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Zinc in PDB 6akr: Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole

Enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole

All present enzymatic activity of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole, PDB code: 6akr was solved by S.Wang, Y.W.Huo, Y.Xie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.64 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.765, 111.429, 159.669, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 22

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole (pdb code 6akr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole, PDB code: 6akr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6akr

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Zinc binding site 1 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:20.3
occ:1.00
 OD2 A:ASP439 2.1 12.7 1.0
NE2 A:HIS438 2.1 14.0 1.0
NE2 A:HIS402 2.3 11.4 1.0
OD1 A:ASP556 2.3 16.0 1.0
O A:HOH860 2.5 17.9 1.0
CD2 A:HIS438 3.0 13.2 1.0
CG A:ASP439 3.1 12.9 1.0
CG A:ASP556 3.1 16.6 1.0
CE1 A:HIS438 3.2 12.8 1.0
CD2 A:HIS402 3.2 12.1 1.0
CE1 A:HIS402 3.2 10.7 1.0
OD2 A:ASP556 3.3 21.3 1.0
OD1 A:ASP439 3.6 14.4 1.0
ZN A:ZN702 3.7 57.5 1.0
CD2 A:HIS398 4.1 14.0 1.0
O A:HOH826 4.1 22.5 1.0
O A:HOH852 4.2 16.3 1.0
CG A:HIS438 4.2 11.1 1.0
ND1 A:HIS438 4.3 12.4 1.0
NE2 A:HIS398 4.3 17.5 1.0
CB A:ASP439 4.3 11.3 1.0
ND1 A:HIS402 4.4 10.2 1.0
CG A:HIS402 4.4 11.2 1.0
CB A:ASP556 4.5 17.1 1.0
CG2 A:VAL406 4.7 8.2 1.0
O A:HOH823 4.9 13.8 1.0

Zinc binding site 2 out of 8 in 6akr

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Zinc binding site 2 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:57.5
occ:1.00
 O A:HOH823 2.3 13.8 1.0
OD1 A:ASP439 2.3 14.4 1.0
O A:HOH826 2.5 22.5 1.0
O A:HOH830 2.5 17.1 1.0
O A:HOH880 2.5 18.1 1.0
CG A:ASP439 3.3 12.9 1.0
OD2 A:ASP439 3.5 12.7 1.0
ZN A:ZN701 3.7 20.3 1.0
CD2 A:HIS438 4.1 13.2 1.0
O A:HOH860 4.1 17.9 1.0
OG1 A:THR509 4.2 13.8 1.0
O A:HIS438 4.2 9.7 1.0
OE2 A:GLU468 4.2 20.2 1.0
O A:HOH910 4.3 21.8 1.0
OD2 A:ASP556 4.4 21.3 1.0
NE2 A:HIS471 4.5 12.1 1.0
NE2 A:HIS438 4.5 14.0 1.0
CD2 A:HIS471 4.5 10.8 1.0
O A:THR509 4.5 18.1 1.0
CB A:ASP439 4.7 11.3 1.0
NE2 A:HIS398 4.7 17.5 1.0
CD2 A:HIS398 4.7 14.0 1.0
CB A:THR509 4.7 15.7 1.0
CD2 A:HIS442 4.8 13.7 1.0
CG A:GLU468 4.9 17.1 1.0
CA A:ASP439 5.0 10.0 1.0
CD A:GLU468 5.0 20.5 1.0

Zinc binding site 3 out of 8 in 6akr

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Zinc binding site 3 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:22.8
occ:1.00
 OD2 B:ASP439 2.2 14.2 1.0
NE2 B:HIS402 2.2 16.9 1.0
NE2 B:HIS438 2.2 15.1 1.0
OD1 B:ASP556 2.3 16.6 1.0
O B:HOH880 2.4 20.5 1.0
CD2 B:HIS438 3.0 16.9 1.0
CG B:ASP556 3.1 19.0 1.0
CD2 B:HIS402 3.2 15.6 1.0
CE1 B:HIS402 3.2 14.1 1.0
CG B:ASP439 3.2 14.8 1.0
OD2 B:ASP556 3.3 20.5 1.0
CE1 B:HIS438 3.3 15.3 1.0
ZN B:ZN702 3.6 59.0 1.0
OD1 B:ASP439 3.7 15.9 1.0
O B:HOH864 4.0 24.4 1.0
O B:HOH870 4.0 22.3 1.0
CG B:HIS438 4.2 14.6 1.0
CD2 B:HIS398 4.2 16.0 1.0
ND1 B:HIS402 4.3 14.5 1.0
CG B:HIS402 4.3 16.6 1.0
ND1 B:HIS438 4.3 14.5 1.0
CB B:ASP439 4.4 14.6 1.0
CB B:ASP556 4.5 19.9 1.0
NE2 B:HIS398 4.6 13.6 1.0
CG2 B:VAL406 4.8 16.3 1.0
O B:HOH808 4.9 13.6 1.0

Zinc binding site 4 out of 8 in 6akr

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Zinc binding site 4 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:59.0
occ:1.00
 OD1 B:ASP439 2.4 15.9 1.0
O B:HOH870 2.4 22.3 1.0
O B:HOH827 2.4 16.8 1.0
O B:HOH808 2.5 13.6 1.0
O B:HOH836 2.6 14.3 1.0
CG B:ASP439 3.3 14.8 1.0
OD2 B:ASP439 3.5 14.2 1.0
O B:HOH880 3.5 20.5 1.0
ZN B:ZN701 3.6 22.8 1.0
OG1 B:THR509 4.1 16.5 1.0
OE2 B:GLU468 4.1 20.2 1.0
CD2 B:HIS438 4.2 16.9 1.0
O B:HOH841 4.2 18.4 1.0
O B:HIS438 4.4 13.5 1.0
OD2 B:ASP556 4.4 20.5 1.0
NE2 B:HIS471 4.5 11.8 1.0
NE2 B:HIS438 4.6 15.1 1.0
O B:THR509 4.6 22.7 1.0
CB B:THR509 4.6 19.1 1.0
CD2 B:HIS471 4.6 13.7 1.0
CB B:ASP439 4.7 14.6 1.0
CD2 B:HIS442 4.8 14.7 1.0
CD2 B:HIS398 4.8 16.0 1.0
NE2 B:HIS398 4.8 13.6 1.0
CD B:GLU468 5.0 17.5 1.0

Zinc binding site 5 out of 8 in 6akr

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Zinc binding site 5 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn701

b:25.4
occ:1.00
 NE2 C:HIS438 2.2 17.1 1.0
OD2 C:ASP439 2.2 17.2 1.0
O C:HOH860 2.3 15.4 1.0
NE2 C:HIS402 2.3 16.7 1.0
OD1 C:ASP556 2.4 19.6 1.0
CD2 C:HIS438 3.1 17.9 1.0
CG C:ASP556 3.2 20.6 1.0
CG C:ASP439 3.2 17.2 1.0
CD2 C:HIS402 3.3 16.7 1.0
OD2 C:ASP556 3.3 28.0 1.0
CE1 C:HIS438 3.3 17.2 1.0
CE1 C:HIS402 3.3 16.7 1.0
ZN C:ZN702 3.6 62.0 1.0
OD1 C:ASP439 3.6 16.8 1.0
O C:HOH836 4.1 19.4 1.0
CD2 C:HIS398 4.1 18.1 1.0
CG C:HIS438 4.3 17.7 1.0
ND1 C:HIS438 4.3 16.4 1.0
ND1 C:HIS402 4.4 20.1 1.0
CG C:HIS402 4.4 17.2 1.0
CB C:ASP439 4.4 16.5 1.0
NE2 C:HIS398 4.5 17.9 1.0
CB C:ASP556 4.6 22.3 1.0
CG2 C:VAL406 4.7 18.8 1.0
O C:HOH801 4.9 18.0 1.0

Zinc binding site 6 out of 8 in 6akr

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Zinc binding site 6 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn702

b:62.0
occ:1.00
 OD1 C:ASP439 2.3 16.8 1.0
O C:HOH801 2.4 18.0 1.0
O C:HOH836 2.5 19.4 1.0
O C:HOH814 2.5 19.0 1.0
O C:HOH840 2.8 19.6 1.0
CG C:ASP439 3.3 17.2 1.0
OD2 C:ASP439 3.5 17.2 1.0
ZN C:ZN701 3.6 25.4 1.0
O C:HOH860 3.7 15.4 1.0
CD2 C:HIS438 4.0 17.9 1.0
OG1 C:THR509 4.0 22.9 1.0
O C:HIS438 4.1 15.9 1.0
OE2 C:GLU468 4.2 20.1 1.0
OD2 C:ASP556 4.2 28.0 1.0
O C:HOH855 4.3 20.0 1.0
NE2 C:HIS438 4.4 17.1 1.0
O C:THR509 4.4 25.0 1.0
NE2 C:HIS471 4.5 14.3 1.0
CB C:THR509 4.6 23.3 1.0
CD2 C:HIS471 4.6 15.0 1.0
CB C:ASP439 4.6 16.5 1.0
CD2 C:HIS398 4.8 18.1 1.0
CD2 C:HIS442 4.9 13.5 1.0
NE2 C:HIS398 4.9 17.9 1.0
CG C:GLU468 4.9 19.6 1.0
C C:HIS438 5.0 17.6 1.0
CA C:ASP439 5.0 14.6 1.0

Zinc binding site 7 out of 8 in 6akr

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Zinc binding site 7 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn701

b:26.9
occ:1.00
 O D:HOH878 2.2 24.9 1.0
OD2 D:ASP439 2.3 18.9 1.0
NE2 D:HIS402 2.3 20.2 1.0
OD1 D:ASP556 2.3 24.0 1.0
NE2 D:HIS438 2.4 18.1 1.0
CD2 D:HIS438 3.1 18.3 1.0
CG D:ASP439 3.1 16.4 1.0
CE1 D:HIS402 3.3 20.3 1.0
CG D:ASP556 3.3 26.6 1.0
CD2 D:HIS402 3.3 18.2 1.0
CE1 D:HIS438 3.4 21.2 1.0
OD1 D:ASP439 3.5 15.9 1.0
ZN D:ZN702 3.5 70.3 1.0
OD2 D:ASP556 3.6 31.0 1.0
O D:HOH874 4.2 25.8 1.0
O D:HOH883 4.2 34.9 1.0
O D:HOH813 4.2 24.1 1.0
CD2 D:HIS398 4.3 19.2 1.0
CG D:HIS438 4.3 20.1 1.0
CB D:ASP439 4.3 19.6 1.0
ND1 D:HIS402 4.4 19.5 1.0
ND1 D:HIS438 4.4 20.2 1.0
CG D:HIS402 4.4 20.6 1.0
CB D:ASP556 4.6 24.8 1.0
NE2 D:HIS398 4.7 19.5 1.0
CG2 D:VAL406 4.8 23.8 1.0
O D:HOH819 4.8 22.3 1.0

Zinc binding site 8 out of 8 in 6akr

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Zinc binding site 8 out of 8 in the Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn702

b:70.3
occ:1.00
 O D:HOH874 2.2 25.8 1.0
OD1 D:ASP439 2.3 15.9 1.0
O D:HOH831 2.4 28.7 1.0
O D:HOH819 2.5 22.3 1.0
O D:HOH818 2.7 22.5 1.0
CG D:ASP439 3.2 16.4 1.0
OD2 D:ASP439 3.4 18.9 1.0
ZN D:ZN701 3.5 26.9 1.0
O D:HOH883 3.5 34.9 1.0
O D:HOH878 3.5 24.9 1.0
O D:HOH854 4.0 22.4 1.0
OE2 D:GLU468 4.2 26.0 1.0
CD2 D:HIS438 4.4 18.3 1.0
NE2 D:HIS471 4.4 19.1 1.0
O D:HIS438 4.4 20.9 1.0
CD2 D:HIS398 4.5 19.2 1.0
OG1 D:THR509 4.6 24.6 1.0
CD2 D:HIS442 4.6 18.1 1.0
NE2 D:HIS398 4.6 19.5 1.0
OD2 D:ASP556 4.6 31.0 1.0
CB D:ASP439 4.6 19.6 1.0
CD2 D:HIS471 4.7 20.2 1.0
NE2 D:HIS442 4.7 16.6 1.0
NE2 D:HIS438 4.7 18.1 1.0
O D:THR509 4.9 25.9 1.0

Reference:

S.Wang, Y.W.Huo, Y.Xie. Crystal Structure of the PDE4D Catalytic Domain in Complex with Osthole To Be Published.
Page generated: Mon Oct 28 17:32:40 2024

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