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Zinc in PDB 3sl4: Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D, PDB code: 3sl4 was solved by S.F.Feil, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.62 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.375, 111.088, 161.215, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 22.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D (pdb code 3sl4). 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 Catalytic Domain of PDE4D2 with Compound 10D, PDB code: 3sl4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3sl4

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Zinc binding site 1 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D


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 Catalytic Domain of PDE4D2 with Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:22.0
occ:1.00
 OD2 A:ASP201 2.1 14.7 1.0
OD1 A:ASP318 2.2 21.1 1.0
O3 A:PO420 2.2 21.0 1.0
NE2 A:HIS164 2.2 18.3 1.0
NE2 A:HIS200 2.3 19.0 1.0
O A:HOH486 2.4 20.6 1.0
CG A:ASP318 3.1 25.6 1.0
CD2 A:HIS200 3.1 18.5 1.0
CG A:ASP201 3.1 17.4 1.0
CD2 A:HIS164 3.1 17.1 1.0
OD2 A:ASP318 3.2 27.4 1.0
CE1 A:HIS164 3.3 18.2 1.0
CE1 A:HIS200 3.4 19.1 1.0
P A:PO420 3.4 24.3 0.2
OD1 A:ASP201 3.6 17.4 1.0
O A:HOH485 3.7 29.6 1.0
O1 A:PO420 3.7 22.2 1.0
ZN A:ZN2 3.8 25.6 0.7
O2 A:PO420 3.9 29.0 0.9
CD2 A:HIS160 4.2 20.6 1.0
CB A:ASP201 4.3 17.2 1.0
CG A:HIS200 4.3 15.1 1.0
CG A:HIS164 4.3 18.9 1.0
ND1 A:HIS164 4.3 18.3 1.0
ND1 A:HIS200 4.4 17.5 1.0
CB A:ASP318 4.5 18.6 1.0
NE2 A:HIS160 4.6 20.6 1.0
CG2 A:VAL168 4.7 21.7 1.0
O4 A:PO420 4.7 32.8 1.0
O A:HOH490 4.8 15.9 1.0
CA A:ASP318 5.0 18.6 1.0

Zinc binding site 2 out of 8 in 3sl4

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Zinc binding site 2 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D


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 Catalytic Domain of PDE4D2 with Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:25.6
occ:0.70
 O A:HOH486 2.0 20.6 1.0
O A:HOH529 2.2 17.3 1.0
OD1 A:ASP201 2.2 17.4 1.0
O A:HOH490 2.2 15.9 1.0
O1 A:PO420 2.3 22.2 1.0
O A:HOH54 2.3 16.7 1.0
CG A:ASP201 3.1 17.4 1.0
P A:PO420 3.4 24.3 0.2
OD2 A:ASP201 3.4 14.7 1.0
O2 A:PO420 3.6 29.0 0.9
ZN A:ZN1 3.8 22.0 1.0
O3 A:PO420 3.8 21.0 1.0
O A:HOH452 4.1 24.6 1.0
NE2 A:HIS233 4.1 16.7 1.0
CD2 A:HIS200 4.2 18.5 1.0
OE2 A:GLU230 4.2 23.1 1.0
O A:HIS200 4.2 14.8 1.0
OG1 A:THR271 4.3 18.7 1.0
CD2 A:HIS233 4.3 15.1 1.0
OD2 A:ASP318 4.4 27.4 1.0
CB A:ASP201 4.5 17.2 1.0
O A:HOH517 4.5 33.2 1.0
CD2 A:HIS204 4.6 19.9 1.0
NE2 A:HIS200 4.6 19.0 1.0
O4 A:PO420 4.7 32.8 1.0
CD2 A:HIS160 4.7 20.6 1.0
CB A:THR271 4.8 16.6 1.0
NE2 A:HIS204 4.8 20.0 1.0
O A:THR271 4.8 21.4 1.0
CA A:ASP201 4.8 17.1 1.0
CG A:GLU230 4.9 15.9 1.0
NE2 A:HIS160 4.9 20.6 1.0
CD A:GLU230 5.0 22.2 1.0
C A:HIS200 5.0 16.5 1.0

Zinc binding site 3 out of 8 in 3sl4

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Zinc binding site 3 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D


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 Catalytic Domain of PDE4D2 with Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:25.9
occ:1.00
 NE2 B:HIS164 2.2 20.9 1.0
O B:HOH489 2.2 23.6 1.0
OD2 B:ASP201 2.2 20.7 1.0
NE2 B:HIS200 2.2 23.3 1.0
OD1 B:ASP318 2.3 20.9 1.0
O1 B:PO420 2.3 25.4 1.0
CE1 B:HIS164 3.1 22.3 1.0
CG B:ASP318 3.1 22.6 1.0
CG B:ASP201 3.1 22.5 1.0
CD2 B:HIS200 3.2 23.9 1.0
CD2 B:HIS164 3.2 21.9 1.0
CE1 B:HIS200 3.2 21.1 1.0
OD2 B:ASP318 3.3 25.0 1.0
P B:PO420 3.5 24.9 0.1
OD1 B:ASP201 3.6 23.4 1.0
O B:HOH510 3.8 28.8 1.0
O4 B:PO420 3.8 24.1 1.0
ZN B:ZN2 3.9 27.2 0.7
O2 B:PO420 4.0 31.2 1.0
ND1 B:HIS164 4.2 22.8 1.0
CD2 B:HIS160 4.3 22.8 1.0
CG B:HIS164 4.3 22.6 1.0
ND1 B:HIS200 4.3 21.0 1.0
CG B:HIS200 4.3 24.3 1.0
CB B:ASP201 4.3 21.0 1.0
CB B:ASP318 4.5 22.7 1.0
CG2 B:VAL168 4.7 22.5 1.0
NE2 B:HIS160 4.7 18.7 1.0
O3 B:PO420 4.8 26.4 0.8
O B:HOH47 4.9 24.1 1.0
CA B:ASP318 5.0 23.1 1.0

Zinc binding site 4 out of 8 in 3sl4

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Zinc binding site 4 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D


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 Catalytic Domain of PDE4D2 with Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:27.2
occ:0.66
 OD1 B:ASP201 2.1 23.4 1.0
O B:HOH484 2.2 21.9 1.0
O B:HOH47 2.2 24.1 1.0
O4 B:PO420 2.2 24.1 1.0
O B:HOH489 2.3 23.6 1.0
O B:HOH57 2.3 18.9 1.0
CG B:ASP201 3.2 22.5 1.0
P B:PO420 3.4 24.9 0.1
OD2 B:ASP201 3.5 20.7 1.0
O2 B:PO420 3.6 31.2 1.0
O1 B:PO420 3.8 25.4 1.0
ZN B:ZN1 3.9 25.9 1.0
O B:HOH451 4.1 20.7 1.0
OE2 B:GLU230 4.2 26.7 1.0
NE2 B:HIS233 4.2 21.4 1.0
O B:HIS200 4.2 22.2 1.0
CD2 B:HIS200 4.2 23.9 1.0
OG1 B:THR271 4.3 26.4 1.0
CD2 B:HIS233 4.4 23.1 1.0
OD2 B:ASP318 4.5 25.0 1.0
CB B:ASP201 4.5 21.0 1.0
CD2 B:HIS204 4.6 20.9 1.0
O B:THR271 4.6 27.6 1.0
O B:HOH487 4.6 35.9 1.0
NE2 B:HIS200 4.6 23.3 1.0
O3 B:PO420 4.6 26.4 0.8
CD2 B:HIS160 4.7 22.8 1.0
CB B:THR271 4.7 27.5 1.0
NE2 B:HIS204 4.8 20.7 1.0
NE2 B:HIS160 4.8 18.7 1.0
CA B:ASP201 4.8 22.3 1.0
CG B:GLU230 4.9 23.4 1.0
CD B:GLU230 4.9 25.1 1.0

Zinc binding site 5 out of 8 in 3sl4

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Zinc binding site 5 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D


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 Catalytic Domain of PDE4D2 with Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1

b:24.9
occ:1.00
 OD2 C:ASP201 2.2 22.7 1.0
NE2 C:HIS164 2.2 20.8 1.0
NE2 C:HIS200 2.3 21.1 1.0
OD1 C:ASP318 2.3 21.3 1.0
O3 C:PO417 2.3 22.5 1.0
O C:HOH487 2.3 21.9 1.0
CD2 C:HIS200 3.2 16.8 1.0
CG C:ASP201 3.2 21.9 1.0
CG C:ASP318 3.2 27.5 1.0
CD2 C:HIS164 3.2 20.1 1.0
CE1 C:HIS164 3.2 20.0 1.0
CE1 C:HIS200 3.3 17.3 1.0
OD2 C:ASP318 3.4 28.2 1.0
P C:PO417 3.5 25.2 0.1
OD1 C:ASP201 3.7 19.7 1.0
ZN C:ZN2 3.8 24.7 0.6
O C:HOH484 3.9 33.7 1.0
O4 C:PO417 3.9 22.9 1.0
O1 C:PO417 4.0 30.4 0.9
CD2 C:HIS160 4.1 22.8 1.0
CG C:HIS200 4.3 18.2 1.0
ND1 C:HIS164 4.3 19.6 1.0
CB C:ASP201 4.3 16.3 1.0
ND1 C:HIS200 4.3 20.7 1.0
CG C:HIS164 4.4 20.2 1.0
NE2 C:HIS160 4.5 22.3 1.0
CB C:ASP318 4.6 21.4 1.0
CG2 C:VAL168 4.7 19.6 1.0
O2 C:PO417 4.8 35.5 1.0
O C:HOH481 4.8 20.8 1.0

Zinc binding site 6 out of 8 in 3sl4

Go back to Zinc Binding Sites List in 3sl4
Zinc binding site 6 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D


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 Catalytic Domain of PDE4D2 with Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn2

b:24.7
occ:0.63
 OD1 C:ASP201 2.1 19.7 1.0
O C:HOH481 2.2 20.8 1.0
O C:HOH491 2.2 19.3 1.0
O C:HOH487 2.2 21.9 1.0
O C:HOH516 2.2 17.6 1.0
O4 C:PO417 2.3 22.9 1.0
CG C:ASP201 3.1 21.9 1.0
P C:PO417 3.4 25.2 0.1
OD2 C:ASP201 3.4 22.7 1.0
O1 C:PO417 3.6 30.4 0.9
O3 C:PO417 3.8 22.5 1.0
ZN C:ZN1 3.8 24.9 1.0
O C:HOH503 4.0 23.2 1.0
CD2 C:HIS200 4.1 16.8 1.0
O C:HIS200 4.2 19.7 1.0
OE2 C:GLU230 4.2 23.9 1.0
OG1 C:THR271 4.2 23.0 1.0
NE2 C:HIS233 4.3 18.1 1.0
CD2 C:HIS233 4.4 15.2 1.0
CB C:ASP201 4.5 16.3 1.0
CD2 C:HIS204 4.5 19.0 1.0
NE2 C:HIS200 4.5 21.1 1.0
OD2 C:ASP318 4.5 28.2 1.0
CD2 C:HIS160 4.6 22.8 1.0
O C:THR271 4.7 24.6 1.0
O2 C:PO417 4.7 35.5 1.0
NE2 C:HIS160 4.7 22.3 1.0
O C:HOH75 4.7 37.0 1.0
NE2 C:HIS204 4.7 16.5 1.0
CB C:THR271 4.7 23.6 1.0
CA C:ASP201 4.8 20.0 1.0
CG C:GLU230 4.9 22.5 1.0
CD C:GLU230 5.0 23.6 1.0
C C:HIS200 5.0 17.1 1.0

Zinc binding site 7 out of 8 in 3sl4

Go back to Zinc Binding Sites List in 3sl4
Zinc binding site 7 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D


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 Catalytic Domain of PDE4D2 with Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1

b:21.3
occ:1.00
 OD2 D:ASP201 2.2 16.6 1.0
NE2 D:HIS164 2.2 15.9 1.0
OD1 D:ASP318 2.2 16.1 1.0
NE2 D:HIS200 2.2 16.8 1.0
O D:HOH482 2.3 18.8 1.0
O3 D:PO424 2.4 25.4 1.0
CG D:ASP318 3.1 19.7 1.0
CD2 D:HIS200 3.1 13.2 1.0
CE1 D:HIS164 3.1 16.2 1.0
CG D:ASP201 3.1 18.1 1.0
CD2 D:HIS164 3.2 16.3 1.0
OD2 D:ASP318 3.2 23.9 1.0
CE1 D:HIS200 3.3 16.3 1.0
P D:PO424 3.6 22.5 0.1
OD1 D:ASP201 3.6 15.2 1.0
ZN D:ZN2 3.8 24.6 0.7
O2 D:PO424 3.8 22.7 1.0
O D:HOH483 3.8 28.5 1.0
O4 D:PO424 4.0 24.9 0.8
CD2 D:HIS160 4.2 24.1 1.0
CG D:HIS200 4.3 15.5 1.0
ND1 D:HIS164 4.3 16.3 1.0
CB D:ASP201 4.3 13.6 1.0
CG D:HIS164 4.3 18.8 1.0
ND1 D:HIS200 4.4 13.2 1.0
CB D:ASP318 4.5 16.7 1.0
NE2 D:HIS160 4.5 25.0 1.0
CG2 D:VAL168 4.7 17.1 1.0
O D:HOH546 4.8 17.2 1.0
O1 D:PO424 4.8 25.8 0.8
CA D:ASP318 5.0 16.5 1.0

Zinc binding site 8 out of 8 in 3sl4

Go back to Zinc Binding Sites List in 3sl4
Zinc binding site 8 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 10D


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 Catalytic Domain of PDE4D2 with Compound 10D within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn2

b:24.6
occ:0.71
 O D:HOH482 2.1 18.8 1.0
OD1 D:ASP201 2.1 15.2 1.0
O D:HOH546 2.1 17.2 1.0
O D:HOH557 2.2 16.1 1.0
O D:HOH76 2.3 18.7 1.0
O2 D:PO424 2.3 22.7 1.0
CG D:ASP201 3.1 18.1 1.0
P D:PO424 3.4 22.5 0.1
OD2 D:ASP201 3.4 16.6 1.0
O4 D:PO424 3.6 24.9 0.8
ZN D:ZN1 3.8 21.3 1.0
O3 D:PO424 3.8 25.4 1.0
O D:HOH518 4.0 23.2 1.0
NE2 D:HIS233 4.2 17.4 1.0
CD2 D:HIS200 4.2 13.2 1.0
OG1 D:THR271 4.2 18.5 1.0
O D:HIS200 4.2 15.4 1.0
OE2 D:GLU230 4.3 21.3 1.0
CD2 D:HIS233 4.4 14.5 1.0
OD2 D:ASP318 4.4 23.9 1.0
CB D:ASP201 4.5 13.6 1.0
CD2 D:HIS204 4.5 16.9 1.0
CD2 D:HIS160 4.6 24.1 1.0
NE2 D:HIS200 4.6 16.8 1.0
NE2 D:HIS160 4.6 25.0 1.0
O D:THR271 4.7 24.7 1.0
O D:HOH481 4.7 34.3 1.0
O1 D:PO424 4.7 25.8 0.8
CB D:THR271 4.8 20.8 1.0
NE2 D:HIS204 4.8 23.6 1.0
CA D:ASP201 4.8 13.6 1.0
CG D:GLU230 4.8 19.2 1.0
CD D:GLU230 5.0 21.2 1.0

Reference:

J.L.Nankervis, S.C.Feil, N.C.Hancock, Z.Zheng, H.L.Ng, C.J.Morton, J.K.Holien, P.W.Ho, M.M.Frazzetto, I.G.Jennings, D.T.Manallack, T.J.Martin, P.E.Thompson, M.W.Parker. Thiophene Inhibitors of PDE4: Crystal Structures Show A Second Binding Mode at the Catalytic Domain of PDE4D2. Bioorg.Med.Chem.Lett. V. 21 7089 2011.
ISSN: ISSN 0960-894X
PubMed: 22030030
DOI: 10.1016/J.BMCL.2011.09.109
Page generated: Sat Oct 26 15:53:50 2024

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