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

Go back to

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

Go back to

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: Mon Oct 7 02:39:51 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1

	© Copyright 2008-2020 by atomistry.com
Home \| Site Map \| Copyright \| Contact us \| Privacy