Magnesium in PDB 2dy9: Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp

Enzymatic activity of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp

All present enzymatic activity of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp, PDB code: 2dy9 was solved by M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama, Rikenstructural Genomics/Proteomics Initiative (Rsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	34.92 / 2.01
*Space group*	P 6₃
*Cell size a, b, c (Å), α, β, γ (°)*	69.835, 69.835, 106.897, 90.00, 90.00, 120.00
*R / R_free (%)*	12.2 / 16.8

Other elements in 2dy9:

The structure of Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp (pdb code 2dy9). 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 Nucleoside Diphosphate Kinase in Complex with Adp, PDB code: 2dy9:

Magnesium binding site 1 out of 1 in 2dy9

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Magnesium Binding Sites List in 2dy9

Magnesium binding site 1 out of 1 in the Crystal Structure of Nucleoside Diphosphate Kinase 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 Nucleoside Diphosphate Kinase in Complex with Adp within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Mg601 b:26.0 occ:1.00	O	A:HOH735	2.3	12.9	1.0
	O1A	A:ADP501	2.3	31.1	1.0
	O	A:HOH774	2.4	13.1	1.0
	O1B	A:ADP501	2.5	28.9	1.0
	O	A:HOH732	2.6	11.5	1.0
	O	A:HOH764	3.6	33.9	1.0
	PB	A:ADP501	3.7	30.1	1.0
	PA	A:ADP501	3.7	30.0	1.0
	NH1	A:ARG91	4.1	22.9	1.0
	O3B	A:ADP501	4.1	30.1	1.0
	OE2	A:GLU57	4.1	28.8	1.0
	O3A	A:ADP501	4.2	32.4	1.0
	O	A:HOH736	4.2	14.0	1.0
	OD2	A:ASP127	4.3	13.4	1.0
	CE1	A:HIS124	4.4	13.3	1.0
	O	A:HOH730	4.5	14.2	1.0
	OE1	A:GLU57	4.5	29.7	1.0
	O	A:HOH766	4.5	16.7	1.0
	NE2	A:HIS58	4.5	20.4	1.0
	CD	A:GLU57	4.6	29.1	1.0
	C5'	A:ADP501	4.6	29.8	1.0
	O5'	A:ADP501	4.6	29.3	1.0
	O2A	A:ADP501	4.7	32.0	1.0
	NH2	A:ARG91	4.7	23.0	1.0
	CB	A:ASP127	4.8	15.9	1.0
	ND1	A:HIS124	4.8	13.3	1.0
	CG	A:ASP127	4.8	15.8	1.0
	CZ	A:ARG91	4.8	24.1	1.0
	O	A:ALA125	4.8	13.9	1.0
	O	A:HOH794	4.9	25.1	1.0
	O	A:HOH714	4.9	12.2	1.0

Reference:

M.Kato-Murayama, K.Murayama, T.Terada, M.Shirouzu, S.Yokoyama. Crystal Structure of Nucleoside Diphosphate Kinase in Complex with Adp To Be Published.

Page generated: Tue Aug 13 22:37:49 2024

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