Sodium in PDB 2gn0: Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation)

Enzymatic activity of Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation)

All present enzymatic activity of Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation):
4.3.1.19;

Protein crystallography data

The structure of Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation), PDB code: 2gn0 was solved by D.K.Simanshu, H.S.Savithri, M.R.Murthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

*Resolution Low / High (Å)*	20.00 / 1.70
*Space group*	P 1
*Cell size a, b, c (Å), α, β, γ (°)*	56.675, 76.827, 78.501, 66.12, 89.16, 77.08
*R / R_free (%)*	18.8 / 22.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation) (pdb code 2gn0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation), PDB code: 2gn0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 2gn0

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Sodium Binding Sites List in 2gn0

Sodium binding site 1 out of 2 in the Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation)

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 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
A:Na800 b:19.0 occ:0.80	O	A:ASP256	2.3	21.9	0.8
	O	A:HOH802	2.4	22.5	0.8
	O	A:HOH801	2.4	22.5	0.8
	O	A:HOH803	2.4	17.2	0.8
	OH	A:TYR220	2.4	19.4	0.8
	C	A:ASP256	3.3	22.8	0.8
	CZ	A:TYR220	3.6	19.0	0.8
	CE2	A:TYR220	3.9	20.1	0.8
	N	A:ASP257	4.1	22.8	0.8
	CA	A:ASP256	4.2	22.9	0.8
	CA	A:ASP257	4.2	23.6	0.8
	O	A:VAL255	4.2	21.7	0.8
	O	A:HOH1058	4.3	31.0	0.8
	O	A:HOH837	4.4	31.5	0.8
	OD1	A:ASP257	4.5	28.9	0.8
	O	A:HOH1040	4.5	33.6	0.8
	O	A:HOH827	4.5	20.3	0.8
	CB	A:ASP257	4.7	23.7	0.8
	CE1	A:TYR220	4.8	19.9	0.8
	CG	A:ASP257	5.0	26.3	0.8

Sodium binding site 2 out of 2 in 2gn0

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Sodium Binding Sites List in 2gn0

Sodium binding site 2 out of 2 in the Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation)

Mono view

Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Dimeric Biodegradative Threonine Deaminase (Tdcb) From Salmonella Typhimurium at 1.7 A Resolution (Triclinic Form with One Complete Subunit Built in Alternate Conformation) within 5.0Å range:

probe	atom	residue	distance (Å)	B	Occ
C:Na801 b:17.9 occ:0.80	O	C:ASP256	2.3	21.3	0.8
	O	B:ARG229	2.3	19.1	0.8
	O	B:HOH338	2.3	16.7	0.8
	O	C:HOH815	2.4	18.5	0.8
	OH	C:TYR220	2.4	21.2	0.8
	O	C:HOH983	2.5	22.8	0.8
	C	C:ASP256	3.3	21.9	0.8
	C	B:ARG229	3.4	19.0	0.8
	CZ	C:TYR220	3.6	21.5	0.8
	N	B:ARG229	3.9	19.4	0.8
	CE2	C:TYR220	3.9	21.5	0.8
	N	C:ASP257	4.1	22.2	0.8
	CA	C:ASP257	4.2	22.4	0.8
	O	C:VAL255	4.2	21.4	0.8
	CA	C:ASP256	4.2	22.3	0.8
	CA	B:ARG229	4.2	19.4	0.8
	O	C:HOH871	4.3	34.4	0.8
	N	B:THR230	4.4	19.6	0.8
	O	B:HOH363	4.5	27.2	0.8
	O	C:HOH819	4.5	20.2	0.8
	O	B:HOH393	4.5	27.9	0.8
	O	C:HOH839	4.6	33.5	0.8
	CA	B:THR230	4.6	19.7	0.8
	OD1	C:ASP257	4.6	25.0	0.8
	CB	C:ASP257	4.7	22.6	0.8
	CE1	C:TYR220	4.7	19.3	0.8
	CG2	B:THR230	4.8	20.7	0.8
	CB	B:ARG229	4.9	19.5	0.8
	C	B:HIS228	5.0	19.1	0.8

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: Tue Dec 15 05:50:00 2020

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