 4.4 26.3 1.0
NE2 B:HIS413 4.4 17.4 1.0
OD1 B:ASP521 4.5 25.0 1.0
CB B:ASP410 4.5 13.6 1.0
CD B:GLU439 4.6 15.6 1.0
O B:HOH802 4.7 12.6 1.0
CA B:ASP410 4.7 13.7 1.0
O B:THR480 4.8 16.9 1.0
CG B:GLU439 4.8 15.1 1.0
NE2 B:HIS409 4.8 13.1 1.0
CD2 B:HIS368 4.9 17.7 1.0

Magnesium binding site 3 out of 8 in 3v94

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Magnesium binding site 3 out of 8 in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg703

b:17.0
occ:1.00
 OD1 C:ASP410 2.1 12.5 1.0
O C:HOH801 2.2 14.7 1.0
O C:HOH803 2.2 19.5 1.0
O C:HOH806 2.3 17.6 1.0
O C:HOH805 2.3 18.3 1.0
O C:HOH804 2.4 8.7 1.0
CG C:ASP410 3.2 18.8 1.0
OD2 C:ASP410 3.7 17.9 1.0
OE2 C:GLU439 3.7 20.8 1.0
NE2 C:HIS442 3.8 18.5 1.0
CD2 C:HIS442 4.0 19.6 1.0
ZN C:ZN702 4.1 23.6 1.0
O C:HIS409 4.2 22.3 1.0
OG1 C:THR480 4.2 14.8 1.0
CD2 C:HIS413 4.3 20.0 1.0
O C:HOH808 4.3 21.4 1.0
OD1 C:ASP521 4.4 27.9 1.0
CD2 C:HIS409 4.4 17.4 1.0
CB C:ASP410 4.5 19.3 1.0
CD C:GLU439 4.6 21.4 1.0
O C:HOH802 4.6 28.6 1.0
CA C:ASP410 4.7 19.5 1.0
NE2 C:HIS413 4.7 21.7 1.0
CG C:GLU439 4.7 20.0 1.0
O C:THR480 4.8 21.8 1.0
CB C:THR480 4.8 18.8 1.0
NE2 C:HIS409 4.9 19.6 1.0
CE1 C:HIS442 4.9 19.3 1.0
C C:HIS409 5.0 20.4 1.0

Magnesium binding site 4 out of 8 in 3v94

Go back to Magnesium Binding Sites List in 3v94
Magnesium binding site 4 out of 8 in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg703

b:33.1
occ:1.00
 OD1 D:ASP410 2.1 23.9 1.0
O D:HOH802 2.4 13.9 1.0
O D:HOH804 2.4 35.6 1.0
O D:HOH805 2.4 17.9 1.0
O D:HOH803 2.5 17.0 1.0
CG D:ASP410 2.9 24.6 1.0
OD2 D:ASP410 3.1 27.9 1.0
ZN D:ZN702 3.2 30.5 1.0
OD1 D:ASP521 3.6 38.1 1.0
CD2 D:HIS409 3.6 21.9 1.0
NE2 D:HIS409 4.0 20.9 1.0
O D:HOH801 4.0 23.4 1.0
OG1 D:THR480 4.2 22.6 1.0
O D:HIS409 4.2 22.0 1.0
CB D:ASP410 4.3 25.7 1.0
OE2 D:GLU439 4.4 21.8 1.0
CD2 D:HIS413 4.6 28.9 1.0
O D:HOH807 4.7 35.6 1.0
NE2 D:HIS442 4.7 21.6 1.0
CG D:ASP521 4.7 34.2 1.0
CB D:THR480 4.7 24.8 1.0
CA D:ASP410 4.8 23.9 1.0
CD2 D:HIS442 4.8 20.8 1.0
CD2 D:HIS368 4.8 27.0 1.0
O D:THR480 4.8 27.7 1.0
CG D:HIS409 4.9 22.0 1.0
NE2 D:HIS368 4.9 28.3 1.0
C D:HIS409 4.9 21.4 1.0
NE2 D:HIS413 4.9 30.9 1.0

Magnesium binding site 5 out of 8 in 3v94

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Magnesium binding site 5 out of 8 in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg703

b:39.9
occ:1.00
 OD1 E:ASP410 2.1 31.4 1.0
O E:HOH804 2.5 47.5 1.0
O E:HOH805 2.5 26.1 1.0
O E:HOH803 2.5 26.7 1.0
O E:HOH802 2.6 28.8 1.0
OD2 E:ASP410 2.7 34.7 1.0
CG E:ASP410 2.7 31.9 1.0
ZN E:ZN702 3.1 43.9 1.0
CD2 E:HIS409 3.6 33.8 1.0
OG1 E:THR480 4.0 37.0 1.0
O E:HOH801 4.1 31.5 1.0
NE2 E:HIS409 4.1 36.3 1.0
O E:HIS409 4.1 33.5 1.0
CB E:ASP410 4.2 34.6 1.0
OD2 E:ASP521 4.2 40.3 1.0
OE2 E:GLU439 4.3 39.5 1.0
CB E:THR480 4.4 35.9 1.0
OD1 E:ASP521 4.4 43.1 1.0
O E:HOH809 4.5 28.6 1.0
NE2 E:HIS442 4.6 30.7 1.0
CG E:ASP521 4.7 39.6 1.0
CA E:ASP410 4.7 34.8 1.0
CD2 E:HIS442 4.7 31.8 1.0
O E:THR480 4.7 38.3 1.0
C E:HIS409 4.8 34.4 1.0
CD2 E:HIS413 4.8 38.2 1.0
CG E:HIS409 4.8 34.4 1.0
CD2 E:HIS368 4.9 40.9 1.0

Magnesium binding site 6 out of 8 in 3v94

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Magnesium binding site 6 out of 8 in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg703

b:15.8
occ:1.00
 OD1 F:ASP410 2.1 9.5 1.0
O F:HOH803 2.2 17.5 1.0
O F:HOH801 2.2 12.5 1.0
O F:HOH804 2.3 11.9 1.0
O F:HOH806 2.4 7.0 1.0
O F:HOH805 2.4 8.1 1.0
CG F:ASP410 3.2 13.9 1.0
OD2 F:ASP410 3.7 17.2 1.0
NE2 F:HIS442 3.7 21.3 1.0
OE2 F:GLU439 3.8 19.9 1.0
CD2 F:HIS442 4.0 18.6 1.0
CD2 F:HIS413 4.0 16.5 1.0
ZN F:ZN702 4.1 20.1 1.0
O F:HOH810 4.2 27.3 1.0
O F:HIS409 4.2 14.6 1.0
CD2 F:HIS409 4.4 11.1 1.0
NE2 F:HIS413 4.4 17.8 1.0
CB F:ASP410 4.5 13.3 1.0
OG1 F:THR480 4.6 11.7 1.0
OD1 F:ASP521 4.6 21.2 1.0
CD F:GLU439 4.7 17.6 1.0
CA F:ASP410 4.7 14.1 1.0
O F:HOH802 4.7 9.5 1.0
CD2 F:HIS368 4.8 21.7 1.0
CE1 F:HIS442 4.8 20.9 1.0
NE2 F:HIS409 4.8 13.5 1.0
O F:THR480 5.0 12.3 1.0
CG F:GLU439 5.0 19.5 1.0

Magnesium binding site 7 out of 8 in 3v94

Go back to Magnesium Binding Sites List in 3v94
Magnesium binding site 7 out of 8 in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg703

b:27.8
occ:1.00
 OD1 G:ASP410 2.1 24.5 1.0
O G:HOH803 2.2 17.7 1.0
O G:HOH801 2.2 18.5 1.0
O G:HOH805 2.3 25.8 1.0
O G:HOH804 2.3 11.8 1.0
O G:HOH806 2.4 14.8 1.0
CG G:ASP410 3.1 23.8 1.0
OE2 G:GLU439 3.4 19.1 1.0
OD2 G:ASP410 3.5 26.4 1.0
NE2 G:HIS442 3.9 26.6 1.0
CD2 G:HIS442 4.0 27.1 1.0
O G:HOH808 4.0 27.5 1.0
ZN G:ZN702 4.1 30.6 1.0
O G:HIS409 4.2 26.1 1.0
CD2 G:HIS409 4.2 17.3 1.0
CD2 G:HIS413 4.2 27.9 1.0
OG1 G:THR480 4.3 22.1 1.0
CD G:GLU439 4.4 22.0 1.0
CB G:ASP410 4.5 25.9 1.0
O G:HOH809 4.5 32.6 1.0
OD1 G:ASP521 4.5 33.8 1.0
O G:HOH802 4.6 13.1 1.0
NE2 G:HIS413 4.6 27.4 1.0
NE2 G:HIS409 4.7 23.3 1.0
O G:HOH807 4.7 46.4 1.0
O G:THR480 4.7 22.7 1.0
CA G:ASP410 4.8 25.2 1.0
CB G:THR480 4.8 23.2 1.0
CG G:GLU439 4.8 21.2 1.0

Magnesium binding site 8 out of 8 in 3v94

Go back to Magnesium Binding Sites List in 3v94
Magnesium binding site 8 out of 8 in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg703

b:24.6
occ:1.00
 OD1 H:ASP410 2.1 20.9 1.0
O H:HOH801 2.3 28.2 1.0
O H:HOH803 2.4 21.6 1.0
O H:HOH804 2.4 21.0 1.0
O H:HOH820 2.4 23.6 1.0
O H:HOH805 2.4 23.2 1.0
CG H:ASP410 3.2 22.3 1.0
OD2 H:ASP410 3.6 24.3 1.0
OE2 H:GLU439 3.7 21.1 1.0
NE2 H:HIS442 3.9 23.1 1.0
ZN H:ZN702 3.9 29.4 1.0
O H:HIS409 4.1 23.8 1.0
CD2 H:HIS442 4.1 20.5 1.0
CD2 H:HIS409 4.2 22.5 1.0
OG1 H:THR480 4.2 19.2 1.0
CD2 H:HIS413 4.4 25.3 1.0
CB H:ASP410 4.5 24.4 1.0
O H:HOH802 4.5 25.1 1.0
O H:HOH866 4.6 40.9 1.0
CD H:GLU439 4.6 22.3 1.0
OD2 H:ASP521 4.6 27.4 1.0
NE2 H:HIS409 4.7 21.8 1.0
CA H:ASP410 4.7 24.4 1.0
O H:THR480 4.7 26.4 1.0
NE2 H:HIS413 4.8 26.2 1.0
CG H:GLU439 4.9 20.1 1.0
C H:HIS409 4.9 23.5 1.0
CB H:THR480 5.0 23.0 1.0
CE1 H:HIS442 5.0 22.6 1.0

Reference:

H.Wang, S.Kunz, G.Chen, T.Seebeck, Y.Wan, H.Robinson, S.Martinelli, H.Ke. TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16 To Be Published.
Page generated: Thu Aug 15 12:46:57 2024

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