Magnesium in PDB 3brb: Crystal Structure of Catalytic Domain of the Proto-Oncogene Tyrosine- Protein Kinase Mer in Complex with Adp

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

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

Protein crystallography data

The structure of Crystal Structure of Catalytic Domain of the Proto-Oncogene Tyrosine- Protein Kinase Mer in Complex with Adp, PDB code: 3brb was solved by J.R.Walker, X.Huang, P.J.Finerty Jr, J.Weigelt, C.H.Arrowsmith, A.M.Edwards, A.Bochkarev, S.Dhe-Paganon, Structural Genomics Consortium(Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	25.05 / 1.90
*Space group*	P 1 2₁ 1
*Cell size a, b, c (Å), α, β, γ (°)*	53.385, 89.880, 69.537, 90.00, 103.09, 90.00
*R / R_free (%)*	19.2 / 24

Other elements in 3brb:

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

Chlorine

(Cl)

5 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Catalytic Domain of the Proto-Oncogene Tyrosine- Protein Kinase Mer in Complex with Adp (pdb code 3brb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Catalytic Domain of the Proto-Oncogene Tyrosine- Protein Kinase Mer in Complex with Adp, PDB code: 3brb:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3brb

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Magnesium Binding Sites List in 3brb

Magnesium binding site 1 out of 2 in the Crystal Structure of Catalytic Domain of the Proto-Oncogene Tyrosine- Protein Kinase Mer in Complex with Adp

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

probe	atom	residue	distance (Å)	B	Occ
A:Mg10 b:40.4 occ:1.00	O	A:HOH240	2.0	43.6	1.0
	O2B	A:ADP901	2.1	46.4	1.0
	OD2	A:ASP741	2.2	52.8	1.0
	O1A	A:ADP901	2.2	43.2	1.0
	OD1	A:ASN728	2.2	43.0	1.0
	O	A:HOH20	2.2	44.8	1.0
	PA	A:ADP901	3.3	47.6	1.0
	CG	A:ASN728	3.3	39.6	1.0
	PB	A:ADP901	3.3	50.3	1.0
	CG	A:ASP741	3.3	52.2	1.0
	O3A	A:ADP901	3.5	46.1	1.0
	NZ	A:LYS619	3.8	64.5	1.0
	ND2	A:ASN728	3.9	37.6	1.0
	CB	A:ASP741	3.9	44.3	1.0
	O1B	A:ADP901	4.0	50.7	1.0
	O5'	A:ADP901	4.1	49.6	1.0
	O	A:ARG727	4.2	33.9	1.0
	OD1	A:ASP741	4.3	56.9	1.0
	O2A	A:ADP901	4.4	48.8	1.0
	CB	A:ASN728	4.5	32.3	1.0
	O3B	A:ADP901	4.5	49.6	1.0
	O	A:HOH21	4.5	41.5	1.0
	CA	A:ASN728	4.6	33.7	1.0
	C	A:ARG727	4.9	32.8	1.0
	CE	A:LYS619	4.9	61.0	1.0
	CG	A:ARG727	5.0	39.8	1.0

Magnesium binding site 2 out of 2 in 3brb

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Magnesium Binding Sites List in 3brb

Magnesium binding site 2 out of 2 in the Crystal Structure of Catalytic Domain of the Proto-Oncogene Tyrosine- Protein Kinase Mer in Complex with Adp

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Catalytic Domain of the Proto-Oncogene Tyrosine- Protein Kinase Mer in Complex with Adp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
B:Mg9 b:41.2 occ:1.00	ND2	B:ASN728	2.0	36.7	1.0
	O	B:HOH238	2.1	49.3	1.0
	O2B	B:ADP901	2.1	49.0	1.0
	OD2	B:ASP741	2.1	51.9	1.0
	O	B:HOH239	2.1	46.9	1.0
	O1A	B:ADP901	2.2	42.2	1.0
	CG	B:ASN728	3.2	32.0	1.0
	CG	B:ASP741	3.3	50.1	1.0
	PB	B:ADP901	3.3	46.0	1.0
	PA	B:ADP901	3.3	42.1	1.0
	O3A	B:ADP901	3.5	44.6	1.0
	OD1	B:ASN728	3.7	43.5	1.0
	O	B:ARG727	3.8	28.0	0.5
	NZ	B:LYS619	3.9	58.5	1.0
	CB	B:ASP741	4.0	41.2	1.0
	NH2	B:ARG727	4.1	21.3	0.5
	O1B	B:ADP901	4.2	50.6	1.0
	OD1	B:ASP741	4.3	59.4	1.0
	O5'	B:ADP901	4.3	45.6	1.0
	CB	B:ASN728	4.3	34.7	1.0
	O3B	B:ADP901	4.4	52.0	1.0
	CA	B:ASN728	4.5	29.8	1.0
	O2A	B:ADP901	4.5	45.6	1.0
	O	B:ARG727	4.6	30.8	0.5
	C	B:ARG727	4.7	31.4	0.5
	O	B:HOH189	4.7	37.2	1.0
	CD	B:ARG727	4.7	23.2	0.5
	C	B:ARG727	4.9	30.2	0.5
	N	B:ASN728	5.0	31.4	1.0
	CE	B:LYS619	5.0	56.2	1.0

Reference:

X.Huang, P.Finerty, J.R.Walker, C.Butler-Cole, M.Vedadi, M.Schapira, S.A.Parker, B.E.Turk, D.A.Thompson, S.Dhe-Paganon. Structural Insights Into the Inhibited States of the Mer Receptor Tyrosine Kinase. J.Struct.Biol. V. 165 88 2009.
ISSN: ISSN 1047-8477
PubMed: 19028587
DOI: 10.1016/J.JSB.2008.10.003

Page generated: Wed Aug 14 09:18:26 2024

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