Atomistry » Zinc » PDB 1pe8-1pud » 1ptw
Atomistry »
  Zinc »
    PDB 1pe8-1pud »
      1ptw »

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

Go back to Zinc Binding Sites List in 1ptw
Zinc binding site 1 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 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

Go back to Zinc Binding Sites List in 1ptw
Zinc binding site 2 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 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

Go back to Zinc Binding Sites List in 1ptw
Zinc binding site 3 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 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

Go back to Zinc Binding Sites List in 1ptw
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

Go back to Zinc Binding Sites List in 1ptw
Zinc binding site 5 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 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

Go back to Zinc Binding Sites List in 1ptw
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

Go back to Zinc Binding Sites List in 1ptw
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

Go back to Zinc Binding Sites List in 1ptw
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy