Chlorine in PDB 4rit: The Yellow Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745

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

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

Protein crystallography data

The structure of The Yellow Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745, PDB code: 4rit 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) 39.59 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 77.483, 118.566, 126.018, 90.00, 90.00, 90.00
R / Rfree (%) 15 / 17.3

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 3 in 4rit

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Chlorine binding site 1 out of 3 in the The Yellow Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Yellow Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:31.6
occ:1.00
O B:HOH709 3.2 26.1 1.0
N B:LEU397 3.3 20.6 1.0
NE B:ARG396 3.7 33.9 0.5
CA B:ARG396 3.8 21.0 0.5
CA B:ARG396 3.8 21.0 0.5
CG B:LEU397 3.9 25.1 1.0
C B:ARG396 4.0 21.6 0.5
CB B:LEU397 4.0 22.0 1.0
C B:ARG396 4.0 21.5 0.5
CG B:ARG396 4.1 36.5 0.5
O B:LEU395 4.2 23.3 1.0
CD1 B:LEU397 4.2 29.5 1.0
CA B:LEU397 4.2 21.2 1.0
CG1 B:VAL389 4.4 22.1 1.0
NH1 B:ARG396 4.4 44.2 0.5
CD B:ARG396 4.4 31.7 0.5
CB B:ARG396 4.5 24.3 0.5
CB B:ARG396 4.5 24.4 0.5
CZ B:ARG396 4.5 38.6 0.5
CD B:ARG396 4.6 47.6 0.5
CA B:ARG390 4.6 25.6 1.0
CG B:ARG390 4.6 30.4 1.0
O B:VAL389 4.8 23.1 1.0
N B:ARG396 4.8 20.4 0.5
N B:ARG396 4.8 20.3 0.5
O B:LEU397 4.9 21.3 1.0
C B:LEU395 4.9 22.4 1.0
N B:ARG390 5.0 21.7 1.0

Chlorine binding site 2 out of 3 in 4rit

Go back to Chlorine Binding Sites List in 4rit
Chlorine binding site 2 out of 3 in the The Yellow Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Yellow Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:30.5
occ:1.00
O A:HOH643 2.8 25.5 1.0
O A:HOH686 2.9 30.3 1.0
O B:HOH616 2.9 22.4 1.0
O B:HOH661 3.1 29.8 1.0
CB A:HIS353 3.7 22.8 1.0
O B:HOH621 3.8 21.3 1.0
CB B:HIS353 3.8 23.8 1.0
OG1 B:THR311 3.9 25.5 1.0
CG A:HIS353 3.9 22.4 1.0
OG1 A:THR311 3.9 25.4 1.0
O B:HOH631 3.9 24.2 1.0
ND1 A:HIS353 4.0 21.4 1.0
CG B:HIS353 4.0 24.2 1.0
ND1 B:HIS353 4.1 25.0 1.0
OD1 A:ASP355 4.3 25.4 1.0
OD1 B:ASP355 4.4 22.4 1.0
OG A:SER149 4.5 20.6 1.0
OG B:SER149 4.6 21.0 1.0
CD2 A:HIS353 4.6 24.0 1.0
CD2 B:HIS353 4.8 24.5 1.0
CE1 A:HIS353 4.8 22.8 1.0
OD2 A:ASP355 4.9 27.0 1.0
CE1 B:HIS353 4.9 24.6 1.0
N B:THR311 5.0 16.0 1.0

Chlorine binding site 3 out of 3 in 4rit

Go back to Chlorine Binding Sites List in 4rit
Chlorine binding site 3 out of 3 in the The Yellow Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Yellow Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:45.4
occ:1.00
N A:LEU397 3.2 30.8 1.0
O A:HOH762 3.5 43.6 1.0
CB A:LEU397 3.7 30.8 1.0
CA A:ARG396 3.8 38.0 1.0
CG A:LEU397 3.9 34.7 1.0
C A:ARG396 4.0 34.3 1.0
CA A:LEU397 4.0 29.1 1.0
CG A:ARG396 4.2 41.3 1.0
O A:LEU395 4.3 43.5 1.0
CD1 A:LEU397 4.3 39.9 1.0
CG1 A:VAL389 4.5 31.3 1.0
CB A:ARG396 4.5 39.4 1.0
O A:LEU397 4.7 28.2 1.0
C A:LEU397 4.9 27.0 1.0
N A:ARG396 4.9 30.3 1.0
CG A:ARG390 4.9 42.1 1.0

Reference:

R.Wu, S.Clancy, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). The Yellow Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 To Be Published.
Page generated: Sat Dec 12 11:11:34 2020

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