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Sodium in PDB 4ym9: Crystal Structure of Porcine Pancreatic Elastase (Ppe) in Complex with the Novel Inhibitor JM102

Enzymatic activity of Crystal Structure of Porcine Pancreatic Elastase (Ppe) in Complex with the Novel Inhibitor JM102

All present enzymatic activity of Crystal Structure of Porcine Pancreatic Elastase (Ppe) in Complex with the Novel Inhibitor JM102:
3.4.21.36;

Protein crystallography data

The structure of Crystal Structure of Porcine Pancreatic Elastase (Ppe) in Complex with the Novel Inhibitor JM102, PDB code: 4ym9 was solved by S.Hofbauer, J.A.Brito, J.Mulchande, P.Nogly, M.Pessanha, R.Moreira, M.Archer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.41 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 51.026, 58.340, 74.923, 90.00, 90.00, 90.00
R / Rfree (%) 12.9 / 15.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Porcine Pancreatic Elastase (Ppe) in Complex with the Novel Inhibitor JM102 (pdb code 4ym9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Porcine Pancreatic Elastase (Ppe) in Complex with the Novel Inhibitor JM102, PDB code: 4ym9:

Sodium binding site 1 out of 1 in 4ym9

Go back to Sodium Binding Sites List in 4ym9
Sodium binding site 1 out of 1 in the Crystal Structure of Porcine Pancreatic Elastase (Ppe) in Complex with the Novel Inhibitor JM102


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Porcine Pancreatic Elastase (Ppe) in Complex with the Novel Inhibitor JM102 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1012

b:14.8
occ:1.00
 O A:GLN75 2.1 21.4 1.0
O A:HOH1233 2.2 26.9 1.0
O A:ASN72 2.3 15.9 1.0
OE1 A:GLU70 2.3 17.2 1.0
OE2 A:GLU80 2.3 24.1 1.0
O A:HOH1246 2.8 20.7 1.0
CD A:GLU70 3.1 15.4 1.0
OE2 A:GLU70 3.2 17.2 1.0
C A:GLN75 3.3 24.5 1.0
C A:ASN72 3.3 15.0 1.0
CD A:GLU80 3.4 20.5 1.0
CG A:GLU80 3.8 19.7 1.0
N A:ASN72 3.9 14.0 1.0
CA A:ASN76 3.9 28.2 1.0
O A:HOH1256 4.0 38.0 1.0
N A:ASN76 4.0 26.1 1.0
CA A:ASN72 4.1 13.6 1.0
N A:ASP77 4.1 28.4 1.0
N A:GLN75 4.2 22.5 1.0
CA A:GLN75 4.3 35.5 1.0
N A:LEU73 4.4 14.3 1.0
CB A:ASN72 4.4 18.4 1.0
OD2 A:ASP77 4.4 37.2 1.0
OE1 A:GLU80 4.5 16.6 1.0
N A:HIS71 4.5 14.0 1.0
CG A:GLU70 4.5 15.0 1.0
C A:ASN76 4.5 36.0 1.0
OH A:TYR82 4.6 25.3 1.0
CA A:LEU73 4.6 15.1 1.0
C A:LEU73 4.7 21.3 1.0
CG A:ASP77 4.8 38.6 1.0
CB A:ASP77 4.9 37.8 1.0
C A:HIS71 4.9 15.5 1.0

Reference:

E.F.Ruivo, L.M.Goncalves, L.A.Carvalho, R.C.Guedes, S.Hofbauer, J.A.Brito, M.Archer, R.Moreira, S.D.Lucas. Clickable 4-Oxo-Beta-Lactam-Based Selective Probing For Human Neutrophil Elastase Related Proteomes. Chemmedchem V. 11 2037 2016.
ISSN: ESSN 1860-7187
PubMed: 27465595
DOI: 10.1002/CMDC.201600258
Page generated: Sun Aug 17 22:38:40 2025

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