Atomistry » Zinc » PDB 3v3g-3vh4 » 3v93
Atomistry »
  Zinc »
    PDB 3v3g-3vh4 »
      3v93 »

Zinc 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:

Magnesium (Mg) 8 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 3v93

Go back to Zinc Binding Sites List in 3v93
Zinc binding site 1 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:18.6
occ:1.00
 OD2 A:ASP410 2.1 12.6 1.0
OD1 A:ASP521 2.1 12.6 1.0
O A:HOH801 2.1 15.0 1.0
NE2 A:HIS409 2.1 12.6 1.0
NE2 A:HIS372 2.1 14.7 1.0
O A:HOH802 2.4 18.9 1.0
CD2 A:HIS409 2.9 12.9 1.0
CG A:ASP521 3.0 16.6 1.0
CD2 A:HIS372 3.1 11.9 1.0
CG A:ASP410 3.1 12.0 1.0
CE1 A:HIS372 3.1 14.2 1.0
CE1 A:HIS409 3.2 11.4 1.0
OD2 A:ASP521 3.3 16.5 1.0
OD1 A:ASP410 3.6 12.2 1.0
MG A:MG702 3.7 18.7 1.0
O A:HOH804 4.0 10.5 1.0
CG A:HIS409 4.1 13.1 1.0
ND1 A:HIS372 4.2 13.4 1.0
CG A:HIS372 4.2 15.5 1.0
ND1 A:HIS409 4.2 12.0 1.0
CB A:ASP410 4.3 11.7 1.0
CD2 A:HIS368 4.3 14.0 1.0
CB A:ASP521 4.4 14.9 1.0
CG2 A:VAL376 4.7 10.5 1.0
NE2 A:HIS368 4.8 12.6 1.0
O A:HOH805 4.8 9.7 1.0
O A:ASP521 4.8 18.3 1.0
CA A:ASP521 4.9 15.8 1.0
CE2 A:TYR367 5.0 14.7 1.0

Zinc binding site 2 out of 8 in 3v93

Go back to Zinc Binding Sites List in 3v93
Zinc binding site 2 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:21.4
occ:1.00
 O B:HOH801 2.0 17.3 1.0
OD1 B:ASP521 2.1 21.4 1.0
OD2 B:ASP410 2.1 18.1 1.0
NE2 B:HIS409 2.1 13.1 1.0
NE2 B:HIS372 2.1 20.9 1.0
O B:HOH802 2.2 16.9 1.0
CD2 B:HIS409 3.0 14.7 1.0
CG B:ASP521 3.0 21.3 1.0
CG B:ASP410 3.0 17.8 1.0
CD2 B:HIS372 3.1 19.7 1.0
CE1 B:HIS372 3.1 19.8 1.0
CE1 B:HIS409 3.2 14.2 1.0
OD2 B:ASP521 3.3 23.6 1.0
OD1 B:ASP410 3.5 16.9 1.0
MG B:MG702 3.7 21.8 1.0
O B:HOH919 3.8 37.5 1.0
O B:HOH804 3.9 14.2 1.0
CG B:HIS409 4.2 14.9 1.0
ND1 B:HIS372 4.2 19.8 1.0
ND1 B:HIS409 4.2 12.1 1.0
CG B:HIS372 4.2 20.4 1.0
CB B:ASP410 4.3 16.3 1.0
O B:HOH808 4.3 19.6 1.0
CD2 B:HIS368 4.4 19.1 1.0
CB B:ASP521 4.4 20.0 1.0
CG2 B:VAL376 4.7 18.0 1.0
NE2 B:HIS368 4.8 19.9 1.0
O B:ASP521 4.9 20.7 1.0
CA B:ASP521 4.9 19.9 1.0
O B:HOH805 4.9 12.9 1.0

Zinc binding site 3 out of 8 in 3v93

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:19.3
occ:1.00
 OD2 C:ASP410 2.1 16.2 1.0
OD1 C:ASP521 2.1 15.5 1.0
O C:HOH801 2.1 16.4 1.0
NE2 C:HIS372 2.1 19.5 1.0
NE2 C:HIS409 2.1 17.1 1.0
O C:HOH802 2.4 19.2 1.0
CD2 C:HIS409 3.0 15.4 1.0
CG C:ASP521 3.0 22.3 1.0
CG C:ASP410 3.0 13.9 1.0
CE1 C:HIS372 3.1 18.6 1.0
CD2 C:HIS372 3.1 19.0 1.0
CE1 C:HIS409 3.2 18.1 1.0
OD2 C:ASP521 3.3 19.3 1.0
OD1 C:ASP410 3.5 13.4 1.0
MG C:MG702 3.6 15.4 1.0
O C:HOH926 3.9 38.8 1.0
O C:HOH804 3.9 14.8 1.0
CG C:HIS409 4.2 16.0 1.0
ND1 C:HIS372 4.2 17.2 1.0
ND1 C:HIS409 4.2 14.1 1.0
CB C:ASP410 4.2 14.8 1.0
CG C:HIS372 4.3 17.0 1.0
O C:HOH808 4.3 20.1 1.0
CD2 C:HIS368 4.4 16.6 1.0
CB C:ASP521 4.4 15.8 1.0
CG2 C:VAL376 4.7 15.2 1.0
O C:ASP521 4.7 20.3 1.0
NE2 C:HIS368 4.8 16.6 1.0
O C:HOH805 4.8 14.3 1.0
CA C:ASP521 4.9 20.2 1.0

Zinc binding site 4 out of 8 in 3v93

Go back to Zinc Binding Sites List in 3v93
Zinc binding site 4 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:34.5
occ:1.00
 OD1 D:ASP521 2.1 30.1 1.0
OD2 D:ASP410 2.1 28.8 1.0
NE2 D:HIS409 2.1 28.9 1.0
NE2 D:HIS372 2.1 35.4 1.0
O D:HOH801 2.1 25.4 1.0
CD2 D:HIS409 2.9 26.3 1.0
CG D:ASP521 3.0 31.3 1.0
CG D:ASP410 3.1 26.9 1.0
O D:HOH802 3.1 32.0 1.0
CE1 D:HIS372 3.1 32.6 1.0
CD2 D:HIS372 3.1 34.8 1.0
CE1 D:HIS409 3.2 28.6 1.0
OD2 D:ASP521 3.2 30.5 1.0
OD1 D:ASP410 3.6 24.6 1.0
MG D:MG702 3.8 31.2 1.0
O D:HOH804 4.0 23.4 1.0
CG D:HIS409 4.1 29.1 1.0
ND1 D:HIS372 4.2 35.4 1.0
ND1 D:HIS409 4.2 26.6 1.0
CG D:HIS372 4.2 35.0 1.0
CB D:ASP410 4.3 27.8 1.0
CB D:ASP521 4.4 31.9 1.0
CD2 D:HIS368 4.5 34.5 1.0
CG2 D:VAL376 4.7 31.5 1.0
O D:ASP521 4.7 33.1 1.0
O D:HOH805 4.8 22.8 1.0
CA D:ASP521 4.9 32.0 1.0

Zinc binding site 5 out of 8 in 3v93

Go back to Zinc Binding Sites List in 3v93
Zinc binding site 5 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn701

b:25.1
occ:1.00
 O E:HOH801 2.0 18.4 1.0
OD2 E:ASP410 2.1 20.1 1.0
OD1 E:ASP521 2.1 23.4 1.0
NE2 E:HIS409 2.1 17.1 1.0
NE2 E:HIS372 2.1 24.3 1.0
O E:HOH802 2.3 22.1 1.0
CG E:ASP521 3.0 22.1 1.0
CD2 E:HIS409 3.0 14.7 1.0
CE1 E:HIS372 3.1 22.7 1.0
CG E:ASP410 3.1 20.2 1.0
CD2 E:HIS372 3.1 23.9 1.0
CE1 E:HIS409 3.2 18.2 1.0
OD2 E:ASP521 3.2 20.7 1.0
OD1 E:ASP410 3.7 21.9 1.0
MG E:MG702 3.7 26.2 1.0
O E:HOH804 4.0 27.2 1.0
CG E:HIS409 4.2 15.4 1.0
ND1 E:HIS372 4.2 21.8 1.0
ND1 E:HIS409 4.2 16.2 1.0
CB E:ASP410 4.2 20.1 1.0
CG E:HIS372 4.3 22.7 1.0
O E:HOH808 4.3 30.8 1.0
CB E:ASP521 4.4 22.6 1.0
CD2 E:HIS368 4.4 22.1 1.0
CG2 E:VAL376 4.6 17.8 1.0
O E:ASP521 4.7 22.8 1.0
NE2 E:HIS368 4.8 23.9 1.0
CA E:ASP521 4.9 21.5 1.0
O E:HOH805 4.9 16.5 1.0

Zinc binding site 6 out of 8 in 3v93

Go back to Zinc Binding Sites List in 3v93
Zinc binding site 6 out of 8 in the Unliganded Structure of TCRPDEC1 Catalytic Domain


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn701

b:20.2
occ:1.00
 OD1 F:ASP521 2.1 16.9 1.0
OD2 F:ASP410 2.1 16.3 1.0
O F:HOH801 2.1 20.5 1.0
NE2 F:HIS409 2.1 15.8 1.0
NE2 F:HIS372 2.1 13.6 1.0
O F:HOH802 2.4 21.1 1.0
CD2 F:HIS409 2.9 14.9 1.0
CG F:ASP521 3.0 16.8 1.0
CD2 F:HIS372 3.1 14.3 1.0
CG F:ASP410 3.1 15.7 1.0
CE1 F:HIS372 3.1 13.6 1.0
CE1 F:HIS409 3.2 15.9 1.0
OD2 F:ASP521 3.3 15.5 1.0
OD1 F:ASP410 3.6 15.1 1.0
MG F:MG702 3.6 19.0 1.0
O F:HOH804 3.8 13.3 1.0
CG F:HIS409 4.2 15.2 1.0
ND1 F:HIS372 4.2 13.7 1.0
CG F:HIS372 4.2 16.5 1.0
CB F:ASP410 4.2 16.3 1.0
ND1 F:HIS409 4.2 12.2 1.0
CD2 F:HIS368 4.4 15.1 1.0
CB F:ASP521 4.4 14.5 1.0
CG2 F:VAL376 4.7 9.8 1.0
O F:ASP521 4.8 20.5 1.0
NE2 F:HIS368 4.8 17.4 1.0
O F:HOH805 4.8 12.4 1.0
CA F:ASP521 4.9 17.6 1.0
CE2 F:TYR367 5.0 18.6 1.0

Zinc binding site 7 out of 8 in 3v93

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn701

b:22.1
occ:1.00
 O G:HOH801 2.0 13.0 1.0
OD2 G:ASP410 2.1 18.5 1.0
OD1 G:ASP521 2.1 20.4 1.0
NE2 G:HIS409 2.1 17.3 1.0
NE2 G:HIS372 2.1 15.9 1.0
O G:HOH802 2.3 19.1 1.0
CD2 G:HIS409 3.0 17.5 1.0
CG G:ASP521 3.0 21.3 1.0
CD2 G:HIS372 3.0 17.0 1.0
CG G:ASP410 3.1 17.0 1.0
CE1 G:HIS372 3.2 16.6 1.0
CE1 G:HIS409 3.2 16.2 1.0
OD2 G:ASP521 3.3 21.6 1.0
OD1 G:ASP410 3.6 17.3 1.0
MG G:MG702 3.7 18.4 1.0
O G:HOH804 3.9 14.3 1.0
CG G:HIS409 4.2 15.7 1.0
CG G:HIS372 4.2 17.8 1.0
ND1 G:HIS409 4.2 14.7 1.0
CB G:ASP410 4.2 16.7 1.0
ND1 G:HIS372 4.2 15.7 1.0
O G:HOH808 4.4 19.8 1.0
CB G:ASP521 4.4 18.9 1.0
CD2 G:HIS368 4.4 15.3 1.0
CG2 G:VAL376 4.7 14.5 1.0
O G:ASP521 4.8 17.0 1.0
O G:HOH805 4.9 12.7 1.0
CA G:ASP521 4.9 17.0 1.0
NE2 G:HIS368 4.9 16.6 1.0

Zinc binding site 8 out of 8 in 3v93

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


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Unliganded Structure of TCRPDEC1 Catalytic Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn701

b:25.1
occ:1.00
 OD2 H:ASP410 2.1 19.5 1.0
OD1 H:ASP521 2.1 20.2 1.0
NE2 H:HIS409 2.1 22.2 1.0
NE2 H:HIS372 2.1 23.0 1.0
O H:HOH801 2.2 23.2 1.0
CD2 H:HIS409 3.0 21.6 1.0
CG H:ASP521 3.0 22.6 1.0
CE1 H:HIS372 3.1 22.1 1.0
CG H:ASP410 3.1 18.0 1.0
O H:HOH802 3.1 31.8 1.0
CD2 H:HIS372 3.1 21.6 1.0
CE1 H:HIS409 3.2 24.5 1.0
OD2 H:ASP521 3.3 21.9 1.0
OD1 H:ASP410 3.6 22.9 1.0
MG H:MG702 3.7 25.8 1.0
O H:HOH804 4.0 20.4 1.0
CG H:HIS409 4.2 23.1 1.0
ND1 H:HIS372 4.2 21.9 1.0
ND1 H:HIS409 4.2 20.7 1.0
CB H:ASP410 4.3 17.7 1.0
CG H:HIS372 4.3 22.0 1.0
CD2 H:HIS368 4.4 18.6 1.0
CB H:ASP521 4.4 22.7 1.0
CG2 H:VAL376 4.7 20.4 1.0
O H:ASP521 4.7 23.4 1.0
NE2 H:HIS368 4.8 19.4 1.0
O H:HOH805 4.8 18.6 1.0
CA H:ASP521 4.9 22.8 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: Wed Aug 20 15:02:03 2025

Last articles

Zn in 4LY1
Zn in 4LY5
Zn in 4LXZ
Zn in 4LXC
Zn in 4LXL
Zn in 4LX9
Zn in 4LV7
Zn in 4LV4
Zn in 4LP6
Zn in 4LUX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy