Magnesium in PDB 5k0k: Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434

Enzymatic activity of Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434

All present enzymatic activity of Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434:
2.7.10.1;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434, PDB code: 5k0k was solved by X.Wang, J.Liu, W.Zhang, M.A.Stashko, J.Nichols, D.Deryckere, M.J.Miley, J.Norris-Drouin, Z.Chen, M.Machius, E.Wood, D.K.Graham, H.S.Earp, K.Graham, D.Kireev, S.V.Frye, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	34.55 / 2.55
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	51.072, 91.315, 69.203, 90.00, 100.42, 90.00
*R / R_free (%)*	19.8 / 25.4

Other elements in 5k0k:

The structure of Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 also contains other interesting chemical elements:

Chlorine

(Cl)

6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 (pdb code 5k0k). 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 the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434, PDB code: 5k0k:

Magnesium binding site 1 out of 1 in 5k0k

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Magnesium Binding Sites List in 5k0k

Magnesium binding site 1 out of 1 in the Crystal Structure of the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434

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 the Catalytic Domain of the Proto-Oncogene Tyrosine-Protein Kinase Mer in Complex with Inhibitor UNC2434 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg903 b:50.0 occ:1.00	OD1	B:ASN728	2.2	66.0	0.7
	OD1	B:ASP741	2.3	49.7	1.0
	HB3	B:ASN728	3.2	73.4	0.3
	CG	B:ASN728	3.3	63.9	0.7
	CG	B:ASP741	3.3	50.7	1.0
	HD22	B:ASN728	3.7	78.3	0.7
	ND2	B:ASN728	3.9	65.2	0.7
	O21	B:6Q1904	4.0	60.0	1.0
	HA	B:ASN728	4.0	70.0	0.7
	HB2	B:ASP741	4.1	57.0	1.0
	HA	B:ASN728	4.1	68.7	0.3
	CB	B:ASN728	4.1	61.2	0.3
	OD2	B:ASP741	4.1	55.1	1.0
	CB	B:ASP741	4.2	47.5	1.0
	HB3	B:ASP741	4.3	57.0	1.0
	HG3	B:ARG727	4.3	56.9	1.0
	CB	B:ASN728	4.4	60.4	0.7
	HB2	B:ASN728	4.4	73.4	0.3
	HD21	B:ASN728	4.4	75.7	0.3
	HD2	B:ARG727	4.5	59.5	1.0
	C20	B:6Q1904	4.5	55.5	1.0
	HB3	B:ASN728	4.5	72.5	0.7
	O	B:ARG727	4.6	51.0	1.0
	CA	B:ASN728	4.6	57.2	0.3
	HE	B:ARG727	4.6	61.0	1.0
	CA	B:ASN728	4.6	58.3	0.7
	HD21	B:ASN728	4.7	78.3	0.7
	HB2	B:ARG727	4.7	54.9	1.0
	H221	B:6Q1904	4.8	68.0	1.0
	C	B:ARG727	4.9	53.0	1.0
	N	B:ASN728	4.9	55.9	0.3
	N	B:ASN728	4.9	55.9	0.7
	H191	B:6Q1904	4.9	65.2	1.0
	N19	B:6Q1904	5.0	54.4	1.0
	H171	B:6Q1904	5.0	59.4	1.0

Reference:

X.Wang, J.Liu, W.Zhang, M.A.Stashko, J.Nichols, M.J.Miley, J.Norris-Drouin, Z.Chen, M.Machius, D.Deryckere, E.Wood, D.K.Graham, H.S.Earp, D.Kireev, S.V.Frye. Design and Synthesis of Novel Macrocyclic Mer Tyrosine Kinase Inhibitors. Acs Med Chem Lett V. 7 1044 2016.
ISSN: ISSN 1948-5875
PubMed: 27994735
DOI: 10.1021/ACSMEDCHEMLETT.6B00221

Page generated: Sun Sep 29 18:04:00 2024

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