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Nickel in PDB 6fet: Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439, PDB code: 6fet 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) 55.35 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 97.190, 110.710, 161.480, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.9

Other elements in 6fet:

The structure of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 also contains other interesting chemical elements:

Fluorine (F) 16 atoms
Magnesium (Mg) 4 atoms
Zinc (Zn) 4 atoms

Nickel Binding Sites:

The binding sites of Nickel atom in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 (pdb code 6fet). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 2 binding sites of Nickel where determined in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439, PDB code: 6fet:
Jump to Nickel binding site number: 1; 2;

Nickel binding site 1 out of 2 in 6fet

Go back to Nickel Binding Sites List in 6fet
Nickel binding site 1 out of 2 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ni525

b:41.0
occ:1.00
OD1 A:ASP156 2.1 40.8 1.0
O C:HOH604 2.3 28.6 1.0
ND1 A:HIS154 2.3 44.7 1.0
ND1 C:HIS154 2.5 49.7 1.0
O A:HOH744 2.5 40.9 1.0
CG A:ASP156 2.9 41.1 1.0
OD2 A:ASP156 2.9 39.9 1.0
CG A:HIS154 3.2 41.9 1.0
CE1 C:HIS154 3.3 50.2 1.0
CE1 A:HIS154 3.3 50.0 1.0
CG C:HIS154 3.4 48.7 1.0
CB A:HIS154 3.5 27.9 1.0
CB C:HIS154 3.8 37.4 1.0
OD1 C:ASP156 4.1 40.2 1.0
NE2 C:HIS154 4.3 53.3 1.0
CA A:HIS154 4.3 31.9 1.0
CB A:ASP156 4.3 35.1 1.0
CD2 A:HIS154 4.4 45.3 1.0
CD2 C:HIS154 4.4 47.1 1.0
NE2 A:HIS154 4.4 45.0 1.0
CA C:HIS154 4.5 35.0 1.0
N A:ASP156 4.7 35.3 1.0
CA A:ASP156 5.0 37.3 1.0
CG C:ASP156 5.0 42.7 1.0

Nickel binding site 2 out of 2 in 6fet

Go back to Nickel Binding Sites List in 6fet
Nickel binding site 2 out of 2 in the Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Human Phosphodiesterase 4D2 Catalytic Domain with Inhibitor Npd-1439 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ni527

b:29.8
occ:0.60
O D:HOH671 2.1 48.0 1.0
OD1 D:ASP156 2.1 36.0 1.0
O B:HOH628 2.3 32.1 1.0
ND1 D:HIS154 2.3 53.5 1.0
ND1 B:HIS154 2.4 51.8 1.0
OD2 D:ASP156 2.7 41.4 1.0
CG D:ASP156 2.8 39.2 1.0
CE1 B:HIS154 3.1 60.0 1.0
CG D:HIS154 3.3 44.1 1.0
CE1 D:HIS154 3.3 61.8 1.0
CB D:HIS154 3.5 34.0 1.0
CG B:HIS154 3.5 44.7 1.0
OD1 B:ASP156 4.0 37.9 1.0
CB B:HIS154 4.0 39.0 1.0
CB D:ASP156 4.3 33.0 1.0
NE2 B:HIS154 4.3 61.7 1.0
CD2 D:HIS154 4.4 48.1 1.0
NE2 D:HIS154 4.4 55.1 1.0
CA D:HIS154 4.5 32.5 1.0
CD2 B:HIS154 4.5 51.9 1.0
CA B:HIS154 4.5 35.5 1.0
N D:ASP156 4.7 30.7 1.0
CA D:ASP156 4.9 32.3 1.0
CG B:ASP156 5.0 39.2 1.0

Reference:

I.G.Salado, C.Moreno, G.Sakaine, A.K.Singh, A.R.Blaazer, M.Siderius, A.Matheeussen, S.Gul, L.Maes, R.Leurs, D.G.Brown, K.Augustyns. HPDE4D2 Structure with Inhibitor Npd-1439 To Be Published.
Page generated: Wed Dec 16 01:51:14 2020

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