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Sodium in PDB 4riz: The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745

Enzymatic activity of The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745

All present enzymatic activity of The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745:
4.1.1.15;

Protein crystallography data

The structure of The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745, PDB code: 4riz was solved by R.Wu, S.Clancy, A.Joachimiak, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.58 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.411, 124.659, 131.849, 90.00, 99.42, 90.00
R / Rfree (%) 15.7 / 19.9

Sodium Binding Sites:

The binding sites of Sodium atom in the The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 (pdb code 4riz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745, PDB code: 4riz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 4riz

Go back to Sodium Binding Sites List in 4riz
Sodium binding site 1 out of 3 in the The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:19.0
occ:1.00
 O A:HOH686 2.9 26.4 1.0
O B:HOH629 2.9 25.5 1.0
O A:HOH685 2.9 18.9 1.0
O B:HOH603 3.2 23.9 1.0
CB B:HIS353 3.6 21.9 1.0
CB A:HIS353 3.7 25.4 1.0
O B:HOH625 3.7 18.4 1.0
O A:HOH829 3.8 20.4 1.0
OG1 B:THR311 3.8 31.5 1.0
OG1 A:THR311 3.8 26.0 1.0
CG B:HIS353 3.9 30.4 1.0
CG A:HIS353 3.9 25.9 1.0
ND1 B:HIS353 4.0 22.7 1.0
ND1 A:HIS353 4.1 19.6 1.0
OD1 B:ASP355 4.3 26.5 1.0
OD1 A:ASP355 4.3 26.5 1.0
OG B:SER149 4.5 23.7 1.0
OG A:SER149 4.5 19.7 1.0
CD2 B:HIS353 4.6 29.8 1.0
CD2 A:HIS353 4.6 21.1 1.0
CE1 B:HIS353 4.8 25.1 1.0
CE1 A:HIS353 4.9 19.0 1.0
N A:THR311 4.9 20.3 1.0
OD2 B:ASP355 5.0 22.6 1.0
OD2 A:ASP355 5.0 31.7 1.0
N B:THR311 5.0 21.4 1.0

Sodium binding site 2 out of 3 in 4riz

Go back to Sodium Binding Sites List in 4riz
Sodium binding site 2 out of 3 in the The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na504

b:59.0
occ:1.00
 O A:GLU171 2.3 33.7 1.0
NH2 B:ARG180 2.3 63.5 1.0
O B:LEU202 2.7 23.7 1.0
CA B:GLY203 3.2 21.8 1.0
N B:ALA206 3.2 31.0 1.0
C B:GLY203 3.2 31.8 1.0
O B:GLY203 3.3 32.5 1.0
N B:ALA205 3.3 26.1 1.0
C A:GLU171 3.4 31.7 1.0
C A:PRO172 3.5 30.3 1.0
CA A:PRO172 3.5 29.3 1.0
O A:PRO172 3.5 32.7 1.0
CB B:ALA205 3.5 24.2 1.0
CZ B:ARG180 3.6 59.8 1.0
C B:ALA205 3.6 29.4 1.0
CA B:ALA205 3.6 26.4 1.0
C B:LEU202 3.6 29.2 1.0
N B:GLY203 3.8 27.3 1.0
N B:THR204 3.9 27.5 1.0
CB B:ALA206 3.9 25.7 1.0
N A:PRO172 4.0 32.3 1.0
CA B:ALA206 4.0 27.4 1.0
N A:GLY173 4.1 29.8 1.0
C B:THR204 4.3 31.7 1.0
NE B:ARG180 4.3 60.0 1.0
NH1 B:ARG180 4.5 61.0 1.0
O B:ALA205 4.5 35.4 1.0
O B:HOH677 4.5 37.2 1.0
CA A:GLU171 4.7 34.6 1.0
CA B:THR204 4.7 27.8 1.0
CA A:GLY173 4.9 27.2 1.0
CB A:PRO172 4.9 30.1 1.0

Sodium binding site 3 out of 3 in 4riz

Go back to Sodium Binding Sites List in 4riz
Sodium binding site 3 out of 3 in the The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na503

b:75.3
occ:1.00
 NH2 D:ARG180 2.4 59.8 1.0
O C:GLU171 2.4 34.5 1.0
O D:LEU202 2.4 42.1 1.0
CA D:GLY203 2.9 31.1 1.0
C D:GLY203 3.0 36.5 1.0
O D:GLY203 3.1 39.0 1.0
N D:ALA206 3.2 40.1 1.0
C D:LEU202 3.3 39.6 1.0
C C:PRO172 3.4 35.4 1.0
N D:ALA205 3.4 42.1 1.0
O C:PRO172 3.4 38.6 1.0
N D:GLY203 3.5 33.1 1.0
C C:GLU171 3.5 41.9 1.0
CA C:PRO172 3.6 35.0 1.0
CB D:ALA205 3.6 35.0 1.0
CZ D:ARG180 3.6 60.7 1.0
CB D:ALA206 3.7 28.8 1.0
C D:ALA205 3.7 37.2 1.0
CA D:ALA205 3.8 38.4 1.0
N D:THR204 3.8 35.5 1.0
N C:GLY173 3.9 36.3 1.0
CA D:ALA206 3.9 37.2 1.0
N C:PRO172 4.1 33.5 1.0
NE D:ARG180 4.3 60.6 1.0
C D:THR204 4.3 40.8 1.0
O D:HOH725 4.4 37.0 1.0
O C:HOH2162 4.5 33.4 1.0
CA C:GLY173 4.6 36.2 1.0
NH1 D:ARG180 4.6 69.5 1.0
O D:ALA205 4.7 41.9 1.0
CA D:THR204 4.7 37.6 1.0
CA D:LEU202 4.7 35.8 1.0
CA C:GLU171 4.8 42.1 1.0

Reference:

R.Wu, S.Clancy, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). The Crystal Structure of Y333Q Mutant Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 To Be Published.
Page generated: Tue Dec 15 07:23:56 2020

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