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Zinc in PDB 1ptw: The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis

Enzymatic activity of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis

All present enzymatic activity of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis:
3.1.4.17;

Protein crystallography data

The structure of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis, PDB code: 1ptw was solved by Q.Huai, J.Colicelli, 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 (°) 99.207, 111.229, 159.650, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 27.4

Zinc Binding Sites:

The binding sites of Zinc atom in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis (pdb code 1ptw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis, PDB code: 1ptw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1ptw

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Zinc binding site 1 out of 8 in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:38.0
occ:1.00
 OD1 A:ASP318 2.0 36.2 1.0
OD2 A:ASP201 2.0 33.7 1.0
NE2 A:HIS200 2.1 34.6 1.0
NE2 A:HIS164 2.1 34.0 1.0
O3P A:AMP507 2.3 59.0 1.0
CD2 A:HIS200 2.9 33.0 1.0
O1P A:AMP507 3.0 57.9 1.0
CG A:ASP318 3.0 34.6 1.0
CE1 A:HIS164 3.1 32.6 1.0
CD2 A:HIS164 3.1 30.3 1.0
P A:AMP507 3.1 57.1 1.0
CE1 A:HIS200 3.1 32.7 1.0
CG A:ASP201 3.2 32.7 1.0
OD2 A:ASP318 3.2 34.3 1.0
OD1 A:ASP201 3.7 42.0 1.0
O A:HOH510 3.9 33.5 1.0
ZN A:ZN502 4.0 63.2 1.0
O2P A:AMP507 4.1 57.4 1.0
CG A:HIS200 4.1 31.9 1.0
ND1 A:HIS164 4.2 32.4 1.0
ND1 A:HIS200 4.2 31.8 1.0
CG A:HIS164 4.2 32.1 1.0
O5' A:AMP507 4.3 57.4 1.0
CB A:ASP318 4.3 34.2 1.0
CB A:ASP201 4.3 32.2 1.0
CD2 A:HIS160 4.4 32.4 1.0
CG2 A:VAL168 4.7 27.3 1.0
NE2 A:HIS160 4.9 34.8 1.0
CA A:ASP318 4.9 35.2 1.0
O A:HOH513 4.9 21.3 1.0
C5' A:AMP507 4.9 55.3 1.0

Zinc binding site 2 out of 8 in 1ptw

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Zinc binding site 2 out of 8 in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:63.2
occ:1.00
 OD1 A:ASP201 2.0 42.0 1.0
O A:HOH508 2.2 24.1 1.0
O3P A:AMP507 2.4 59.0 1.0
O A:HOH513 2.6 21.3 1.0
O A:HOH509 2.7 42.0 1.0
O2P A:AMP507 3.0 57.4 1.0
CG A:ASP201 3.0 32.7 1.0
P A:AMP507 3.2 57.1 1.0
OD2 A:ASP201 3.4 33.7 1.0
O A:HOH512 3.8 34.4 1.0
NE2 A:HIS233 4.0 27.0 1.0
O5' A:AMP507 4.0 57.4 1.0
ZN A:ZN501 4.0 38.0 1.0
OE2 A:GLU230 4.0 36.8 1.0
CD2 A:HIS233 4.3 27.5 1.0
CD2 A:HIS200 4.3 33.0 1.0
O A:HIS200 4.3 27.9 1.0
OG1 A:THR271 4.4 36.9 1.0
CB A:ASP201 4.4 32.2 1.0
CD2 A:HIS204 4.5 30.6 1.0
O1P A:AMP507 4.5 57.9 1.0
NE2 A:HIS204 4.7 32.9 1.0
CD2 A:HIS160 4.7 32.4 1.0
NE2 A:HIS200 4.7 34.6 1.0
CA A:ASP201 4.8 29.7 1.0
NE2 A:HIS160 4.9 34.8 1.0
OD2 A:ASP318 4.9 34.3 1.0
CD A:GLU230 4.9 34.6 1.0
CB A:THR271 4.9 37.4 1.0

Zinc binding site 3 out of 8 in 1ptw

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Zinc binding site 3 out of 8 in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:47.1
occ:1.00
 OD2 B:ASP201 2.0 46.9 1.0
OD1 B:ASP318 2.0 46.7 1.0
NE2 B:HIS164 2.1 41.4 1.0
NE2 B:HIS200 2.1 39.9 1.0
O3P B:AMP508 2.4 66.5 1.0
CG B:ASP318 3.0 45.0 1.0
CE1 B:HIS200 3.0 38.9 1.0
CD2 B:HIS164 3.0 40.7 1.0
CE1 B:HIS164 3.1 38.9 1.0
CG B:ASP201 3.1 44.9 1.0
CD2 B:HIS200 3.1 38.5 1.0
P B:AMP508 3.3 65.8 1.0
O1P B:AMP508 3.3 66.3 1.0
OD2 B:ASP318 3.3 46.4 1.0
OD1 B:ASP201 3.6 50.3 1.0
O B:HOH516 3.7 30.2 1.0
ZN B:ZN502 3.9 68.2 1.0
ND1 B:HIS200 4.1 40.3 1.0
ND1 B:HIS164 4.1 39.5 1.0
CG B:HIS164 4.2 41.1 1.0
CG B:HIS200 4.2 39.3 1.0
O2P B:AMP508 4.2 66.8 1.0
CB B:ASP201 4.3 43.9 1.0
CB B:ASP318 4.4 45.9 1.0
CD2 B:HIS160 4.4 39.8 1.0
O5' B:AMP508 4.5 64.2 1.0
CG2 B:VAL168 4.8 51.5 1.0
CE2 B:TYR159 4.9 37.7 1.0
CA B:ASP318 4.9 45.4 1.0

Zinc binding site 4 out of 8 in 1ptw

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Zinc binding site 4 out of 8 in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:68.2
occ:1.00
 OD1 B:ASP201 2.0 50.3 1.0
O3P B:AMP508 2.5 66.5 1.0
O B:HOH512 2.5 38.9 1.0
O B:HOH509 2.5 32.9 1.0
O B:HOH510 2.6 41.2 1.0
O2P B:AMP508 2.7 66.8 1.0
CG B:ASP201 3.0 44.9 1.0
P B:AMP508 3.1 65.8 1.0
OD2 B:ASP201 3.4 46.9 1.0
ZN B:ZN501 3.9 47.1 1.0
NE2 B:HIS233 3.9 35.1 1.0
O5' B:AMP508 4.0 64.2 1.0
O B:HIS200 4.1 38.2 1.0
CD2 B:HIS200 4.2 38.5 1.0
CD2 B:HIS233 4.2 35.2 1.0
O1P B:AMP508 4.4 66.3 1.0
CB B:ASP201 4.4 43.9 1.0
CD2 B:HIS204 4.4 30.9 1.0
NE2 B:HIS200 4.5 39.9 1.0
OE2 B:GLU230 4.5 34.5 1.0
CD2 B:HIS160 4.7 39.8 1.0
OG1 B:THR271 4.7 46.4 1.0
CA B:ASP201 4.7 41.3 1.0
OD2 B:ASP318 4.8 46.4 1.0
NE2 B:HIS204 4.8 33.4 1.0
CE1 B:HIS233 4.9 35.7 1.0
C B:HIS200 4.9 40.0 1.0

Zinc binding site 5 out of 8 in 1ptw

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Zinc binding site 5 out of 8 in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:44.3
occ:1.00
 OD2 C:ASP201 2.0 42.7 1.0
OD1 C:ASP318 2.0 43.7 1.0
NE2 C:HIS200 2.1 35.6 1.0
NE2 C:HIS164 2.1 39.5 1.0
O3P C:AMP509 2.2 59.6 1.0
CE1 C:HIS164 2.9 38.8 1.0
CD2 C:HIS200 3.0 33.4 1.0
CG C:ASP318 3.0 41.2 1.0
CE1 C:HIS200 3.1 34.0 1.0
CG C:ASP201 3.1 40.0 1.0
CD2 C:HIS164 3.2 38.0 1.0
OD2 C:ASP318 3.4 42.0 1.0
P C:AMP509 3.5 61.6 1.0
OD1 C:ASP201 3.7 46.8 1.0
O C:HOH512 3.7 50.2 1.0
ZN C:ZN502 3.8 67.9 1.0
ND1 C:HIS164 4.0 39.1 1.0
O2P C:AMP509 4.1 58.7 1.0
O1P C:AMP509 4.1 61.0 1.0
CG C:HIS200 4.2 34.1 1.0
ND1 C:HIS200 4.2 33.5 1.0
CG C:HIS164 4.2 38.9 1.0
CB C:ASP201 4.3 36.6 1.0
CB C:ASP318 4.4 41.8 1.0
CD2 C:HIS160 4.4 34.1 1.0
O5' C:AMP509 4.6 60.2 1.0
CG2 C:VAL168 4.8 33.3 1.0
NE2 C:HIS160 4.9 33.9 1.0
CA C:ASP318 5.0 40.6 1.0
CE2 C:TYR159 5.0 37.0 1.0

Zinc binding site 6 out of 8 in 1ptw

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Zinc binding site 6 out of 8 in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:67.9
occ:1.00
 OD1 C:ASP201 2.0 46.8 1.0
O2P C:AMP509 2.4 58.7 1.0
O C:HOH513 2.5 27.3 1.0
O C:HOH515 2.5 30.9 1.0
O C:HOH514 2.6 31.0 1.0
CG C:ASP201 3.0 40.0 1.0
O3P C:AMP509 3.1 59.6 1.0
P C:AMP509 3.2 61.6 1.0
OD2 C:ASP201 3.3 42.7 1.0
ZN C:ZN501 3.8 44.3 1.0
O C:HIS200 3.9 33.9 1.0
CD2 C:HIS200 3.9 33.4 1.0
O5' C:AMP509 4.0 60.2 1.0
O C:HOH510 4.1 37.2 1.0
OG1 C:THR271 4.2 39.5 1.0
NE2 C:HIS233 4.2 29.5 1.0
OE2 C:GLU230 4.2 39.5 1.0
NE2 C:HIS200 4.4 35.6 1.0
CD2 C:HIS233 4.4 27.1 1.0
CB C:ASP201 4.4 36.6 1.0
O1P C:AMP509 4.5 61.0 1.0
CB C:THR271 4.7 41.0 1.0
OD2 C:ASP318 4.7 42.0 1.0
CD2 C:HIS160 4.7 34.1 1.0
CD2 C:HIS204 4.7 25.7 1.0
O C:THR271 4.8 41.5 1.0
CA C:ASP201 4.8 33.2 1.0
C C:HIS200 4.8 34.0 1.0

Zinc binding site 7 out of 8 in 1ptw

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Zinc binding site 7 out of 8 in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:38.4
occ:1.00
 OD2 D:ASP201 2.0 36.4 1.0
OD1 D:ASP318 2.0 33.9 1.0
NE2 D:HIS200 2.0 30.2 1.0
NE2 D:HIS164 2.1 28.2 1.0
O3P D:AMP510 2.3 63.1 1.0
CD2 D:HIS200 2.9 25.7 1.0
CG D:ASP318 3.0 32.8 1.0
CE1 D:HIS164 3.0 27.6 1.0
CD2 D:HIS164 3.1 27.0 1.0
CE1 D:HIS200 3.1 27.9 1.0
CG D:ASP201 3.1 35.7 1.0
OD2 D:ASP318 3.3 37.5 1.0
P D:AMP510 3.3 62.6 1.0
O1P D:AMP510 3.4 62.2 1.0
OD1 D:ASP201 3.7 44.0 1.0
ZN D:ZN502 3.8 64.0 1.0
CG D:HIS200 4.1 24.4 1.0
ND1 D:HIS164 4.1 26.3 1.0
ND1 D:HIS200 4.2 26.6 1.0
CG D:HIS164 4.2 26.6 1.0
O2P D:AMP510 4.3 61.8 1.0
CB D:ASP201 4.3 32.7 1.0
CB D:ASP318 4.4 32.9 1.0
O5' D:AMP510 4.5 62.6 1.0
CD2 D:HIS160 4.5 34.8 1.0
CG2 D:VAL168 4.7 23.1 1.0
C5' D:AMP510 4.9 59.3 1.0
CA D:ASP318 5.0 31.2 1.0

Zinc binding site 8 out of 8 in 1ptw

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Zinc binding site 8 out of 8 in the The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:64.0
occ:1.00
 OD1 D:ASP201 2.0 44.0 1.0
O D:HOH513 2.3 20.9 1.0
O D:HOH511 2.4 36.2 1.0
O3P D:AMP510 2.5 63.1 1.0
O D:HOH512 2.6 28.4 1.0
O2P D:AMP510 2.7 61.8 1.0
CG D:ASP201 2.9 35.7 1.0
P D:AMP510 3.0 62.6 1.0
OD2 D:ASP201 3.2 36.4 1.0
ZN D:ZN501 3.8 38.4 1.0
O5' D:AMP510 3.9 62.6 1.0
CD2 D:HIS200 4.0 25.7 1.0
O D:HIS200 4.1 27.1 1.0
NE2 D:HIS233 4.2 26.8 1.0
O D:HOH514 4.3 45.8 1.0
OG1 D:THR271 4.3 36.2 1.0
O1P D:AMP510 4.3 62.2 1.0
OE2 D:GLU230 4.3 37.4 1.0
CB D:ASP201 4.4 32.7 1.0
CD2 D:HIS233 4.4 25.7 1.0
NE2 D:HIS200 4.4 30.2 1.0
CD2 D:HIS204 4.6 34.8 1.0
CD2 D:HIS160 4.6 34.8 1.0
OD2 D:ASP318 4.7 37.5 1.0
NE2 D:HIS204 4.8 37.2 1.0
CA D:ASP201 4.8 27.6 1.0
O D:THR271 4.8 36.9 1.0
CB D:THR271 4.8 36.6 1.0
NE2 D:HIS160 4.9 35.7 1.0
C D:HIS200 4.9 25.2 1.0

Reference:

Q.Huai, J.Colicelli, H.Ke. The Crystal Structure of Amp-Bound PDE4 Suggests A Mechanism For Phosphodiesterase Catalysis Biochemistry V. 42 13220 2003.
ISSN: ISSN 0006-2960
PubMed: 14609333
DOI: 10.1021/BI034653E
Page generated: Wed Oct 16 17:54:54 2024

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