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Zinc in PDB 1oyn: Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram

Enzymatic activity of Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram

All present enzymatic activity of Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram, PDB code: 1oyn was solved by Q.Huai, H.Wang, Y.Sun, H.Y.Kim, Y.Liu, H.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 99.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.785, 111.529, 160.025, 90.00, 90.00, 90.00
R / Rfree (%) 23.3 / 26.6

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram (pdb code 1oyn). 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 PDE4D2 in Complex with (R,S)-Rolipram, PDB code: 1oyn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1oyn

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Zinc binding site 1 out of 8 in the Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram


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 PDE4D2 in Complex with (R,S)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:33.0
occ:1.00
 OD2 A:ASP201 2.0 30.1 1.0
OD1 A:ASP318 2.0 29.9 1.0
NE2 A:HIS200 2.1 27.1 1.0
NE2 A:HIS164 2.1 26.5 1.0
O A:HOH560 2.5 28.4 1.0
CD2 A:HIS200 3.0 24.8 1.0
CG A:ASP318 3.0 29.4 1.0
CE1 A:HIS164 3.0 24.7 1.0
CD2 A:HIS164 3.1 25.7 1.0
CE1 A:HIS200 3.1 25.2 1.0
CG A:ASP201 3.2 28.2 1.0
OD2 A:ASP318 3.4 30.5 1.0
OD1 A:ASP201 3.8 33.4 1.0
ZN A:ZN502 3.9 56.9 1.0
O A:HOH528 4.1 36.0 1.0
CG A:HIS200 4.1 24.8 1.0
ND1 A:HIS200 4.1 24.7 1.0
ND1 A:HIS164 4.2 25.5 1.0
CG A:HIS164 4.2 26.7 1.0
CD2 A:HIS160 4.2 21.4 1.0
CB A:ASP201 4.3 25.3 1.0
O A:HOH559 4.3 30.1 1.0
CB A:ASP318 4.4 28.5 1.0
NE2 A:HIS160 4.6 22.1 1.0
CG2 A:VAL168 4.7 22.7 1.0
CA A:ASP318 4.9 28.0 1.0

Zinc binding site 2 out of 8 in 1oyn

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Zinc binding site 2 out of 8 in the Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram


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 PDE4D2 in Complex with (R,S)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:56.9
occ:1.00
 OD1 A:ASP201 2.0 33.4 1.0
O A:HOH557 2.4 26.3 1.0
O A:HOH558 2.4 18.3 1.0
O A:HOH559 2.5 30.1 1.0
O A:HOH540 2.5 27.7 1.0
CG A:ASP201 3.0 28.2 1.0
OD2 A:ASP201 3.3 30.1 1.0
ZN A:ZN501 3.9 33.0 1.0
O A:HIS200 4.0 23.0 1.0
NE2 A:HIS233 4.1 21.2 1.0
CD2 A:HIS200 4.2 24.8 1.0
O A:HOH560 4.2 28.4 1.0
OE2 A:GLU230 4.3 28.7 1.0
CD2 A:HIS233 4.3 22.4 1.0
O A:HOH563 4.3 31.2 1.0
CB A:ASP201 4.3 25.3 1.0
OG1 A:THR271 4.5 29.8 1.0
NE2 A:HIS200 4.6 27.1 1.0
CD2 A:HIS204 4.6 22.8 1.0
CA A:ASP201 4.7 23.5 1.0
CD2 A:HIS160 4.7 21.4 1.0
O A:HOH564 4.7 45.0 1.0
NE2 A:HIS160 4.8 22.1 1.0
OD2 A:ASP318 4.9 30.5 1.0
C A:HIS200 4.9 22.4 1.0
O A:THR271 4.9 31.8 1.0
CB A:THR271 5.0 30.5 1.0

Zinc binding site 3 out of 8 in 1oyn

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Zinc binding site 3 out of 8 in the Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram


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 PDE4D2 in Complex with (R,S)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:36.8
occ:1.00
 OD2 B:ASP201 2.0 38.2 1.0
OD1 B:ASP318 2.0 34.9 1.0
NE2 B:HIS164 2.1 31.8 1.0
NE2 B:HIS200 2.1 30.9 1.0
O B:HOH531 2.4 30.5 1.0
CD2 B:HIS200 2.9 29.2 1.0
CG B:ASP318 3.0 35.3 1.0
CG B:ASP201 3.0 37.2 1.0
CE1 B:HIS164 3.0 30.6 1.0
CD2 B:HIS164 3.1 31.7 1.0
CE1 B:HIS200 3.1 30.4 1.0
OD2 B:ASP318 3.3 36.4 1.0
OD1 B:ASP201 3.5 44.9 1.0
ZN B:ZN504 3.7 67.1 1.0
O B:HOH533 4.1 36.7 1.0
CG B:HIS200 4.1 30.6 1.0
ND1 B:HIS200 4.1 29.8 1.0
ND1 B:HIS164 4.1 30.6 1.0
CG B:HIS164 4.2 31.9 1.0
CD2 B:HIS160 4.3 29.9 1.0
CB B:ASP201 4.3 35.4 1.0
CB B:ASP318 4.4 35.0 1.0
NE2 B:HIS160 4.7 28.6 1.0
CG2 B:VAL168 4.7 36.5 1.0
O B:HOH529 4.8 31.4 1.0
CA B:ASP318 5.0 35.4 1.0

Zinc binding site 4 out of 8 in 1oyn

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Zinc binding site 4 out of 8 in the Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram


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 PDE4D2 in Complex with (R,S)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:67.1
occ:1.00
 OD1 B:ASP201 2.0 44.9 1.0
O B:HOH532 2.5 25.9 1.0
O B:HOH529 2.5 31.4 1.0
O B:HOH513 2.6 25.2 1.0
CG B:ASP201 3.0 37.2 1.0
OD2 B:ASP201 3.3 38.2 1.0
ZN B:ZN503 3.7 36.8 1.0
O B:HOH531 4.0 30.5 1.0
NE2 B:HIS233 4.0 32.1 1.0
O B:HIS200 4.1 30.6 1.0
CD2 B:HIS204 4.3 25.9 1.0
CD2 B:HIS233 4.3 30.0 1.0
CD2 B:HIS200 4.3 29.2 1.0
CD2 B:HIS160 4.3 29.9 1.0
CB B:ASP201 4.3 35.4 1.0
O B:HOH534 4.4 44.9 1.0
OE2 B:GLU230 4.4 29.2 1.0
NE2 B:HIS160 4.5 28.6 1.0
NE2 B:HIS204 4.6 26.5 1.0
NE2 B:HIS200 4.6 30.9 1.0
CA B:ASP201 4.7 32.0 1.0
OD2 B:ASP318 4.8 36.4 1.0
OG1 B:THR271 4.8 34.3 1.0
C B:HIS200 5.0 30.6 1.0

Zinc binding site 5 out of 8 in 1oyn

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Zinc binding site 5 out of 8 in the Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram


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 PDE4D2 in Complex with (R,S)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:37.2
occ:1.00
 OD2 C:ASP201 2.0 37.1 1.0
OD1 C:ASP318 2.0 35.7 1.0
NE2 C:HIS200 2.1 31.6 1.0
O C:HOH536 2.1 25.5 1.0
NE2 C:HIS164 2.1 31.2 1.0
O C:HOH519 2.4 31.1 1.0
CE1 C:HIS164 3.0 30.1 1.0
CD2 C:HIS200 3.0 29.4 1.0
CE1 C:HIS200 3.0 31.1 1.0
CG C:ASP318 3.1 35.0 1.0
CD2 C:HIS164 3.1 30.6 1.0
CG C:ASP201 3.1 35.0 1.0
OD2 C:ASP318 3.5 34.8 1.0
OD1 C:ASP201 3.6 41.6 1.0
ZN C:ZN506 3.9 60.5 1.0
O C:HOH535 4.1 29.9 1.0
ND1 C:HIS164 4.1 31.4 1.0
ND1 C:HIS200 4.1 30.7 1.0
CG C:HIS200 4.2 30.1 1.0
O C:HOH537 4.2 44.8 1.0
CG C:HIS164 4.2 30.9 1.0
CD2 C:HIS160 4.3 29.4 1.0
CB C:ASP201 4.3 32.2 1.0
CB C:ASP318 4.4 34.2 1.0
CG2 C:VAL168 4.7 29.8 1.0
NE2 C:HIS160 4.7 29.4 1.0
O C:HOH539 5.0 30.7 1.0
CA C:ASP318 5.0 34.3 1.0

Zinc binding site 6 out of 8 in 1oyn

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Zinc binding site 6 out of 8 in the Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram


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 PDE4D2 in Complex with (R,S)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn506

b:60.5
occ:1.00
 OD1 C:ASP201 2.0 41.6 1.0
O C:HOH539 2.3 30.7 1.0
O C:HOH535 2.4 29.9 1.0
O C:HOH538 2.5 34.6 1.0
O C:HOH519 2.5 31.1 1.0
O C:HOH526 2.5 29.4 1.0
CG C:ASP201 3.1 35.0 1.0
OD2 C:ASP201 3.5 37.1 1.0
NE2 C:HIS233 3.9 22.5 1.0
ZN C:ZN505 3.9 37.2 1.0
O C:HIS200 4.0 27.5 1.0
CD2 C:HIS200 4.0 29.4 1.0
OE2 C:GLU230 4.1 33.6 1.0
OG1 C:THR271 4.2 36.6 1.0
O C:HOH536 4.2 25.5 1.0
CD2 C:HIS233 4.2 21.6 1.0
CB C:ASP201 4.4 32.2 1.0
NE2 C:HIS200 4.4 31.6 1.0
O C:HOH533 4.5 36.9 1.0
CD2 C:HIS204 4.5 21.7 1.0
CD2 C:HIS160 4.7 29.4 1.0
CA C:ASP201 4.7 28.6 1.0
CB C:THR271 4.8 37.3 1.0
C C:HIS200 4.9 28.5 1.0
NE2 C:HIS204 4.9 22.9 1.0
NE2 C:HIS160 4.9 29.4 1.0
O C:THR271 4.9 39.0 1.0
CE1 C:HIS233 5.0 19.7 1.0
CD C:GLU230 5.0 32.7 1.0
OD2 C:ASP318 5.0 34.8 1.0

Zinc binding site 7 out of 8 in 1oyn

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Zinc binding site 7 out of 8 in the Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram


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 PDE4D2 in Complex with (R,S)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn507

b:33.1
occ:1.00
 OD2 D:ASP201 2.0 32.8 1.0
OD1 D:ASP318 2.0 29.2 1.0
NE2 D:HIS200 2.1 25.2 1.0
NE2 D:HIS164 2.1 26.8 1.0
O D:HOH558 2.4 30.2 1.0
CG D:ASP318 2.9 29.2 1.0
CE1 D:HIS164 3.0 24.8 1.0
CE1 D:HIS200 3.0 25.5 1.0
CD2 D:HIS200 3.0 23.9 1.0
CD2 D:HIS164 3.1 24.2 1.0
CG D:ASP201 3.1 34.4 1.0
OD2 D:ASP318 3.2 29.6 1.0
OD1 D:ASP201 3.7 42.4 1.0
ZN D:ZN508 4.0 63.3 1.0
CD2 D:HIS160 4.1 27.5 1.0
ND1 D:HIS200 4.1 24.1 1.0
ND1 D:HIS164 4.1 24.8 1.0
CG D:HIS200 4.2 23.4 1.0
CG D:HIS164 4.2 25.3 1.0
O D:HOH544 4.2 36.8 1.0
CB D:ASP201 4.2 31.2 1.0
CB D:ASP318 4.3 28.9 1.0
NE2 D:HIS160 4.4 28.1 1.0
CG2 D:VAL168 4.7 20.7 1.0
O D:HOH557 4.9 25.1 1.0
CA D:ASP318 4.9 27.6 1.0

Zinc binding site 8 out of 8 in 1oyn

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Zinc binding site 8 out of 8 in the Crystal Structure of PDE4D2 in Complex with (R,S)-Rolipram


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 PDE4D2 in Complex with (R,S)-Rolipram within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn508

b:63.3
occ:1.00
 OD1 D:ASP201 2.0 42.4 1.0
O D:HOH557 2.2 25.1 1.0
O D:HOH525 2.5 23.8 1.0
O D:HOH556 2.5 27.9 1.0
CG D:ASP201 3.0 34.4 1.0
OD2 D:ASP201 3.4 32.8 1.0
O D:HIS200 3.9 24.6 1.0
NE2 D:HIS233 4.0 24.4 1.0
ZN D:ZN507 4.0 33.1 1.0
OE2 D:GLU230 4.0 29.7 1.0
CD2 D:HIS200 4.2 23.9 1.0
CD2 D:HIS233 4.2 23.6 1.0
CB D:ASP201 4.4 31.2 1.0
OG1 D:THR271 4.4 34.2 1.0
O D:HOH558 4.4 30.2 1.0
CD2 D:HIS204 4.5 27.6 1.0
O D:HOH555 4.5 46.2 1.0
NE2 D:HIS200 4.5 25.2 1.0
CA D:ASP201 4.6 26.8 1.0
CD2 D:HIS160 4.7 27.5 1.0
NE2 D:HIS160 4.8 28.1 1.0
OD2 D:ASP318 4.8 29.6 1.0
NE2 D:HIS204 4.8 29.4 1.0
C D:HIS200 4.8 24.2 1.0
CD D:GLU230 4.9 30.2 1.0
CG D:GLU230 4.9 28.2 1.0
CB D:THR271 4.9 33.6 1.0
O D:THR271 5.0 32.7 1.0

Reference:

Q.Huai, H.Wang, Y.Sun, H.Y.Kim, Y.Liu, H.Ke. Three-Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity Structure V. 11 865 2003.
ISSN: ISSN 0969-2126
PubMed: 12842049
DOI: 10.1016/S0969-2126(03)00123-0
Page generated: Wed Oct 16 17:37:07 2024

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