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Zinc 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:

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 8 binding sites of Zinc where determined in the TCRPDEC1 Catalytic Domain in Complex with Inhibitor WYQ16, PDB code: 3v94:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3v94

Go back to Zinc Binding Sites List in 3v94
Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:20.1
occ:1.00
 OD2 A:ASP410 2.1 12.7 1.0
OD1 A:ASP521 2.1 19.1 1.0
NE2 A:HIS409 2.1 15.5 1.0
NE2 A:HIS372 2.1 15.7 1.0
O A:HOH801 2.3 4.1 1.0
OD2 A:ASP521 2.3 20.1 1.0
CG A:ASP521 2.5 15.9 1.0
O A:HOH802 2.9 10.2 1.0
CD2 A:HIS409 2.9 9.9 1.0
CD2 A:HIS372 3.1 14.6 1.0
CG A:ASP410 3.1 13.9 1.0
CE1 A:HIS372 3.1 13.2 1.0
CE1 A:HIS409 3.2 13.7 1.0
OD1 A:ASP410 3.6 12.5 1.0
MG A:MG703 3.9 15.1 1.0
O A:HOH803 4.0 7.5 1.0
CB A:ASP521 4.0 15.1 1.0
CG A:HIS409 4.2 13.4 1.0
CG A:HIS372 4.2 14.2 1.0
ND1 A:HIS372 4.2 15.6 1.0
ND1 A:HIS409 4.2 12.9 1.0
CD2 A:HIS368 4.3 20.3 1.0
CB A:ASP410 4.3 13.6 1.0
O A:HOH956 4.5 29.2 1.0
O A:HOH805 4.7 8.0 1.0
O A:ASP521 4.7 14.2 1.0
CG2 A:VAL376 4.7 11.2 1.0
NE2 A:HIS368 4.8 20.4 1.0
CA A:ASP521 4.8 14.1 1.0

Zinc binding site 2 out of 8 in 3v94

Go back to Zinc Binding Sites List in 3v94
Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:20.4
occ:1.00
 OD2 B:ASP410 2.1 16.4 1.0
OD1 B:ASP521 2.1 25.0 1.0
NE2 B:HIS409 2.1 13.1 1.0
NE2 B:HIS372 2.1 16.5 1.0
O B:HOH801 2.4 4.8 1.0
OD2 B:ASP521 2.5 28.6 1.0
CG B:ASP521 2.6 21.9 1.0
CD2 B:HIS409 2.9 9.1 1.0
O B:HOH802 3.0 12.6 1.0
CG B:ASP410 3.1 13.5 1.0
CD2 B:HIS372 3.1 16.6 1.0
CE1 B:HIS372 3.1 15.9 1.0
CE1 B:HIS409 3.2 11.6 1.0
OD1 B:ASP410 3.6 9.7 1.0
O B:HOH804 3.9 12.0 1.0
CB B:ASP521 4.0 22.1 1.0
MG B:MG703 4.1 15.4 1.0
CG B:HIS409 4.2 12.9 1.0
ND1 B:HIS372 4.2 16.4 1.0
ND1 B:HIS409 4.2 10.6 1.0
CG B:HIS372 4.3 18.8 1.0
CB B:ASP410 4.3 13.6 1.0
CD2 B:HIS368 4.4 17.7 1.0
O B:HOH912 4.6 26.3 1.0
CG2 B:VAL376 4.7 12.5 1.0
O B:ASP521 4.7 17.1 1.0
O B:HOH805 4.7 12.8 1.0
CA B:ASP521 4.8 19.6 1.0
NE2 B:HIS368 4.9 16.9 1.0

Zinc binding site 3 out of 8 in 3v94

Go back to Zinc Binding Sites List in 3v94
Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:23.6
occ:1.00
 OD2 C:ASP410 2.1 17.9 1.0
OD1 C:ASP521 2.1 27.9 1.0
NE2 C:HIS409 2.1 19.6 1.0
NE2 C:HIS372 2.1 21.4 1.0
O C:HOH801 2.2 14.7 1.0
OD2 C:ASP521 2.2 26.0 1.0
CG C:ASP521 2.5 25.9 1.0
O C:HOH802 2.8 28.6 1.0
CD2 C:HIS409 2.9 17.4 1.0
CE1 C:HIS372 3.0 17.5 1.0
CG C:ASP410 3.1 18.8 1.0
CD2 C:HIS372 3.2 20.0 1.0
CE1 C:HIS409 3.2 20.4 1.0
OD1 C:ASP410 3.6 12.5 1.0
O C:HOH804 3.8 8.7 1.0
CB C:ASP521 4.0 23.7 1.0
MG C:MG703 4.1 17.0 1.0
CG C:HIS409 4.1 18.3 1.0
ND1 C:HIS372 4.2 17.9 1.0
ND1 C:HIS409 4.2 18.1 1.0
CG C:HIS372 4.3 21.2 1.0
CB C:ASP410 4.3 19.3 1.0
CD2 C:HIS368 4.4 23.1 1.0
CG2 C:VAL376 4.6 21.2 1.0
O C:ASP521 4.7 25.8 1.0
NE2 C:HIS368 4.7 23.0 1.0
CA C:ASP521 4.7 22.6 1.0
O C:HOH840 4.9 34.5 1.0
O C:HOH805 4.9 18.3 1.0

Zinc binding site 4 out of 8 in 3v94

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Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:30.5
occ:1.00
 OD2 D:ASP410 2.1 27.9 1.0
OD1 D:ASP521 2.1 38.1 1.0
NE2 D:HIS409 2.1 20.9 1.0
NE2 D:HIS372 2.1 34.6 1.0
OD2 D:ASP521 2.3 36.5 1.0
CG D:ASP521 2.5 34.2 1.0
O D:HOH801 3.0 23.4 1.0
CD2 D:HIS409 3.0 21.9 1.0
CE1 D:HIS372 3.0 33.9 1.0
CG D:ASP410 3.1 24.6 1.0
MG D:MG703 3.2 33.1 1.0
CE1 D:HIS409 3.2 22.2 1.0
CD2 D:HIS372 3.2 33.5 1.0
OD1 D:ASP410 3.6 23.9 1.0
CB D:ASP521 4.0 31.2 1.0
O D:HOH805 4.1 17.9 1.0
ND1 D:HIS372 4.2 34.2 1.0
CG D:HIS409 4.2 22.0 1.0
ND1 D:HIS409 4.2 19.7 1.0
CD2 D:HIS368 4.3 27.0 1.0
CG D:HIS372 4.3 34.5 1.0
CB D:ASP410 4.4 25.7 1.0
CG2 D:VAL376 4.7 24.5 1.0
NE2 D:HIS368 4.7 28.3 1.0
O D:HOH804 4.7 35.6 1.0
O D:ASP521 4.7 29.1 1.0
CA D:ASP521 4.8 29.2 1.0

Zinc binding site 5 out of 8 in 3v94

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Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:43.9
occ:1.00
 OD2 E:ASP410 2.0 34.7 1.0
OD1 E:ASP521 2.1 43.1 1.0
NE2 E:HIS372 2.1 43.4 1.0
NE2 E:HIS409 2.1 36.3 1.0
CD2 E:HIS409 2.8 33.8 1.0
CG E:ASP521 3.0 39.6 1.0
O E:HOH801 3.0 31.5 1.0
CE1 E:HIS372 3.1 42.7 1.0
CD2 E:HIS372 3.1 41.9 1.0
MG E:MG703 3.1 39.9 1.0
CG E:ASP410 3.2 31.9 1.0
CE1 E:HIS409 3.3 35.1 1.0
OD2 E:ASP521 3.3 40.3 1.0
OD1 E:ASP410 3.8 31.4 1.0
CG E:HIS409 4.1 34.4 1.0
O E:HOH803 4.1 26.7 1.0
ND1 E:HIS372 4.2 42.9 1.0
CB E:ASP410 4.2 34.6 1.0
CG E:HIS372 4.2 41.4 1.0
ND1 E:HIS409 4.3 33.8 1.0
CB E:ASP521 4.4 40.5 1.0
CD2 E:HIS368 4.4 40.9 1.0
CG2 E:VAL376 4.5 35.2 1.0
O E:ASP521 4.7 39.7 1.0
CA E:ASP521 4.9 38.6 1.0

Zinc binding site 6 out of 8 in 3v94

Go back to Zinc Binding Sites List in 3v94
Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:20.1
occ:1.00
 OD2 F:ASP410 2.1 17.2 1.0
OD1 F:ASP521 2.1 21.2 1.0
NE2 F:HIS409 2.1 13.5 1.0
NE2 F:HIS372 2.1 15.7 1.0
OD2 F:ASP521 2.3 25.3 1.0
O F:HOH801 2.3 12.5 1.0
CG F:ASP521 2.5 19.6 1.0
O F:HOH802 2.8 9.5 1.0
CD2 F:HIS409 2.9 11.1 1.0
CE1 F:HIS372 3.1 13.1 1.0
CG F:ASP410 3.1 13.9 1.0
CD2 F:HIS372 3.1 13.9 1.0
CE1 F:HIS409 3.2 14.6 1.0
OD1 F:ASP410 3.6 9.5 1.0
O F:HOH806 4.0 7.0 1.0
CB F:ASP521 4.1 18.8 1.0
MG F:MG703 4.1 15.8 1.0
CG F:HIS409 4.1 11.5 1.0
ND1 F:HIS372 4.2 12.8 1.0
ND1 F:HIS409 4.2 9.4 1.0
CG F:HIS372 4.3 14.8 1.0
CD2 F:HIS368 4.3 21.7 1.0
CB F:ASP410 4.4 13.3 1.0
O F:HOH804 4.5 11.9 1.0
CG2 F:VAL376 4.7 12.0 1.0
O F:ASP521 4.7 17.1 1.0
NE2 F:HIS368 4.7 20.8 1.0
CA F:ASP521 4.8 16.5 1.0

Zinc binding site 7 out of 8 in 3v94

Go back to Zinc Binding Sites List in 3v94
Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:30.6
occ:1.00
 OD2 G:ASP410 2.1 26.4 1.0
OD1 G:ASP521 2.1 33.8 1.0
NE2 G:HIS409 2.1 23.3 1.0
NE2 G:HIS372 2.1 25.0 1.0
O G:HOH801 2.2 18.5 1.0
O G:HOH802 2.7 13.1 1.0
CG G:ASP521 2.7 29.1 1.0
OD2 G:ASP521 2.9 37.2 1.0
CD2 G:HIS409 3.0 17.3 1.0
CE1 G:HIS372 3.1 21.0 1.0
CD2 G:HIS372 3.1 21.2 1.0
CE1 G:HIS409 3.1 21.4 1.0
CG G:ASP410 3.2 23.8 1.0
O G:HOH806 3.7 14.8 1.0
OD1 G:ASP410 3.8 24.5 1.0
CB G:ASP521 4.1 25.0 1.0
MG G:MG703 4.1 27.8 1.0
ND1 G:HIS372 4.2 22.2 1.0
CG G:HIS409 4.2 20.6 1.0
ND1 G:HIS409 4.2 18.9 1.0
CG G:HIS372 4.2 22.6 1.0
CB G:ASP410 4.3 25.9 1.0
CD2 G:HIS368 4.5 24.6 1.0
O G:HOH807 4.6 46.4 1.0
CG2 G:VAL376 4.6 22.6 1.0
O G:ASP521 4.7 23.1 1.0
CA G:ASP521 4.8 24.4 1.0
O G:HOH805 4.8 25.8 1.0

Zinc binding site 8 out of 8 in 3v94

Go back to Zinc Binding Sites List in 3v94
Zinc 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 Zinc with other atoms in the Zn 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:Zn702

b:29.4
occ:1.00
 OD1 H:ASP521 2.1 29.8 1.0
OD2 H:ASP410 2.1 24.3 1.0
NE2 H:HIS372 2.1 30.5 1.0
NE2 H:HIS409 2.1 21.8 1.0
O H:HOH801 2.1 28.2 1.0
O H:HOH802 2.7 25.1 1.0
CD2 H:HIS409 2.9 22.5 1.0
CG H:ASP521 3.0 26.3 1.0
CD2 H:HIS372 3.0 27.4 1.0
CG H:ASP410 3.1 22.3 1.0
CE1 H:HIS372 3.1 29.4 1.0
CE1 H:HIS409 3.2 23.1 1.0
OD2 H:ASP521 3.3 27.4 1.0
OD1 H:ASP410 3.5 20.9 1.0
O H:HOH804 3.6 21.0 1.0
MG H:MG703 3.9 24.6 1.0
CG H:HIS409 4.1 21.5 1.0
CG H:HIS372 4.2 29.1 1.0
CD2 H:HIS368 4.2 28.8 1.0
ND1 H:HIS372 4.2 30.4 1.0
ND1 H:HIS409 4.2 19.9 1.0
CB H:ASP410 4.3 24.4 1.0
CB H:ASP521 4.3 24.4 1.0
CG2 H:VAL376 4.6 24.4 1.0
NE2 H:HIS368 4.6 30.5 1.0
O H:HOH866 4.7 40.9 1.0
O H:HOH820 4.7 23.6 1.0
O H:ASP521 4.8 24.7 1.0
CA H:ASP521 4.8 25.0 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: Sat Oct 26 17:37:04 2024

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