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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 / Rfree (%) 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

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