Fluorine in PDB 1mkd: Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex:
3.1.4.17;

The structure of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex, PDB code: 1mkd was solved by M.E.Lee, J.Markowitz, J.-O.Lee, H.Lee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	97.325, 164.572, 325.540, 90.00, 90.00, 90.00
R / Rfree (%)	24.5 / 26

The structure of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex also contains other interesting chemical elements:

Magnesium	(Mg)	12 atoms
Zinc	(Zn)	12 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex (pdb code 1mkd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 24 binding sites of Fluorine where determined in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex, PDB code: 1mkd:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F3001 b:62.1 occ:1.00 F16 A:ZAR3001 0.0 62.1 1.0 C14 A:ZAR3001 1.4 62.1 1.0 F17 A:ZAR3001 2.2 63.3 1.0 O15 A:ZAR3001 2.3 62.1 1.0 C11 A:ZAR3001 3.1 62.3 1.0 CB A:ASN418 3.1 32.7 1.0 C12 A:ZAR3001 3.2 63.2 1.0 OD1 A:ASN418 3.6 31.1 1.0 CE1 A:TYR426 3.6 37.7 1.0 CD A:PRO419 3.7 32.9 1.0 CG A:PRO419 3.8 33.0 1.0 CG A:ASN418 3.8 32.9 1.0 CD1 A:TYR426 4.0 37.4 1.0 OE1 A:GLN466 4.1 46.0 1.0 CE2 A:PHE469 4.2 38.5 1.0 N A:PRO419 4.2 32.7 1.0 CA A:ASN418 4.3 32.6 1.0 C10 A:ZAR3001 4.4 61.9 1.0 OG1 A:THR430 4.5 37.6 1.0 C A:ASN418 4.5 31.9 1.0 C13 A:ZAR3001 4.6 64.4 1.0 CB A:TRP429 4.6 34.4 1.0 CD2 A:PHE469 4.6 39.7 1.0 CZ A:TYR426 4.7 38.8 1.0 O18 A:ZAR3001 4.8 61.0 1.0 OH A:TYR426 4.9 39.6 1.0 N A:ASN418 4.9 33.2 1.0 CD A:GLN466 4.9 47.4 1.0 N A:THR430 4.9 36.1 1.0

Fluorine binding site 2 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F3001 b:63.3 occ:1.00 F17 A:ZAR3001 0.0 63.3 1.0 C14 A:ZAR3001 1.4 62.1 1.0 F16 A:ZAR3001 2.2 62.1 1.0 O15 A:ZAR3001 2.3 62.1 1.0 C11 A:ZAR3001 3.1 62.3 1.0 C12 A:ZAR3001 3.2 63.2 1.0 N A:THR430 3.3 36.1 1.0 C A:TRP429 3.3 36.3 1.0 O A:TRP429 3.5 34.9 1.0 CA A:THR430 3.5 37.2 1.0 CG2 A:ILE433 3.5 40.6 1.0 CB A:TRP429 3.6 34.4 1.0 OD1 A:ASN418 3.7 31.1 1.0 CB A:ILE433 3.9 39.5 1.0 CE1 A:TYR256 3.9 34.6 1.0 OG1 A:THR430 3.9 37.6 1.0 CA A:TRP429 4.1 36.8 1.0 CB A:ASN418 4.3 32.7 1.0 CB A:THR430 4.3 36.1 1.0 C10 A:ZAR3001 4.4 61.9 1.0 CG A:ASN418 4.4 32.9 1.0 C13 A:ZAR3001 4.6 64.4 1.0 CD1 A:TYR256 4.6 34.7 1.0 C A:THR430 4.6 38.1 1.0 CZ A:TYR256 4.7 33.7 1.0 CG1 A:ILE433 4.7 38.0 1.0 OH A:TYR256 4.7 32.8 1.0 CE1 A:TYR426 4.7 37.7 1.0 O A:TYR426 4.8 40.0 1.0 OE1 A:GLN466 4.8 46.0 1.0 CG A:TRP429 4.9 33.5 1.0 NE2 A:GLN466 4.9 47.5 1.0 O18 A:ZAR3001 4.9 61.0 1.0 CD1 A:TYR426 4.9 37.4 1.0 O A:THR430 4.9 38.5 1.0

Fluorine binding site 3 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F3002 b:60.2 occ:1.00 F16 B:ZAR3002 0.0 60.2 1.0 C14 B:ZAR3002 1.4 59.6 1.0 F17 B:ZAR3002 2.2 60.8 1.0 O15 B:ZAR3002 2.3 61.2 1.0 C11 B:ZAR3002 3.1 61.6 1.0 CB B:ASN418 3.1 29.5 1.0 C12 B:ZAR3002 3.2 61.9 1.0 OD1 B:ASN418 3.5 28.2 1.0 CE1 B:TYR426 3.6 36.4 1.0 CD B:PRO419 3.7 31.2 1.0 CG B:PRO419 3.7 31.1 1.0 CG B:ASN418 3.8 29.8 1.0 CD1 B:TYR426 4.0 36.3 1.0 OE1 B:GLN466 4.1 43.3 1.0 CE2 B:PHE469 4.1 35.1 1.0 N B:PRO419 4.2 30.9 1.0 CA B:ASN418 4.3 29.6 1.0 C10 B:ZAR3002 4.3 61.5 1.0 OG1 B:THR430 4.5 36.1 1.0 C B:ASN418 4.5 31.0 1.0 C13 B:ZAR3002 4.6 63.2 1.0 CD2 B:PHE469 4.6 36.1 1.0 CZ B:TYR426 4.7 36.8 1.0 CB B:TRP429 4.7 35.0 1.0 O18 B:ZAR3002 4.8 60.6 1.0 OH B:TYR426 4.9 36.5 1.0 N B:ASN418 4.9 29.9 1.0 CD B:GLN466 4.9 43.9 1.0 N B:THR430 5.0 35.2 1.0

Fluorine binding site 4 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:F3002 b:60.8 occ:1.00 F17 B:ZAR3002 0.0 60.8 1.0 C14 B:ZAR3002 1.4 59.6 1.0 F16 B:ZAR3002 2.2 60.2 1.0 O15 B:ZAR3002 2.3 61.2 1.0 C11 B:ZAR3002 3.1 61.6 1.0 C12 B:ZAR3002 3.2 61.9 1.0 N B:THR430 3.4 35.2 1.0 C B:TRP429 3.4 35.8 1.0 O B:TRP429 3.5 36.5 1.0 CA B:THR430 3.5 35.6 1.0 CG2 B:ILE433 3.6 37.7 1.0 OD1 B:ASN418 3.6 28.2 1.0 CB B:TRP429 3.7 35.0 1.0 CE1 B:TYR256 3.9 30.1 1.0 OG1 B:THR430 3.9 36.1 1.0 CB B:ILE433 4.0 37.4 1.0 CA B:TRP429 4.2 36.1 1.0 CB B:ASN418 4.3 29.5 1.0 CB B:THR430 4.3 36.2 1.0 CG B:ASN418 4.4 29.8 1.0 C10 B:ZAR3002 4.4 61.5 1.0 C13 B:ZAR3002 4.6 63.2 1.0 CD1 B:TYR256 4.6 31.5 1.0 OH B:TYR256 4.6 31.0 1.0 CZ B:TYR256 4.7 30.3 1.0 C B:THR430 4.7 35.8 1.0 CE1 B:TYR426 4.7 36.4 1.0 CG1 B:ILE433 4.7 37.3 1.0 O B:TYR426 4.8 37.8 1.0 OE1 B:GLN466 4.8 43.3 1.0 NE2 B:GLN466 4.9 44.9 1.0 CG B:TRP429 4.9 33.0 1.0 O18 B:ZAR3002 4.9 60.6 1.0 CD1 B:TYR426 4.9 36.3 1.0 O B:THR430 5.0 34.4 1.0

Fluorine binding site 5 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F3003 b:61.6 occ:1.00 F16 C:ZAR3003 0.0 61.6 1.0 C14 C:ZAR3003 1.4 60.9 1.0 F17 C:ZAR3003 2.3 61.1 1.0 O15 C:ZAR3003 2.3 60.8 1.0 C11 C:ZAR3003 3.1 61.2 1.0 CB C:ASN418 3.1 31.2 1.0 C12 C:ZAR3003 3.2 62.6 1.0 OD1 C:ASN418 3.5 30.5 1.0 CE1 C:TYR426 3.6 35.2 1.0 CD C:PRO419 3.7 33.0 1.0 CG C:PRO419 3.8 33.0 1.0 CG C:ASN418 3.8 30.6 1.0 CD1 C:TYR426 4.0 34.4 1.0 OE1 C:GLN466 4.1 42.4 1.0 CE2 C:PHE469 4.2 37.9 1.0 N C:PRO419 4.3 32.6 1.0 C10 C:ZAR3003 4.3 61.2 1.0 CA C:ASN418 4.4 31.7 1.0 OG1 C:THR430 4.4 38.3 1.0 C C:ASN418 4.5 31.9 1.0 C13 C:ZAR3003 4.6 64.4 1.0 CD2 C:PHE469 4.6 38.6 1.0 CB C:TRP429 4.6 35.4 1.0 CZ C:TYR426 4.7 35.8 1.0 O18 C:ZAR3003 4.8 60.0 1.0 N C:THR430 4.9 35.6 1.0 OH C:TYR426 4.9 36.0 1.0 CD C:GLN466 4.9 43.1 1.0 N C:ASN418 5.0 32.0 1.0

Fluorine binding site 6 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:F3003 b:61.1 occ:1.00 F17 C:ZAR3003 0.0 61.1 1.0 C14 C:ZAR3003 1.4 60.9 1.0 F16 C:ZAR3003 2.3 61.6 1.0 O15 C:ZAR3003 2.3 60.8 1.0 C11 C:ZAR3003 3.1 61.2 1.0 C12 C:ZAR3003 3.2 62.6 1.0 N C:THR430 3.3 35.6 1.0 C C:TRP429 3.3 35.7 1.0 O C:TRP429 3.4 34.4 1.0 CA C:THR430 3.5 35.6 1.0 CG2 C:ILE433 3.5 37.2 1.0 CB C:TRP429 3.6 35.4 1.0 OD1 C:ASN418 3.7 30.5 1.0 CE1 C:TYR256 3.9 31.3 1.0 CB C:ILE433 3.9 37.6 1.0 OG1 C:THR430 3.9 38.3 1.0 CA C:TRP429 4.1 35.9 1.0 CB C:THR430 4.3 36.2 1.0 CB C:ASN418 4.3 31.2 1.0 C10 C:ZAR3003 4.4 61.2 1.0 CG C:ASN418 4.4 30.6 1.0 CD1 C:TYR256 4.5 31.7 1.0 C13 C:ZAR3003 4.5 64.4 1.0 C C:THR430 4.6 37.0 1.0 CZ C:TYR256 4.6 31.7 1.0 CG1 C:ILE433 4.6 38.2 1.0 OH C:TYR256 4.7 31.9 1.0 CE1 C:TYR426 4.8 35.2 1.0 O C:TYR426 4.8 35.3 1.0 O18 C:ZAR3003 4.9 60.0 1.0 CG C:TRP429 4.9 34.5 1.0 NE2 C:GLN466 4.9 44.4 1.0 OE1 C:GLN466 4.9 42.4 1.0 O C:THR430 4.9 37.2 1.0 CD1 C:TYR426 5.0 34.4 1.0

Fluorine binding site 7 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:F3004 b:61.4 occ:1.00 F16 D:ZAR3004 0.0 61.4 1.0 C14 D:ZAR3004 1.4 60.5 1.0 F17 D:ZAR3004 2.2 61.0 1.0 O15 D:ZAR3004 2.3 60.5 1.0 C11 D:ZAR3004 3.1 61.9 1.0 CB D:ASN418 3.1 33.1 1.0 C12 D:ZAR3004 3.2 62.9 1.0 CE1 D:TYR426 3.5 36.7 1.0 OD1 D:ASN418 3.6 32.3 1.0 CD D:PRO419 3.7 33.1 1.0 CG D:PRO419 3.8 32.3 1.0 CG D:ASN418 3.9 33.2 1.0 CD1 D:TYR426 4.0 36.5 1.0 OE1 D:GLN466 4.0 45.6 1.0 CE2 D:PHE469 4.2 37.3 1.0 N D:PRO419 4.2 33.4 1.0 C10 D:ZAR3004 4.3 62.2 1.0 CA D:ASN418 4.4 33.2 1.0 OG1 D:THR430 4.4 38.7 1.0 C D:ASN418 4.5 33.5 1.0 C13 D:ZAR3004 4.6 65.4 1.0 CZ D:TYR426 4.6 37.7 1.0 CD2 D:PHE469 4.6 37.4 1.0 CB D:TRP429 4.7 37.1 1.0 O18 D:ZAR3004 4.8 62.2 1.0 OH D:TYR426 4.9 35.3 1.0 N D:THR430 4.9 37.9 1.0 CD D:GLN466 4.9 44.0 1.0 N D:ASN418 5.0 32.9 1.0

Fluorine binding site 8 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:F3004 b:61.0 occ:1.00 F17 D:ZAR3004 0.0 61.0 1.0 C14 D:ZAR3004 1.4 60.5 1.0 F16 D:ZAR3004 2.2 61.4 1.0 O15 D:ZAR3004 2.3 60.5 1.0 C11 D:ZAR3004 3.1 61.9 1.0 C12 D:ZAR3004 3.2 62.9 1.0 N D:THR430 3.3 37.9 1.0 C D:TRP429 3.3 38.1 1.0 CA D:THR430 3.4 38.0 1.0 O D:TRP429 3.4 38.0 1.0 CG2 D:ILE433 3.5 40.0 1.0 CB D:TRP429 3.6 37.1 1.0 OD1 D:ASN418 3.7 32.3 1.0 OG1 D:THR430 3.9 38.7 1.0 CB D:ILE433 3.9 40.2 1.0 CE1 D:TYR256 3.9 34.5 1.0 CA D:TRP429 4.1 37.9 1.0 CB D:THR430 4.3 37.6 1.0 CB D:ASN418 4.3 33.1 1.0 C10 D:ZAR3004 4.4 62.2 1.0 CG D:ASN418 4.4 33.2 1.0 C13 D:ZAR3004 4.5 65.4 1.0 C D:THR430 4.6 38.5 1.0 CD1 D:TYR256 4.6 34.8 1.0 CZ D:TYR256 4.7 34.0 1.0 O D:TYR426 4.7 38.8 1.0 CE1 D:TYR426 4.7 36.7 1.0 CG1 D:ILE433 4.7 38.7 1.0 OH D:TYR256 4.7 31.8 1.0 OE1 D:GLN466 4.8 45.6 1.0 CG D:TRP429 4.9 35.9 1.0 NE2 D:GLN466 4.9 44.5 1.0 O18 D:ZAR3004 4.9 62.2 1.0 O D:THR430 4.9 37.9 1.0 CD1 D:TYR426 4.9 36.5 1.0

Fluorine binding site 9 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:F3005 b:62.5 occ:1.00 F16 E:ZAR3005 0.0 62.5 1.0 C14 E:ZAR3005 1.4 61.8 1.0 F17 E:ZAR3005 2.2 62.9 1.0 O15 E:ZAR3005 2.3 62.4 1.0 C11 E:ZAR3005 3.1 62.9 1.0 CB E:ASN418 3.1 31.1 1.0 C12 E:ZAR3005 3.3 64.0 1.0 CE1 E:TYR426 3.5 39.6 1.0 OD1 E:ASN418 3.5 28.6 1.0 CD E:PRO419 3.7 33.1 1.0 CG E:PRO419 3.8 32.2 1.0 CG E:ASN418 3.8 30.4 1.0 CD1 E:TYR426 3.9 38.6 1.0 OE1 E:GLN466 4.0 44.3 1.0 N E:PRO419 4.2 31.8 1.0 CE2 E:PHE469 4.3 38.4 1.0 CA E:ASN418 4.3 31.8 1.0 C10 E:ZAR3005 4.4 62.4 1.0 OG1 E:THR430 4.4 38.6 1.0 C E:ASN418 4.5 32.0 1.0 C13 E:ZAR3005 4.6 65.4 1.0 CB E:TRP429 4.6 35.7 1.0 CZ E:TYR426 4.6 39.8 1.0 CD2 E:PHE469 4.7 39.0 1.0 O18 E:ZAR3005 4.8 60.7 1.0 N E:THR430 4.9 36.2 1.0 CD E:GLN466 4.9 44.8 1.0 OH E:TYR426 4.9 40.5 1.0 N E:ASN418 4.9 30.8 1.0

Fluorine binding site 10 out of 24 in the Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of PDE4D Catalytic Domain and Zardaverine Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:F3005 b:62.9 occ:1.00 F17 E:ZAR3005 0.0 62.9 1.0 C14 E:ZAR3005 1.4 61.8 1.0 F16 E:ZAR3005 2.2 62.5 1.0 O15 E:ZAR3005 2.3 62.4 1.0 C11 E:ZAR3005 3.1 62.9 1.0 C12 E:ZAR3005 3.2 64.0 1.0 N E:THR430 3.3 36.2 1.0 C E:TRP429 3.3 37.1 1.0 O E:TRP429 3.4 37.3 1.0 CA E:THR430 3.4 37.1 1.0 CG2 E:ILE433 3.6 37.2 1.0 CB E:TRP429 3.6 35.7 1.0 OD1 E:ASN418 3.7 28.6 1.0 CE1 E:TYR256 3.9 34.2 1.0 OG1 E:THR430 3.9 38.6 1.0 CB E:ILE433 4.0 39.0 1.0 CA E:TRP429 4.1 37.1 1.0 CB E:ASN418 4.3 31.1 1.0 CB E:THR430 4.3 37.2 1.0 CG E:ASN418 4.4 30.4 1.0 C10 E:ZAR3005 4.4 62.4 1.0 C13 E:ZAR3005 4.6 65.4 1.0 CD1 E:TYR256 4.6 34.0 1.0 C E:THR430 4.6 38.3 1.0 CZ E:TYR256 4.7 34.4 1.0 OH E:TYR256 4.7 36.0 1.0 CE1 E:TYR426 4.7 39.6 1.0 O E:TYR426 4.8 40.1 1.0 CG1 E:ILE433 4.8 38.5 1.0 OE1 E:GLN466 4.8 44.3 1.0 CG E:TRP429 4.9 34.8 1.0 O18 E:ZAR3005 4.9 60.7 1.0 CD1 E:TYR426 4.9 38.6 1.0 NE2 E:GLN466 4.9 46.1 1.0 O E:THR430 5.0 37.9 1.0

M.E.Lee, J.Markowitz, J.-O.Lee, H.Lee. Crystal Structure of Phosphodiesterase 4D and Inhibitor Complex Febs Lett. V. 530 53 2002.
ISSN: ISSN 0014-5793
PubMed: 12387865
DOI: 10.1016/S0014-5793(02)03396-3