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Sodium in PDB 5gjp: Crystal Strcuture of Srldc in Complex with Plp and Cadaverine

Enzymatic activity of Crystal Strcuture of Srldc in Complex with Plp and Cadaverine

All present enzymatic activity of Crystal Strcuture of Srldc in Complex with Plp and Cadaverine:
4.1.1.18;

Protein crystallography data

The structure of Crystal Strcuture of Srldc in Complex with Plp and Cadaverine, PDB code: 5gjp 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 / 2.50
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 111.734, 111.734, 112.976, 90.00, 90.00, 120.00
R / Rfree (%) 19.8 / 27.9

Other elements in 5gjp:

The structure of Crystal Strcuture of Srldc in Complex with Plp and Cadaverine also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Strcuture of Srldc in Complex with Plp and Cadaverine (pdb code 5gjp). 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 Strcuture of Srldc in Complex with Plp and Cadaverine, PDB code: 5gjp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5gjp

Go back to Sodium Binding Sites List in 5gjp
Sodium binding site 1 out of 2 in the Crystal Strcuture of Srldc in Complex with Plp and Cadaverine


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 in Complex with Plp and Cadaverine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na406

b:47.6
occ:1.00
OE2 A:GLU348 3.7 54.0 1.0
OG1 A:THR347 3.8 33.1 1.0
NE2 A:HIS306 3.9 60.8 1.0
CE1 A:HIS306 4.1 58.5 1.0
CG A:ARG5 4.2 60.5 1.0
OE1 A:GLU348 4.2 70.3 1.0
CB A:THR347 4.3 32.0 1.0
CD A:GLU348 4.4 60.9 1.0
CG2 A:THR347 4.4 35.4 1.0
OD1 A:ASN3 4.5 74.7 1.0
NE A:ARG5 4.6 65.1 1.0
CB A:ASN3 4.9 55.7 1.0
CD A:ARG5 5.0 64.3 1.0

Sodium binding site 2 out of 2 in 5gjp

Go back to Sodium Binding Sites List in 5gjp
Sodium binding site 2 out of 2 in the Crystal Strcuture of Srldc in Complex with Plp and Cadaverine


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 in Complex with Plp and Cadaverine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na407

b:54.0
occ:1.00
C A:LEU83 4.0 42.7 1.0
O A:LEU83 4.1 47.5 1.0
O A:GLU82 4.2 40.2 1.0
N A:GLY84 4.3 43.3 1.0
CA A:GLY84 4.5 41.9 1.0
CA A:LEU83 4.5 39.6 1.0

Reference:

H.-Y.Sagong, H.F.Son, S.Kim, Y.-H.Kim, I.-K.Kim, K.-J.Kim. Crystal Structure and Pyridoxal 5-Phosphate Binding Property of Lysine Decarboxylase From Selenomonas Ruminantium Plos One V. 11 66667 2016.
ISSN: ESSN 1932-6203
PubMed: 27861532
DOI: 10.1371/JOURNAL.PONE.0166667
Page generated: Tue Dec 15 11:01:41 2020

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