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Zinc in PDB 6iag: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637, PDB code: 6iag was solved by A.K.Singh, D.G.Brown, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 84.50 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 99.108, 110.311, 160.722, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 24.6

Other elements in 6iag:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637 also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637 (pdb code 6iag). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637, PDB code: 6iag:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 6iag

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:29.2
occ:1.00
 OD2 A:ASP201 1.9 25.2 1.0
OD1 A:ASP318 2.1 30.0 1.0
NE2 A:HIS200 2.2 25.2 1.0
NE2 A:HIS164 2.2 24.1 1.0
O A:HOH634 2.3 19.8 1.0
O A:HOH690 2.3 29.3 1.0
CG A:ASP318 3.0 33.2 1.0
CG A:ASP201 3.0 22.2 1.0
CD2 A:HIS200 3.0 22.8 1.0
CD2 A:HIS164 3.1 24.5 1.0
OD2 A:ASP318 3.2 39.2 1.0
CE1 A:HIS164 3.2 26.5 1.0
CE1 A:HIS200 3.3 26.7 1.0
OD1 A:ASP201 3.5 22.6 1.0
O A:HOH703 3.6 25.3 1.0
MG A:MG502 3.7 19.4 1.0
O A:HOH742 4.0 42.9 1.0
O A:HOH644 4.1 35.5 1.0
CB A:ASP201 4.2 23.6 1.0
CD2 A:HIS160 4.2 28.4 1.0
CG A:HIS200 4.2 24.2 1.0
CG A:HIS164 4.3 25.3 1.0
ND1 A:HIS164 4.3 24.3 1.0
ND1 A:HIS200 4.4 23.6 1.0
CB A:ASP318 4.4 29.9 1.0
NE2 A:HIS160 4.5 29.3 1.0
O A:HOH629 4.6 23.2 1.0
CG2 A:VAL168 4.8 25.1 1.0
CA A:ASP318 5.0 29.3 1.0

Zinc binding site 2 out of 4 in 6iag

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:31.3
occ:1.00
 OD2 B:ASP201 2.0 31.2 1.0
NE2 B:HIS164 2.2 28.0 1.0
OD1 B:ASP318 2.2 28.3 1.0
NE2 B:HIS200 2.3 25.7 1.0
O B:HOH729 2.3 25.6 1.0
O B:HOH648 2.3 23.5 1.0
CG B:ASP318 3.0 27.1 1.0
CG B:ASP201 3.0 25.5 1.0
CD2 B:HIS164 3.1 27.7 1.0
CE1 B:HIS164 3.1 27.8 1.0
CD2 B:HIS200 3.2 26.2 1.0
OD2 B:ASP318 3.2 29.9 1.0
CE1 B:HIS200 3.2 26.4 1.0
OD1 B:ASP201 3.5 25.9 1.0
MG B:MG502 3.7 17.8 1.0
O B:HOH708 3.7 26.6 1.0
O B:HOH638 4.0 36.6 1.0
CB B:ASP201 4.2 29.4 1.0
CD2 B:HIS160 4.2 28.1 1.0
ND1 B:HIS164 4.3 26.9 1.0
CG B:HIS164 4.3 28.2 1.0
ND1 B:HIS200 4.3 25.1 1.0
CG B:HIS200 4.3 25.1 1.0
CB B:ASP318 4.4 26.9 1.0
O B:HOH623 4.6 20.6 1.0
NE2 B:HIS160 4.7 24.9 1.0
CG2 B:VAL168 4.8 25.4 1.0
O B:HOH701 4.9 21.0 1.0
CA B:ASP318 5.0 27.1 1.0

Zinc binding site 3 out of 4 in 6iag

Go back to Zinc Binding Sites List in 6iag
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:31.0
occ:1.00
 OD2 C:ASP201 2.0 26.5 1.0
OD1 C:ASP318 2.2 29.6 1.0
NE2 C:HIS200 2.2 25.8 1.0
O C:HOH680 2.2 27.7 1.0
NE2 C:HIS164 2.2 27.3 1.0
O C:HOH667 2.3 22.9 1.0
CG C:ASP201 3.0 22.1 1.0
CD2 C:HIS200 3.1 24.7 1.0
CG C:ASP318 3.1 30.3 1.0
CE1 C:HIS164 3.2 27.2 1.0
CD2 C:HIS164 3.2 26.7 1.0
CE1 C:HIS200 3.2 25.4 1.0
OD2 C:ASP318 3.4 31.9 1.0
OD1 C:ASP201 3.5 23.0 1.0
MG C:MG502 3.7 17.3 1.0
O C:HOH695 3.8 21.7 1.0
O C:HOH639 4.2 39.4 1.0
CD2 C:HIS160 4.2 24.4 1.0
CB C:ASP201 4.2 21.8 1.0
CG C:HIS200 4.2 24.5 1.0
ND1 C:HIS200 4.3 24.7 1.0
ND1 C:HIS164 4.3 24.0 1.0
CG C:HIS164 4.4 27.0 1.0
CB C:ASP318 4.5 29.7 1.0
NE2 C:HIS160 4.5 24.6 1.0
O C:HOH624 4.6 22.5 1.0
CG2 C:VAL168 4.8 26.0 1.0
CA C:ASP318 5.0 28.8 1.0
O C:HOH666 5.0 20.2 1.0

Zinc binding site 4 out of 4 in 6iag

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637


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 Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-637 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:26.1
occ:1.00
 OD2 D:ASP201 2.0 21.8 1.0
NE2 D:HIS200 2.1 20.8 1.0
OD1 D:ASP318 2.2 25.7 1.0
NE2 D:HIS164 2.2 24.3 1.0
O D:HOH742 2.3 25.3 1.0
O D:HOH659 2.3 20.7 1.0
CG D:ASP201 3.0 21.0 1.0
CG D:ASP318 3.0 25.0 1.0
CD2 D:HIS200 3.1 19.8 1.0
CD2 D:HIS164 3.2 21.8 1.0
CE1 D:HIS200 3.2 21.3 1.0
CE1 D:HIS164 3.2 21.7 1.0
OD2 D:ASP318 3.3 25.1 1.0
OD1 D:ASP201 3.5 19.0 1.0
O D:HOH740 3.7 24.4 1.0
MG D:MG502 3.7 15.5 1.0
O D:HOH720 4.1 31.0 1.0
CD2 D:HIS160 4.2 29.3 1.0
CG D:HIS200 4.2 19.9 1.0
CB D:ASP201 4.2 22.3 1.0
ND1 D:HIS200 4.3 18.1 1.0
CG D:HIS164 4.3 21.4 1.0
ND1 D:HIS164 4.3 20.0 1.0
CB D:ASP318 4.4 21.8 1.0
NE2 D:HIS160 4.6 29.8 1.0
O D:HOH613 4.6 17.9 1.0
CG2 D:VAL168 4.7 22.4 1.0
CA D:ASP318 5.0 21.9 1.0
O D:HOH692 5.0 21.8 1.0

Reference:

A.K.Singh, D.G.Brown. HPDE4D2 Structure with Inhibitor Npd-637 To Be Published.
Page generated: Mon Oct 28 23:37:22 2024

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