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Sodium in PDB 5gjo: Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp

Enzymatic activity of Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp

All present enzymatic activity of Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp:
4.1.1.18;

Protein crystallography data

The structure of Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp, PDB code: 5gjo was solved by H.-Y.Sagong, K.-J.Kim, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.917, 122.859, 136.853, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp (pdb code 5gjo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp, PDB code: 5gjo:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 5gjo

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Sodium binding site 1 out of 4 in the Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:35.9
occ:1.00
NH1 A:ARG199 3.0 27.9 1.0
O A:HOH515 3.0 29.5 1.0
NH2 A:ARG199 3.3 25.4 1.0
O A:HOH797 3.3 34.1 1.0
CZ A:ARG199 3.5 23.9 1.0
CA A:GLU157 3.6 25.0 1.0
O A:VAL156 3.8 19.4 1.0
CB A:GLU157 3.9 32.3 1.0
N A:GLU157 3.9 20.9 1.0
C A:VAL156 4.0 20.2 1.0
CG2 A:VAL156 4.0 27.3 1.0
CD2 A:LEU200 4.1 19.3 1.0
O A:HOH653 4.2 18.9 1.0
OE2 A:GLU203 4.5 39.4 1.0
CB A:VAL156 4.6 23.4 1.0
C A:GLU157 4.8 22.3 1.0
NE A:ARG199 4.8 20.9 1.0
CA A:VAL156 5.0 19.4 1.0

Sodium binding site 2 out of 4 in 5gjo

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Sodium binding site 2 out of 4 in the Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na408

b:49.4
occ:1.00
OH A:TYR298 2.4 25.9 1.0
O B:SER356 2.8 14.8 1.0
CZ A:TYR298 3.1 23.6 1.0
CE2 A:TYR298 3.2 23.5 1.0
CG2 B:THR358 3.3 16.0 1.0
NA B:NA405 3.3 48.8 1.0
CB B:SER294 3.6 14.4 1.0
CE2 B:TYR298 3.8 25.7 1.0
C B:SER356 4.0 14.7 1.0
O B:TYR290 4.2 14.1 1.0
O B:ILE289 4.2 14.7 1.0
CE1 A:TYR298 4.3 18.4 1.0
OG B:SER294 4.4 17.2 1.0
CA B:TYR290 4.4 13.0 1.0
CG2 A:THR358 4.4 17.1 1.0
CD2 A:TYR298 4.5 20.1 1.0
CD2 B:TYR298 4.5 22.2 1.0
C B:TYR290 4.5 15.8 1.0
CB B:THR358 4.5 15.0 1.0
OG1 B:THR358 4.6 14.1 1.0
O A:SER356 4.6 12.2 1.0
CA B:SER294 4.7 14.9 1.0
CD1 B:TYR290 4.8 13.4 1.0
C B:ALA357 4.8 12.9 1.0
N B:THR358 4.8 14.0 1.0
CA B:ALA357 4.8 13.3 1.0
CZ B:TYR298 4.8 22.4 1.0
N B:ALA357 4.9 13.4 1.0
CB B:SER356 4.9 15.7 1.0
OH B:TYR298 4.9 23.4 1.0
CA B:SER356 4.9 14.8 1.0

Sodium binding site 3 out of 4 in 5gjo

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Sodium binding site 3 out of 4 in the Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na409

b:55.9
occ:1.00
OD2 A:ASP202 3.1 29.7 1.0
CA A:ARG199 3.6 20.1 1.0
CB A:ARG199 3.9 19.4 1.0
CG A:ASP202 4.0 27.3 1.0
O A:HOH503 4.1 37.2 1.0
CG A:ARG199 4.1 21.3 1.0
CB A:ASP202 4.2 23.0 1.0
N A:ARG199 4.3 20.1 1.0
O A:ARG198 4.5 20.0 1.0
C A:ARG198 4.6 19.6 1.0
C A:ARG199 4.7 18.4 1.0
O A:ARG199 4.7 17.1 1.0

Sodium binding site 4 out of 4 in 5gjo

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Sodium binding site 4 out of 4 in the Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Strcuture of Srldc Mutant (A225C/T302C) in Complex with Plp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na405

b:48.8
occ:1.00
OH B:TYR298 2.5 23.4 1.0
O A:SER356 2.8 12.2 1.0
CZ B:TYR298 3.2 22.4 1.0
CG2 A:THR358 3.2 17.1 1.0
CE2 B:TYR298 3.3 25.7 1.0
NA A:NA408 3.3 49.4 1.0
CB A:SER294 3.6 12.2 1.0
CE2 A:TYR298 3.8 23.5 1.0
C A:SER356 4.0 11.9 1.0
CG2 B:THR358 4.2 16.0 1.0
O A:TYR290 4.3 13.8 1.0
O A:ILE289 4.4 13.6 1.0
CE1 B:TYR298 4.4 16.7 1.0
OG A:SER294 4.4 13.3 1.0
CA A:TYR290 4.4 12.7 1.0
CD2 A:TYR298 4.5 20.1 1.0
CB A:THR358 4.5 15.6 1.0
CD2 B:TYR298 4.5 22.2 1.0
O B:SER356 4.5 14.8 1.0
C A:TYR290 4.6 14.5 1.0
OG1 A:THR358 4.7 15.6 1.0
C A:ALA357 4.7 12.5 1.0
CZ A:TYR298 4.7 23.6 1.0
OH A:TYR298 4.7 25.9 1.0
N A:THR358 4.7 13.2 1.0
CA A:ALA357 4.7 11.8 1.0
CB A:SER356 4.8 13.4 1.0
CD1 A:TYR290 4.8 14.8 1.0
CA A:SER294 4.8 12.6 1.0
N A:ALA357 4.8 11.2 1.0
CA A:SER356 4.9 12.4 1.0

Reference:

H.-Y.Sagong, K.-J.Kim. Lysine Decarboxylase with An Enhanced Affinity For Pyridoxal 5-Phosphate By Disulfide Bond-Mediated Spatial Reconstitution Plos One V. 12 70163 2017.
ISSN: ESSN 1932-6203
PubMed: 28095457
DOI: 10.1371/JOURNAL.PONE.0170163
Page generated: Tue Dec 15 11:01:40 2020

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