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Zinc in PDB 1q9m: Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity

Enzymatic activity of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity

All present enzymatic activity of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity:
3.1.4.17;

Protein crystallography data

The structure of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity, PDB code: 1q9m 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 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.272, 112.493, 160.908, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 25.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity (pdb code 1q9m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity, PDB code: 1q9m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1q9m

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Zinc binding site 1 out of 8 in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:30.2
occ:1.00
 OD2 A:ASP201 2.0 26.1 1.0
OD1 A:ASP318 2.0 24.8 1.0
NE2 A:HIS164 2.1 23.4 1.0
NE2 A:HIS200 2.1 24.3 1.0
O A:HOH548 2.6 27.8 1.0
CD2 A:HIS200 3.0 22.3 1.0
CG A:ASP318 3.0 23.2 1.0
CD2 A:HIS164 3.0 22.5 1.0
CE1 A:HIS164 3.1 21.7 1.0
CE1 A:HIS200 3.1 24.4 1.0
CG A:ASP201 3.1 24.7 1.0
OD2 A:ASP318 3.4 25.4 1.0
OD1 A:ASP201 3.7 33.8 1.0
ZN A:ZN502 3.8 61.6 1.0
O A:HOH552 4.0 32.1 1.0
CG A:HIS200 4.1 22.6 1.0
CD2 A:HIS160 4.1 18.6 1.0
ND1 A:HIS200 4.1 23.4 1.0
ND1 A:HIS164 4.2 21.7 1.0
CG A:HIS164 4.2 21.9 1.0
O A:HOH512 4.2 27.6 1.0
CB A:ASP201 4.3 23.9 1.0
CB A:ASP318 4.4 23.6 1.0
NE2 A:HIS160 4.4 19.6 1.0
CG2 A:VAL168 4.7 19.3 1.0
O A:HOH551 5.0 18.3 1.0

Zinc binding site 2 out of 8 in 1q9m

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Zinc binding site 2 out of 8 in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:61.6
occ:1.00
 OD1 A:ASP201 2.0 33.8 1.0
O A:HOH552 2.3 32.1 1.0
O A:HOH546 2.4 16.1 1.0
O A:HOH551 2.5 18.3 1.0
O A:HOH547 2.6 26.8 1.0
CG A:ASP201 3.0 24.7 1.0
OD2 A:ASP201 3.4 26.1 1.0
ZN A:ZN501 3.8 30.2 1.0
NE2 A:HIS233 4.1 20.5 1.0
O A:HOH550 4.1 26.4 1.0
OE2 A:GLU230 4.1 25.6 1.0
O A:HIS200 4.2 21.0 1.0
CD2 A:HIS200 4.2 22.3 1.0
OG1 A:THR271 4.2 23.6 1.0
O A:HOH548 4.2 27.8 1.0
CD2 A:HIS233 4.4 20.8 1.0
CB A:ASP201 4.4 23.9 1.0
CD2 A:HIS204 4.5 20.9 1.0
NE2 A:HIS160 4.6 19.6 1.0
CD2 A:HIS160 4.6 18.6 1.0
NE2 A:HIS200 4.6 24.3 1.0
CA A:ASP201 4.8 20.5 1.0
CB A:THR271 4.8 26.9 1.0
O A:THR271 4.8 27.8 1.0
OD2 A:ASP318 4.9 25.4 1.0
NE2 A:HIS204 4.9 22.2 1.0
C A:HIS200 5.0 19.7 1.0

Zinc binding site 3 out of 8 in 1q9m

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Zinc binding site 3 out of 8 in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:35.0
occ:1.00
 OD2 B:ASP201 2.0 35.7 1.0
OD1 B:ASP318 2.0 35.6 1.0
NE2 B:HIS164 2.1 31.4 1.0
NE2 B:HIS200 2.1 29.5 1.0
O B:HOH527 2.6 26.2 1.0
CD2 B:HIS200 2.9 28.6 1.0
CD2 B:HIS164 3.0 31.2 1.0
CG B:ASP201 3.1 34.2 1.0
CE1 B:HIS164 3.1 30.3 1.0
CG B:ASP318 3.1 34.4 1.0
CE1 B:HIS200 3.1 29.3 1.0
OD2 B:ASP318 3.5 35.0 1.0
OD1 B:ASP201 3.5 42.5 1.0
ZN B:ZN504 3.6 64.7 1.0
CD2 B:HIS160 4.1 27.3 1.0
CG B:HIS200 4.1 27.9 1.0
ND1 B:HIS200 4.2 28.5 1.0
ND1 B:HIS164 4.2 29.8 1.0
CG B:HIS164 4.2 31.3 1.0
NE2 B:HIS160 4.3 27.8 1.0
CB B:ASP201 4.3 32.6 1.0
O B:HOH524 4.4 34.1 1.0
CB B:ASP318 4.4 35.1 1.0
O B:HOH535 4.7 23.9 1.0
CG2 B:VAL168 4.8 35.3 1.0
CA B:ASP318 5.0 35.0 1.0

Zinc binding site 4 out of 8 in 1q9m

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Zinc binding site 4 out of 8 in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:64.7
occ:1.00
 OD1 B:ASP201 2.0 42.5 1.0
O B:HOH524 2.5 34.1 1.0
O B:HOH535 2.6 23.9 1.0
O B:HOH529 2.6 27.4 1.0
O B:HOH536 2.6 39.7 1.0
CG B:ASP201 3.0 34.2 1.0
OD2 B:ASP201 3.4 35.7 1.0
ZN B:ZN503 3.6 35.0 1.0
O B:HOH527 3.8 26.2 1.0
OE2 B:GLU230 4.1 27.1 1.0
NE2 B:HIS233 4.2 24.5 1.0
CD2 B:HIS200 4.2 28.6 1.0
O B:HIS200 4.2 27.4 1.0
O B:HOH528 4.3 27.6 1.0
CD2 B:HIS204 4.3 21.3 1.0
CD2 B:HIS160 4.3 27.3 1.0
NE2 B:HIS160 4.4 27.8 1.0
CB B:ASP201 4.4 32.6 1.0
CD2 B:HIS233 4.5 24.4 1.0
NE2 B:HIS200 4.5 29.5 1.0
NE2 B:HIS204 4.5 21.2 1.0
O B:HOH537 4.5 40.8 1.0
OG1 B:THR271 4.6 33.6 1.0
CA B:ASP201 4.8 29.4 1.0
OD2 B:ASP318 4.9 35.0 1.0
O B:THR271 5.0 33.7 1.0
OD1 B:ASP318 5.0 35.6 1.0

Zinc binding site 5 out of 8 in 1q9m

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Zinc binding site 5 out of 8 in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:32.6
occ:1.00
 OD2 C:ASP201 2.0 32.0 1.0
OD1 C:ASP318 2.0 34.7 1.0
NE2 C:HIS200 2.1 28.0 1.0
NE2 C:HIS164 2.1 29.3 1.0
O C:HOH535 2.4 33.1 1.0
CD2 C:HIS200 2.9 26.1 1.0
CE1 C:HIS164 3.0 26.9 1.0
CG C:ASP318 3.0 34.5 1.0
CE1 C:HIS200 3.1 27.3 1.0
CD2 C:HIS164 3.1 27.8 1.0
CG C:ASP201 3.2 29.4 1.0
OD2 C:ASP318 3.4 36.1 1.0
OD1 C:ASP201 3.7 38.4 1.0
ZN C:ZN506 3.9 59.7 1.0
ND1 C:HIS164 4.1 27.0 1.0
CG C:HIS200 4.1 26.0 1.0
ND1 C:HIS200 4.2 26.2 1.0
CD2 C:HIS160 4.2 21.2 1.0
CG C:HIS164 4.2 26.3 1.0
CB C:ASP201 4.3 27.6 1.0
CB C:ASP318 4.4 34.7 1.0
O C:HOH534 4.5 30.7 1.0
NE2 C:HIS160 4.6 21.7 1.0
CG2 C:VAL168 4.7 23.7 1.0
O C:HOH536 4.9 27.4 1.0
CA C:ASP318 5.0 33.7 1.0

Zinc binding site 6 out of 8 in 1q9m

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Zinc binding site 6 out of 8 in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn506

b:59.7
occ:1.00
 OD1 C:ASP201 2.0 38.4 1.0
O C:HOH534 2.4 30.7 1.0
O C:HOH537 2.5 23.9 1.0
O C:HOH536 2.5 27.4 1.0
O C:HOH538 2.6 26.6 1.0
CG C:ASP201 3.0 29.4 1.0
OD2 C:ASP201 3.3 32.0 1.0
ZN C:ZN505 3.9 32.6 1.0
O C:HOH535 4.0 33.1 1.0
OE2 C:GLU230 4.1 28.6 1.0
NE2 C:HIS233 4.2 15.6 1.0
CD2 C:HIS200 4.2 26.1 1.0
O C:HIS200 4.2 21.6 1.0
O C:HOH530 4.3 22.2 1.0
CB C:ASP201 4.4 27.6 1.0
OG1 C:THR271 4.4 34.1 1.0
CD2 C:HIS204 4.4 16.9 1.0
CD2 C:HIS233 4.5 16.5 1.0
CD2 C:HIS160 4.5 21.2 1.0
NE2 C:HIS200 4.6 28.0 1.0
NE2 C:HIS160 4.6 21.7 1.0
NE2 C:HIS204 4.7 17.4 1.0
O C:THR271 4.8 35.9 1.0
CA C:ASP201 4.8 24.3 1.0
CB C:THR271 4.9 34.4 1.0
OD2 C:ASP318 4.9 36.1 1.0

Zinc binding site 7 out of 8 in 1q9m

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Zinc binding site 7 out of 8 in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn507

b:31.1
occ:1.00
 OD2 D:ASP201 2.0 29.8 1.0
OD1 D:ASP318 2.0 28.9 1.0
NE2 D:HIS200 2.1 24.3 1.0
NE2 D:HIS164 2.1 25.9 1.0
O D:HOH538 2.4 29.2 1.0
CG D:ASP318 3.0 26.3 1.0
CD2 D:HIS200 3.0 22.8 1.0
CE1 D:HIS164 3.1 24.7 1.0
CE1 D:HIS200 3.1 23.8 1.0
CD2 D:HIS164 3.1 24.2 1.0
CG D:ASP201 3.1 28.6 1.0
OD2 D:ASP318 3.3 28.3 1.0
OD1 D:ASP201 3.7 37.7 1.0
ZN D:ZN508 3.9 61.4 1.0
O D:HOH551 4.1 36.1 1.0
ND1 D:HIS200 4.2 22.2 1.0
CG D:HIS200 4.2 21.6 1.0
ND1 D:HIS164 4.2 23.9 1.0
CD2 D:HIS160 4.2 24.1 1.0
CG D:HIS164 4.2 23.3 1.0
CB D:ASP201 4.3 26.1 1.0
CB D:ASP318 4.3 25.6 1.0
NE2 D:HIS160 4.5 24.4 1.0
CG2 D:VAL168 4.7 16.9 1.0
CA D:ASP318 4.9 24.8 1.0

Zinc binding site 8 out of 8 in 1q9m

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Zinc binding site 8 out of 8 in the Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Three Dimensional Structures of PDE4D in Complex with Roliprams and Implication on Inhibitor Selectivity within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn508

b:61.4
occ:1.00
 OD1 D:ASP201 2.0 37.7 1.0
O D:HOH553 2.4 25.8 1.0
O D:HOH551 2.5 36.1 1.0
O D:HOH552 2.6 29.2 1.0
O D:HOH542 2.6 24.9 1.0
CG D:ASP201 3.0 28.6 1.0
OD2 D:ASP201 3.4 29.8 1.0
ZN D:ZN507 3.9 31.1 1.0
NE2 D:HIS233 3.9 17.9 1.0
O D:HIS200 3.9 20.0 1.0
CD2 D:HIS200 4.0 22.8 1.0
CD2 D:HIS233 4.2 18.1 1.0
OE2 D:GLU230 4.3 29.4 1.0
O D:HOH538 4.3 29.2 1.0
OG1 D:THR271 4.3 24.3 1.0
CB D:ASP201 4.4 26.1 1.0
NE2 D:HIS200 4.4 24.3 1.0
O D:HOH547 4.5 30.6 1.0
CD2 D:HIS204 4.6 21.4 1.0
CA D:ASP201 4.7 22.6 1.0
CD2 D:HIS160 4.7 24.1 1.0
CB D:THR271 4.8 26.6 1.0
NE2 D:HIS160 4.8 24.4 1.0
O D:THR271 4.8 27.1 1.0
C D:HIS200 4.8 19.8 1.0
OD2 D:ASP318 4.9 28.3 1.0
NE2 D:HIS204 4.9 22.8 1.0
CG D:GLU230 5.0 27.9 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 18:06:43 2024

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