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Zinc in PDB 6lrm: Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin

Enzymatic activity of Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin

All present enzymatic activity of Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin, PDB code: 6lrm was solved by X.L.Zhang, M.J.Li, Y.C.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.42 / 1.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.879, 80.448, 163.733, 90, 90, 90
R / Rfree (%) 18.1 / 20.2

Other elements in 6lrm:

The structure of Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin (pdb code 6lrm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin, PDB code: 6lrm:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6lrm

Go back to Zinc Binding Sites List in 6lrm
Zinc binding site 1 out of 2 in the Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin


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 PDE4D Catalytic Domain in Complex with Arctigenin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:11.3
occ:1.00
OD1 A:ASP318 2.1 7.7 1.0
OD2 A:ASP201 2.1 6.8 1.0
O A:HOH632 2.1 7.8 1.0
O A:HOH742 2.1 9.1 1.0
NE2 A:HIS164 2.2 7.1 1.0
NE2 A:HIS200 2.2 6.8 1.0
CG A:ASP318 3.1 8.2 1.0
CD2 A:HIS200 3.1 6.7 1.0
CG A:ASP201 3.1 6.8 1.0
CE1 A:HIS164 3.2 7.2 1.0
CD2 A:HIS164 3.2 7.1 1.0
CE1 A:HIS200 3.3 6.9 1.0
OD2 A:ASP318 3.3 11.6 1.0
OD1 A:ASP201 3.6 6.9 1.0
MG A:MG502 3.7 6.8 1.0
O A:HOH769 3.8 9.1 1.0
O A:HOH704 4.1 12.2 1.0
ND1 A:HIS160 4.2 7.9 1.0
CB A:ASP201 4.3 6.8 1.0
CG A:HIS200 4.3 6.7 1.0
ND1 A:HIS164 4.3 7.3 1.0
CE1 A:HIS160 4.3 9.7 1.0
CG A:HIS164 4.3 7.3 1.0
ND1 A:HIS200 4.4 6.9 1.0
CB A:ASP318 4.4 7.3 1.0
O A:HOH631 4.7 8.9 1.0
CG2 A:VAL168 4.7 8.6 1.0
CE A:MET273 4.9 17.8 1.0
CA A:ASP318 4.9 7.5 1.0

Zinc binding site 2 out of 2 in 6lrm

Go back to Zinc Binding Sites List in 6lrm
Zinc binding site 2 out of 2 in the Crystal Structure of PDE4D Catalytic Domain in Complex with Arctigenin


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 PDE4D Catalytic Domain in Complex with Arctigenin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:14.6
occ:1.00
OD2 B:ASP201 2.0 11.4 1.0
O B:HOH617 2.1 11.2 1.0
OD2 B:ASP318 2.1 15.0 1.0
NE2 B:HIS164 2.2 12.5 1.0
O B:HOH681 2.2 11.5 1.0
NE2 B:HIS200 2.2 12.1 1.0
CG B:ASP201 3.1 11.1 1.0
CD2 B:HIS200 3.1 11.8 1.0
CG B:ASP318 3.1 13.8 1.0
CE1 B:HIS164 3.1 13.0 1.0
CD2 B:HIS164 3.2 12.6 1.0
CE1 B:HIS200 3.3 12.7 1.0
OD1 B:ASP318 3.3 11.8 1.0
OD1 B:ASP201 3.5 10.7 1.0
MG B:MG501 3.7 10.3 1.0
O B:HOH716 3.9 11.0 1.0
CD2 B:HIS160 4.2 11.2 1.0
O B:HOH674 4.2 14.4 1.0
CG B:HIS200 4.3 12.1 1.0
ND1 B:HIS164 4.3 13.3 1.0
CB B:ASP201 4.3 11.4 1.0
CG B:HIS164 4.3 13.2 1.0
NE2 B:HIS160 4.3 13.2 1.0
ND1 B:HIS200 4.3 12.7 1.0
CB B:ASP318 4.5 12.9 1.0
O B:HOH624 4.7 10.8 1.0
CG2 B:VAL168 4.7 14.1 1.0
CE B:MET273 4.9 20.1 1.0
CA B:ASP318 5.0 13.6 1.0

Reference:

H.Li, X.L.Zhang, M.T.Liu, C.L.Feng, C.Fan, H.X.Su, Y.Zhou, Q.Qi, Y.C.Xu, W.Tang. Identification of PDE4 As the Therapeutic Target of Arctigenin in Alleviating Psoriatic Skin Inflammation To Be Published.
Page generated: Sat Apr 17 17:39:56 2021

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