Magnesium in PDB 7cwa: Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine

Enzymatic activity of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine

All present enzymatic activity of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine:
3.1.4.53;

Protein crystallography data

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine, PDB code: 7cwa was solved by Y.Huang, X.-N.Wu, Q.Zhou, Y.Wu, H.-B.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	24.26 / 2.80
*Space group*	C 2 2 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	76.261, 132.246, 101.916, 90, 90, 90
*R / R_free (%)*	28.9 / 33.3

Other elements in 7cwa:

The structure of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine also contains other interesting chemical elements:

Zinc	(Zn)	1 atom
Chlorine	(Cl)	1 atom
Fluorine	(F)	1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine (pdb code 7cwa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine, PDB code: 7cwa:

Magnesium binding site 1 out of 1 in 7cwa

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Magnesium Binding Sites List in 7cwa

Magnesium binding site 1 out of 1 in the Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of PDE8A Catalytic Domain in Complex with Clofarabine within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg902 b:42.2 occ:1.00	O	A:HOH1023	2.0	30.1	1.0
	O	A:HOH1005	2.2	31.7	1.0
	O	A:HOH1040	2.4	28.6	1.0
	OE2	A:GLU626	2.6	31.0	1.0
	OD1	A:ASP597	3.4	29.0	1.0
	OG1	A:THR668	3.5	32.0	1.0
	CD	A:GLU626	3.8	30.7	1.0
	O	A:THR668	3.9	32.6	1.0
	O	A:HOH1006	4.0	25.7	1.0
	CB	A:THR668	4.0	32.0	1.0
	O	A:HOH1001	4.1	43.1	1.0
	ZN	A:ZN901	4.2	46.7	1.0
	CG	A:GLU626	4.2	30.6	1.0
	C	A:THR668	4.4	32.6	1.0
	CG	A:ASP597	4.4	29.2	1.0
	C5'	A:CFB903	4.7	33.1	1.0
	OD2	A:ASP726	4.8	25.9	1.0
	OD2	A:ASP597	4.8	29.6	1.0
	OE1	A:GLU626	4.8	30.6	1.0
	O	A:HIS596	4.9	29.2	1.0
	N	A:GLU669	4.9	33.3	1.0
	CA	A:THR668	4.9	32.1	1.0
	CD2	A:HIS629	5.0	31.1	1.0

Reference:

Y.Huang, X.Wu, Q.Zhou, H.-B.Luo. Discovery of Highly Selective and Orally Bioavailable Phosphodiesterase-8A Inhibitors. Structure-Activity Relationship, Crystal Structures, and in Vivo Studies To Be Published.

Page generated: Wed Oct 2 14:39:58 2024

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