Sodium in PDB 2gn1: Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 2.2A Resolution (Triclinic Form with One Dimer of Tdcb in the Asymmetric Unit)

Enzymatic activity of Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 2.2A Resolution (Triclinic Form with One Dimer of Tdcb in the Asymmetric Unit)

All present enzymatic activity of Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 2.2A Resolution (Triclinic Form with One Dimer of Tdcb in the Asymmetric Unit):
4.3.1.19;

Protein crystallography data

The structure of Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 2.2A Resolution (Triclinic Form with One Dimer of Tdcb in the Asymmetric Unit), PDB code: 2gn1 was solved by D.K.Simanshu, H.S.Savithri, M.R.N.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	25.00 / 2.20
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	46.317, 55.300, 67.235, 103.09, 94.70, 112.94
*R / R_free (%)*	21 / 25.3

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 2.2A Resolution (Triclinic Form with One Dimer of Tdcb in the Asymmetric Unit) (pdb code 2gn1). 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 Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 2.2A Resolution (Triclinic Form with One Dimer of Tdcb in the Asymmetric Unit), PDB code: 2gn1:

Sodium binding site 1 out of 1 in 2gn1

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Sodium Binding Sites List in 2gn1

Sodium binding site 1 out of 1 in the Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 2.2A Resolution (Triclinic Form with One Dimer of Tdcb in the Asymmetric Unit)

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 Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 2.2A Resolution (Triclinic Form with One Dimer of Tdcb in the Asymmetric Unit) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na400 b:24.7 occ:1.00	O	A:ASP256	2.4	31.8	1.0
	O	A:HOH465	2.4	23.0	1.0
	O	A:HOH466	2.5	23.7	1.0
	OH	A:TYR220	2.5	32.6	1.0
	O	A:HOH550	2.5	28.1	1.0
	C	A:ASP256	3.4	32.2	1.0
	CZ	A:TYR220	3.6	32.9	1.0
	CE2	A:TYR220	4.0	32.4	1.0
	O	A:VAL255	4.2	32.6	1.0
	CA	A:ASP256	4.2	32.4	1.0
	N	A:ASP257	4.2	31.7	1.0
	CA	A:ASP257	4.3	32.1	1.0
	O	A:HOH504	4.3	30.1	1.0
	OD1	A:ASP257	4.3	37.0	1.0
	O	A:HOH479	4.6	45.3	1.0
	O	A:HOH484	4.6	25.9	1.0
	CE1	A:TYR220	4.8	32.3	1.0
	CB	A:ASP257	4.8	32.5	1.0

Reference:

D.K.Simanshu, H.S.Savithri, M.R.Murthy. Crystal Structures of Salmonella Typhimurium Biodegradative Threonine Deaminase and Its Complex with Cmp Provide Structural Insights Into Ligand-Induced Oligomerization and Enzyme Activation. J.Biol.Chem. V. 281 39630 2006.
ISSN: ISSN 0021-9258
PubMed: 17046821
DOI: 10.1074/JBC.M605721200

Page generated: Sun Aug 17 10:38:45 2025

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