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Zinc in PDB 4ogb: Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2, PDB code: 4ogb was solved by S.C.Feil, M.W.Parker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.22 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.838, 111.550, 160.072, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.3

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 4ogb

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Zinc binding site 1 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn509

b:29.0
occ:1.00
 OD2 A:ASP201 2.0 19.9 1.0
NE2 A:HIS164 2.2 20.4 1.0
NE2 A:HIS200 2.3 22.6 1.0
O A:HOH668 2.3 28.3 1.0
O A:HOH707 2.4 32.1 1.0
OD1 A:ASP318 2.4 25.7 1.0
CD2 A:HIS200 3.0 20.6 1.0
CD2 A:HIS164 3.1 19.9 1.0
CG A:ASP201 3.1 22.2 1.0
CG A:ASP318 3.2 28.1 1.0
CE1 A:HIS164 3.3 21.6 1.0
OD2 A:ASP318 3.4 31.5 1.0
CE1 A:HIS200 3.4 20.8 1.0
OD1 A:ASP201 3.7 21.4 1.0
ZN A:ZN510 3.8 30.5 0.7
O A:HOH708 3.9 30.8 1.0
O A:HOH706 4.0 36.3 1.0
CD2 A:HIS160 4.1 23.1 1.0
CB A:ASP201 4.3 17.1 1.0
CG A:HIS164 4.3 20.8 1.0
CG A:HIS200 4.3 22.1 1.0
ND1 A:HIS164 4.3 20.7 1.0
ND1 A:HIS200 4.4 19.7 1.0
NE2 A:HIS160 4.4 25.0 1.0
CB A:ASP318 4.5 21.9 1.0
CG2 A:VAL168 4.7 22.9 1.0

Zinc binding site 2 out of 8 in 4ogb

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn510

b:30.5
occ:0.68
 O A:HOH668 2.1 28.3 1.0
O A:HOH708 2.2 30.8 1.0
OD1 A:ASP201 2.2 21.4 1.0
O A:HOH614 2.3 23.7 1.0
O A:HOH606 2.4 20.9 1.0
O A:HOH616 2.4 24.6 1.0
CG A:ASP201 3.1 22.2 1.0
OD2 A:ASP201 3.3 19.9 1.0
ZN A:ZN509 3.8 29.0 1.0
O A:HOH707 3.9 32.1 1.0
O A:HOH657 4.0 32.0 1.0
NE2 A:HIS233 4.2 21.9 1.0
CD2 A:HIS200 4.2 20.6 1.0
O A:HIS200 4.2 20.7 1.0
OE2 A:GLU230 4.3 26.5 1.0
CD2 A:HIS233 4.3 20.6 1.0
OG1 A:THR271 4.4 22.5 1.0
CB A:ASP201 4.5 17.1 1.0
CD2 A:HIS204 4.5 20.0 1.0
CD2 A:HIS160 4.6 23.1 1.0
NE2 A:HIS160 4.7 25.0 1.0
NE2 A:HIS200 4.7 22.6 1.0
OD2 A:ASP318 4.7 31.5 1.0
NE2 A:HIS204 4.8 24.6 1.0
CA A:ASP201 4.8 17.6 1.0
CB A:THR271 4.9 20.9 1.0
CG A:GLU230 4.9 20.0 1.0
O A:THR271 5.0 28.4 1.0
O05 A:2SR501 5.0 59.2 1.0

Zinc binding site 3 out of 8 in 4ogb

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Zinc binding site 3 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:34.1
occ:1.00
 O B:HOH617 1.8 27.3 1.0
NE2 B:HIS164 2.0 22.6 1.0
O B:HOH690 2.1 29.4 1.0
OD2 B:ASP201 2.3 27.6 1.0
OD1 B:ASP318 2.3 29.1 1.0
NE2 B:HIS200 2.4 29.6 1.0
CE1 B:HIS164 2.9 29.0 1.0
CD2 B:HIS164 3.1 27.7 1.0
CG B:ASP201 3.1 24.0 1.0
CG B:ASP318 3.2 33.9 1.0
CD2 B:HIS200 3.3 27.0 1.0
CE1 B:HIS200 3.4 26.6 1.0
OD2 B:ASP318 3.5 25.5 1.0
OD1 B:ASP201 3.5 25.0 1.0
O B:HOH689 3.8 33.7 1.0
ZN B:ZN503 3.9 35.1 0.7
ND1 B:HIS164 4.0 26.7 1.0
O B:HOH613 4.1 38.5 1.0
CG B:HIS164 4.2 29.8 1.0
CD2 B:HIS160 4.3 30.4 1.0
CB B:ASP201 4.3 28.5 1.0
CG B:HIS200 4.4 25.2 1.0
ND1 B:HIS200 4.5 30.4 1.0
CB B:ASP318 4.6 29.3 1.0
CG2 B:VAL168 4.7 23.7 1.0
NE2 B:HIS160 4.8 24.8 1.0
O B:HOH603 4.9 30.2 1.0

Zinc binding site 4 out of 8 in 4ogb

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Zinc binding site 4 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:35.1
occ:0.66
 O B:HOH689 2.1 33.7 1.0
O B:HOH603 2.1 30.2 1.0
OD1 B:ASP201 2.2 25.0 1.0
O B:HOH609 2.3 24.8 1.0
O B:HOH606 2.5 29.2 1.0
O B:HOH617 2.5 27.3 1.0
CG B:ASP201 3.2 24.0 1.0
OD2 B:ASP201 3.6 27.6 1.0
O B:HOH690 3.8 29.4 1.0
ZN B:ZN502 3.9 34.1 1.0
OE2 B:GLU230 4.1 28.2 1.0
O B:HIS200 4.2 30.1 1.0
NE2 B:HIS233 4.2 30.1 1.0
OG1 B:THR271 4.3 37.5 1.0
CD2 B:HIS200 4.3 27.0 1.0
O B:HOH637 4.3 29.6 1.0
CD2 B:HIS233 4.4 27.3 1.0
OD2 B:ASP318 4.6 25.5 1.0
O B:THR271 4.6 33.5 1.0
CB B:ASP201 4.6 28.5 1.0
CD2 B:HIS204 4.6 24.7 1.0
O B:HOH693 4.6 40.1 1.0
CB B:THR271 4.7 32.0 1.0
CD2 B:HIS160 4.7 30.4 1.0
NE2 B:HIS200 4.8 29.6 1.0
CA B:ASP201 4.9 29.3 1.0
O05 B:2SR501 4.9 54.4 1.0
NE2 B:HIS160 4.9 24.8 1.0
C04 B:2SR501 4.9 46.2 1.0
NE2 B:HIS204 4.9 27.6 1.0
CD B:GLU230 5.0 30.6 1.0

Zinc binding site 5 out of 8 in 4ogb

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Zinc binding site 5 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn510

b:33.4
occ:1.00
 OD2 C:ASP201 2.2 29.9 1.0
NE2 C:HIS200 2.2 28.4 1.0
NE2 C:HIS164 2.2 23.8 1.0
O C:HOH666 2.2 33.3 1.0
O C:HOH601 2.2 30.1 1.0
OD1 C:ASP318 2.3 29.9 1.0
CD2 C:HIS200 3.0 23.9 1.0
CG C:ASP201 3.1 24.2 1.0
CE1 C:HIS164 3.2 23.2 1.0
CG C:ASP318 3.2 31.9 1.0
CD2 C:HIS164 3.2 24.4 1.0
CE1 C:HIS200 3.3 24.3 1.0
OD2 C:ASP318 3.4 29.8 1.0
OD1 C:ASP201 3.6 27.0 1.0
ZN C:ZN511 3.8 32.9 0.6
O C:HOH664 3.9 32.5 1.0
O C:HOH609 4.1 37.7 1.0
CG C:HIS200 4.2 25.3 1.0
CD2 C:HIS160 4.3 25.3 1.0
ND1 C:HIS164 4.3 25.4 1.0
ND1 C:HIS200 4.3 25.4 1.0
CB C:ASP201 4.3 23.4 1.0
CG C:HIS164 4.3 24.3 1.0
CB C:ASP318 4.5 27.8 1.0
CG2 C:VAL168 4.7 24.7 1.0
NE2 C:HIS160 4.7 29.5 1.0
O C:HOH602 4.9 26.7 1.0

Zinc binding site 6 out of 8 in 4ogb

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Zinc binding site 6 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn511

b:32.9
occ:0.64
 O C:HOH664 2.1 32.5 1.0
OD1 C:ASP201 2.2 27.0 1.0
O C:HOH602 2.2 26.7 1.0
O C:HOH665 2.3 27.4 1.0
O C:HOH666 2.3 33.3 1.0
O C:HOH613 2.5 24.9 1.0
CG C:ASP201 3.2 24.2 1.0
OD2 C:ASP201 3.5 29.9 1.0
ZN C:ZN510 3.8 33.4 1.0
O C:HOH601 3.8 30.1 1.0
O C:HOH653 3.9 32.5 1.0
O C:HIS200 4.0 26.3 1.0
OE2 C:GLU230 4.1 34.1 1.0
CD2 C:HIS200 4.2 23.9 1.0
OG1 C:THR271 4.2 29.8 1.0
NE2 C:HIS233 4.2 23.7 1.0
CD2 C:HIS233 4.4 19.2 1.0
CB C:ASP201 4.5 23.4 1.0
CD2 C:HIS204 4.5 19.1 1.0
OD2 C:ASP318 4.7 29.8 1.0
NE2 C:HIS200 4.7 28.4 1.0
CD2 C:HIS160 4.7 25.3 1.0
O C:THR271 4.7 28.2 1.0
CB C:THR271 4.8 31.9 1.0
CA C:ASP201 4.8 27.2 1.0
NE2 C:HIS160 4.8 29.5 1.0
NE2 C:HIS204 4.9 20.4 1.0
C C:HIS200 4.9 26.3 1.0

Zinc binding site 7 out of 8 in 4ogb

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Zinc binding site 7 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with Compound 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn512

b:27.5
occ:1.00
 O D:HOH711 2.1 24.6 1.0
NE2 D:HIS200 2.1 24.2 1.0
OD2 D:ASP201 2.2 22.1 1.0
NE2 D:HIS164 2.2 22.4 1.0
OD1 D:ASP318 2.2 23.6 1.0
O D:HOH712 2.3 32.2 1.0
CD2 D:HIS200 3.1 18.9 1.0
CG D:ASP318 3.1 26.0 1.0
CG D:ASP201 3.1 25.8 1.0
CE1 D:HIS200 3.1 18.6 1.0
CE1 D:HIS164 3.2 19.4 1.0
CD2 D:HIS164 3.2 21.4 1.0
OD2 D:ASP318 3.4 31.0 1.0
OD1 D:ASP201 3.6 22.5 1.0
ZN D:ZN513 3.8 33.2 0.7
O D:HOH713 3.9 32.6 1.0
O D:HOH716 4.1 30.2 1.0
CD2 D:HIS160 4.1 31.3 1.0
CG D:HIS200 4.2 17.6 1.0
ND1 D:HIS200 4.2 20.3 1.0
ND1 D:HIS164 4.3 20.8 1.0
CG D:HIS164 4.3 20.5 1.0
CB D:ASP201 4.3 22.3 1.0
NE2 D:HIS160 4.4 33.7 1.0
CB D:ASP318 4.5 19.3 1.0
CG2 D:VAL168 4.7 17.9 1.0
O D:HOH606 4.7 24.1 1.0
CA D:ASP318 5.0 21.6 1.0

Zinc binding site 8 out of 8 in 4ogb

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn513

b:33.2
occ:0.71
 O D:HOH606 2.0 24.1 1.0
O D:HOH713 2.2 32.6 1.0
OD1 D:ASP201 2.2 22.5 1.0
O D:HOH711 2.2 24.6 1.0
O D:HOH662 2.4 30.4 1.0
O D:HOH623 2.4 28.5 1.0
CG D:ASP201 3.2 25.8 1.0
OD2 D:ASP201 3.5 22.1 1.0
ZN D:ZN512 3.8 27.5 1.0
O D:HOH712 3.9 32.2 1.0
O D:HOH723 4.1 36.0 1.0
CD2 D:HIS200 4.2 18.9 1.0
NE2 D:HIS233 4.3 24.2 1.0
OG1 D:THR271 4.3 23.4 1.0
O D:HIS200 4.3 26.9 1.0
OE2 D:GLU230 4.3 26.0 1.0
CD2 D:HIS233 4.4 19.5 1.0
CD2 D:HIS160 4.5 31.3 1.0
NE2 D:HIS160 4.5 33.7 1.0
OD2 D:ASP318 4.5 31.0 1.0
O D:HOH730 4.5 38.6 1.0
CD2 D:HIS204 4.5 25.8 1.0
NE2 D:HIS200 4.6 24.2 1.0
CB D:ASP201 4.6 22.3 1.0
NE2 D:HIS204 4.7 27.5 1.0
O D:THR271 4.8 27.5 1.0
CB D:THR271 4.8 25.7 1.0
CG D:GLU230 4.8 25.9 1.0
CA D:ASP201 4.9 19.2 1.0

Reference:

B.L.Howard, J.L.Nankervis, S.C.Feil, D.T.Manallack, J.K.Holien, Z.Zhen, I.G.Jennings, B.M.Abbott, M.W.Parker, P.E.Thompson. The Pde Inhibition Profile of LY294002 and Tetrahydropyranyl Analogues Reveals A Chromone Motif For the Development of Pde Inhibitors To Be Published.
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