Sodium in PDB 1pj5: Crystal Structure of Dimethylglycine Oxidase of Arthrobacter Globiformis in Complex with Acetate

Enzymatic activity of Crystal Structure of Dimethylglycine Oxidase of Arthrobacter Globiformis in Complex with Acetate

All present enzymatic activity of Crystal Structure of Dimethylglycine Oxidase of Arthrobacter Globiformis in Complex with Acetate:
1.5.3.10;

Protein crystallography data

The structure of Crystal Structure of Dimethylglycine Oxidase of Arthrobacter Globiformis in Complex with Acetate, PDB code: 1pj5 was solved by D.Leys, J.Basran, N.S.Scrutton, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	14.99 / 1.61
*Space group*	C 2 2 2
*Cell size a, b, c (Å), α, β, γ (°)*	71.381, 226.680, 120.661, 90.00, 90.00, 90.00
*R / R_free (%)*	16 / 19.8

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dimethylglycine Oxidase of Arthrobacter Globiformis in Complex with Acetate (pdb code 1pj5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Dimethylglycine Oxidase of Arthrobacter Globiformis in Complex with Acetate, PDB code: 1pj5:

Sodium binding site 1 out of 1 in 1pj5

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Sodium Binding Sites List in 1pj5

Sodium binding site 1 out of 1 in the Crystal Structure of Dimethylglycine Oxidase of Arthrobacter Globiformis in Complex with Acetate

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Dimethylglycine Oxidase of Arthrobacter Globiformis in Complex with Acetate within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na2001 b:13.4 occ:1.00	O	A:HOH2198	2.1	14.4	1.0
	OD2	A:ASP257	2.1	14.2	1.0
	O	A:HOH2237	2.1	15.4	1.0
	O	A:HOH2152	2.1	13.3	1.0
	O	A:VAL412	2.1	13.3	1.0
	O	A:HOH2147	2.2	12.7	1.0
	CG	A:ASP257	3.0	14.8	1.0
	C	A:VAL412	3.2	13.6	1.0
	OD1	A:ASP257	3.3	16.7	1.0
	OD1	A:ASP416	3.9	17.4	1.0
	CA	A:VAL412	3.9	12.5	1.0
	O	A:HOH2494	4.1	26.9	1.0
	O	A:HOH3092	4.1	30.7	1.0
	O	A:TYR272	4.1	13.3	1.0
	O	A:HOH2475	4.2	24.6	1.0
	O	A:PHE411	4.2	12.2	1.0
	N	A:GLU413	4.2	13.3	1.0
	O	A:HOH2215	4.3	20.1	1.0
	CB	A:ASP257	4.4	11.8	1.0
	CG1	A:VAL412	4.4	14.5	1.0
	O	A:HOH2639	4.5	27.0	1.0
	CA	A:GLU413	4.5	13.3	1.0
	N	A:ILE414	4.6	11.9	1.0
	C	A:GLU413	4.8	13.2	1.0
	CG	A:ASP416	4.8	17.9	1.0
	CB	A:VAL412	4.8	14.3	1.0
	CG2	A:ILE414	4.9	14.0	1.0
	O	A:HOH2351	5.0	23.2	1.0

Reference:

D.Leys, J.Basran, N.S.Scrutton. Channelling and Formation of 'Active' Formaldehyde in Dimethylglycine Oxidase. Embo J. V. 22 4038 2003.
ISSN: ISSN 0261-4189
PubMed: 12912903
DOI: 10.1093/EMBOJ/CDG395

Page generated: Sun Oct 6 21:19:02 2024

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