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Potassium in PDB 4rlg: The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745

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

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

Protein crystallography data

The structure of The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745, PDB code: 4rlg 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) 39.70 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.320, 124.981, 132.760, 90.00, 99.49, 90.00
R / Rfree (%) 16.2 / 19.1

Potassium Binding Sites:

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

Potassium binding site 1 out of 4 in 4rlg

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Potassium binding site 1 out of 4 in the The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2003

b:44.4
occ:1.00
 O A:VAL389 2.7 42.9 1.0
O A:LEU395 2.7 41.7 1.0
O A:ARG392 2.8 50.2 1.0
O A:HOH2276 3.2 41.4 1.0
C A:ARG392 3.6 42.2 1.0
C A:VAL389 3.7 43.4 1.0
O A:ARG390 3.8 47.3 1.0
C A:LEU395 3.9 40.4 1.0
CA A:ARG390 4.0 44.7 1.0
C A:ARG390 4.1 44.9 1.0
CA A:PRO393 4.1 46.1 1.0
O A:HOH2185 4.1 40.1 1.0
CG1 A:VAL389 4.2 36.2 1.0
N A:ARG390 4.2 45.8 1.0
N A:PRO393 4.3 47.0 1.0
N A:ARG392 4.4 40.9 1.0
C A:PRO393 4.5 43.1 1.0
N A:LEU395 4.6 48.9 1.0
CA A:ARG392 4.6 36.6 1.0
O A:PRO393 4.6 50.3 1.0
CA A:LEU395 4.6 44.2 1.0
CB A:LEU395 4.7 38.1 1.0
CA A:VAL389 4.8 35.8 1.0
N A:ARG396 4.8 36.8 1.0
CA A:ARG396 4.9 35.6 1.0
N A:GLN391 4.9 46.3 1.0

Potassium binding site 2 out of 4 in 4rlg

Go back to Potassium Binding Sites List in 4rlg
Potassium binding site 2 out of 4 in the The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:38.1
occ:1.00
 O B:LEU395 2.6 32.1 1.0
O B:VAL389 2.7 35.3 1.0
O B:ARG392 2.7 35.6 1.0
O B:HOH805 3.2 39.8 1.0
C B:ARG392 3.6 35.0 1.0
C B:LEU395 3.7 30.7 1.0
C B:VAL389 3.8 31.8 1.0
O B:ARG390 4.0 42.1 1.0
O B:HOH700 4.0 29.4 1.0
CA B:ARG390 4.0 37.4 1.0
C B:ARG390 4.2 36.0 1.0
CG1 B:VAL389 4.2 25.1 1.0
CA B:PRO393 4.2 33.9 1.0
N B:PRO393 4.3 36.8 1.0
N B:ARG392 4.3 31.5 1.0
N B:ARG390 4.4 35.0 1.0
O B:PRO393 4.5 35.8 1.0
C B:PRO393 4.5 37.0 1.0
CA B:ARG392 4.5 31.3 1.0
CA B:LEU395 4.5 29.5 1.0
N B:LEU395 4.6 33.8 1.0
CB B:LEU395 4.6 27.9 1.0
N B:ARG396 4.7 33.0 1.0
CA B:ARG396 4.8 30.6 1.0
CA B:VAL389 4.9 26.1 1.0

Potassium binding site 3 out of 4 in 4rlg

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Potassium binding site 3 out of 4 in the The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K505

b:49.6
occ:1.00
 O D:LEU395 2.6 51.6 1.0
O D:VAL389 2.7 48.9 1.0
O D:ARG392 3.0 52.6 1.0
O D:ARG390 3.5 67.0 1.0
C D:ARG392 3.6 51.9 1.0
C D:VAL389 3.7 50.0 1.0
O D:HOH815 3.8 44.4 1.0
C D:LEU395 3.8 52.2 1.0
C D:ARG390 4.0 59.4 1.0
CA D:ARG390 4.0 51.7 1.0
CA D:PRO393 4.1 43.5 1.0
N D:PRO393 4.2 48.0 1.0
CG1 D:VAL389 4.2 39.7 1.0
N D:ARG392 4.2 45.9 1.0
N D:ARG390 4.3 44.9 1.0
C D:PRO393 4.5 46.9 1.0
CA D:ARG392 4.5 47.3 1.0
N D:LEU395 4.6 46.5 1.0
CA D:LEU395 4.6 49.7 1.0
O D:PRO393 4.6 49.9 1.0
CB D:LEU395 4.6 40.9 1.0
N D:ARG396 4.8 44.4 1.0
CA D:ARG396 4.8 45.1 1.0
CA D:VAL389 4.9 43.0 1.0

Potassium binding site 4 out of 4 in 4rlg

Go back to Potassium Binding Sites List in 4rlg
Potassium binding site 4 out of 4 in the The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:40.1
occ:1.00
 O C:LEU395 2.6 32.2 1.0
O C:VAL389 2.7 33.0 1.0
O C:ARG392 2.8 42.1 1.0
C C:ARG392 3.6 38.1 1.0
C C:VAL389 3.8 37.1 1.0
C C:LEU395 3.8 34.3 1.0
O C:ARG390 3.8 50.4 1.0
O C:HOH709 4.0 33.6 1.0
CA C:ARG390 4.0 37.1 1.0
C C:ARG390 4.1 49.3 1.0
CA C:PRO393 4.2 36.7 1.0
N C:PRO393 4.2 39.7 1.0
O C:PRO393 4.2 47.6 1.0
N C:ARG392 4.3 36.8 1.0
C C:PRO393 4.3 37.5 1.0
N C:ARG390 4.3 30.3 1.0
CG1 C:VAL389 4.4 27.6 1.0
N C:LEU395 4.4 37.1 1.0
CA C:LEU395 4.5 36.6 1.0
CA C:ARG392 4.5 33.5 1.0
CB C:LEU395 4.6 33.9 1.0
N C:ARG396 4.8 32.4 1.0
CA C:ARG396 4.8 32.3 1.0
N C:GLN391 4.9 43.8 1.0
CA C:VAL389 4.9 30.7 1.0

Reference:

R.Wu, S.Clancy, A.Joachimiak, Midwest Center For Structural Genomics (Mcsg). The Clear Crystal Structure of Pyridoxal-Dependent Decarboxylase From Sphaerobacter Thermophilus Dsm 20745 To Be Published.
Page generated: Sat Aug 9 07:48:23 2025

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