Magnesium in PDB 5byb: Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4:
2.7.4.21; 2.7.4.24;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4, PDB code: 5byb was solved by H.Wang, S.B.Shears, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	35.57 / 2.30
*Space group*	P 2₁ 2₁ 2₁
*Cell size a, b, c (Å), α, β, γ (°)*	88.807, 110.411, 41.423, 90.00, 90.00, 90.00
*R / R_free (%)*	18.9 / 24.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4 (pdb code 5byb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4, PDB code: 5byb:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 5byb

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Magnesium Binding Sites List in 5byb

Magnesium binding site 1 out of 3 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4

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 Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg403 b:10.7 occ:1.00	O	A:HOH583	2.0	6.3	1.0
	O1B	A:ADP401	2.1	11.2	1.0
	OD1	A:ASN323	2.2	10.8	1.0
	OD2	A:ASP321	2.2	10.9	1.0
	OD1	A:ASP321	2.2	10.8	1.0
	CG	A:ASP321	2.5	10.6	1.0
	CG	A:ASN323	3.1	11.0	1.0
	PB	A:ADP401	3.2	11.6	1.0
	O3B	A:ADP401	3.4	11.2	1.0
	O	A:HOH645	3.4	10.6	1.0
	ND2	A:ASN323	3.5	10.4	1.0
	MG	A:MG404	3.7	11.0	1.0
	CB	A:ASP321	4.1	10.6	1.0
	NH1	A:ARG134	4.1	13.8	1.0
	O	A:HOH593	4.2	28.6	1.0
	O3A	A:ADP401	4.2	11.7	1.0
	O2B	A:ADP401	4.3	11.9	1.0
	CE1	A:HIS194	4.3	13.1	1.0
	O	A:ALA191	4.4	16.2	1.0
	CB	A:ASN323	4.4	11.3	1.0
	O2A	A:ADP401	4.5	11.3	1.0
	ND1	A:HIS194	4.6	12.0	1.0
	O	A:HOH634	4.8	14.2	1.0
	PA	A:ADP401	4.9	12.1	1.0
	CA	A:ASN323	4.9	11.6	1.0
	NH2	A:ARG134	5.0	12.2	1.0

Magnesium binding site 2 out of 3 in 5byb

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Magnesium Binding Sites List in 5byb

Magnesium binding site 2 out of 3 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4

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 the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg404 b:11.0 occ:1.00	O	A:HOH525	2.1	8.5	1.0
	O3B	A:ADP401	2.1	11.2	1.0
	OD2	A:ASP309	2.1	11.0	1.0
	OD2	A:ASP321	2.2	10.9	1.0
	O2A	A:ADP401	2.2	11.3	1.0
	O	A:HOH645	2.2	10.6	1.0
	CG	A:ASP309	3.3	11.7	1.0
	CG	A:ASP321	3.3	10.6	1.0
	PB	A:ADP401	3.4	11.6	1.0
	PA	A:ADP401	3.6	12.1	1.0
	MG	A:MG403	3.7	10.7	1.0
	CB	A:ASP321	3.7	10.6	1.0
	OD1	A:ASP309	3.8	12.3	1.0
	NZ	A:LYS248	3.8	19.6	1.0
	O3A	A:ADP401	3.9	11.7	1.0
	O1B	A:ADP401	3.9	11.2	1.0
	ND2	A:ASN323	4.0	10.4	1.0
	OD1	A:ASP321	4.3	10.8	1.0
	O3'	A:ADP401	4.3	12.1	1.0
	C5'	A:ADP401	4.4	12.0	1.0
	CB	A:ASP309	4.5	11.4	1.0
	O5'	A:ADP401	4.5	12.0	1.0
	O2B	A:ADP401	4.6	11.9	1.0
	O1A	A:ADP401	4.7	11.2	1.0
	OD1	A:ASN323	4.7	10.8	1.0
	CG	A:ASN323	4.8	11.0	1.0
	CE	A:LYS248	4.8	18.7	1.0
	C3'	A:ADP401	4.9	12.2	1.0
	O	A:HOH640	5.0	46.9	1.0

Magnesium binding site 3 out of 3 in 5byb

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Magnesium Binding Sites List in 5byb

Magnesium binding site 3 out of 3 in the Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4

Mono view

Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of the Catalytic Domain of Human Diphosphoinositol Pentakisphosphate Kinase 2 (PPIP5K2) in Complex with Adp and 1,5- (Pa)2-IP4 within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg405 b:21.8 occ:1.00	O	A:SER68	2.2	21.8	1.0
	O	A:PHE70	2.2	21.5	1.0
	O	A:ILE73	2.2	20.0	1.0
	O	A:HOH664	2.4	16.0	1.0
	O	A:HOH684	2.7	35.5	1.0
	C	A:SER68	3.2	19.7	1.0
	C	A:PHE70	3.4	23.4	1.0
	C	A:ILE73	3.4	18.9	1.0
	CA	A:SER68	3.8	18.7	1.0
	N	A:ILE73	4.0	20.4	1.0
	N	A:PHE70	4.1	22.3	1.0
	CA	A:ILE73	4.1	18.4	1.0
	N	A:LYS71	4.3	24.4	1.0
	CA	A:PHE70	4.3	21.5	1.0
	OE1	A:GLN43	4.3	30.5	1.0
	N	A:LEU69	4.3	20.1	1.0
	O	A:LYS71	4.3	25.9	1.0
	C	A:LYS71	4.3	25.7	1.0
	C	A:LEU69	4.3	21.4	1.0
	CA	A:LYS71	4.4	26.4	1.0
	N	A:THR74	4.5	18.2	1.0
	CB	A:ILE73	4.5	17.8	1.0
	CB	A:SER68	4.5	18.9	1.0
	CA	A:LEU69	4.6	20.8	1.0
	O	A:ILE67	4.7	16.8	1.0
	CA	A:THR74	4.8	18.1	1.0
	N	A:TYR72	4.9	25.0	1.0
	CB	A:PHE70	4.9	21.1	1.0
	O	A:LEU69	4.9	21.7	1.0

Reference:

A.M.Riley, H.Wang, S.B.Shears, B.V.L Potter. Synthetic Tools For Studying the Chemical Biology of INSP8. Chem.Commun.(Camb.) V. 51 12605 2015.
ISSN: ESSN 1364-548X
PubMed: 26153667
DOI: 10.1039/C5CC05017K

Page generated: Sun Sep 29 01:46:52 2024

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