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Sodium in PDB 8oyh: X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol

Enzymatic activity of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol

All present enzymatic activity of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol, PDB code: 8oyh was solved by S.O.Dahms, H.Brandstetter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.53 / 1.80
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.245, 131.245, 154.618, 90, 90, 120
R / Rfree (%) 17.4 / 18.8

Other elements in 8oyh:

The structure of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Calcium (Ca) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol (pdb code 8oyh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol, PDB code: 8oyh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 8oyh

Go back to Sodium Binding Sites List in 8oyh
Sodium binding site 1 out of 3 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:28.5
occ:1.00
 O A:SER311 2.3 25.4 1.0
OG1 A:THR314 2.4 25.6 1.0
O A:THR309 2.4 23.9 1.0
O A:HOH778 2.4 23.9 1.0
O A:THR314 2.4 26.7 1.0
HG1 A:THR314 2.8 30.8 1.0
HB2 A:SER316 3.0 33.4 1.0
C A:THR314 3.2 26.7 1.0
H A:THR314 3.3 30.7 1.0
H A:SER316 3.4 33.2 1.0
C A:THR309 3.4 26.5 1.0
C A:SER311 3.5 26.3 1.0
CB A:THR314 3.6 25.4 1.0
HA A:THR309 3.8 28.9 1.0
CA A:THR314 3.8 27.1 1.0
H A:SER311 3.8 31.3 1.0
O A:HOH839 3.8 34.1 1.0
N A:SER311 3.8 26.0 1.0
HE1 A:MET534 3.8 31.3 1.0
N A:SER316 3.9 27.6 1.0
CB A:SER316 3.9 27.8 1.0
N A:THR314 3.9 25.5 1.0
HE3 A:MET534 4.0 31.3 1.0
HE2 A:MET534 4.0 31.3 1.0
HB3 A:SER316 4.0 33.4 1.0
HB A:THR314 4.1 30.5 1.0
HB3 A:SER311 4.1 31.9 1.0
CE A:MET534 4.1 26.0 1.0
O A:TYR308 4.2 28.5 1.0
CA A:SER311 4.2 25.5 1.0
C A:ASN310 4.2 28.8 1.0
CA A:THR309 4.2 24.0 1.0
N A:LEU315 4.3 26.4 1.0
HA A:ILE312 4.3 31.1 1.0
HA A:LEU315 4.3 34.1 1.0
HB2 A:SER335 4.3 31.3 1.0
N A:ASN310 4.4 24.0 1.0
HA A:ASN310 4.4 30.2 1.0
O A:SER335 4.4 24.7 1.0
CA A:SER316 4.4 26.0 1.0
C A:LEU315 4.5 28.6 1.0
CA A:ASN310 4.6 25.1 1.0
N A:ILE312 4.6 25.6 1.0
CA A:LEU315 4.6 28.3 1.0
HG23 A:THR314 4.6 32.7 1.0
CB A:SER311 4.7 26.6 1.0
CG2 A:THR314 4.7 27.2 1.0
HA A:THR314 4.7 32.6 1.0
O A:ASN310 4.7 27.4 1.0
CA A:ILE312 4.8 25.8 1.0
HA A:SER316 4.8 31.3 1.0
C A:ILE312 4.8 26.1 1.0
H A:LEU315 5.0 31.8 1.0
HG21 A:THR314 5.0 32.7 1.0
OG A:SER316 5.0 29.8 1.0

Sodium binding site 2 out of 3 in 8oyh

Go back to Sodium Binding Sites List in 8oyh
Sodium binding site 2 out of 3 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:39.1
occ:1.00
 O A:SER279 2.3 33.7 1.0
O A:HOH992 2.4 41.9 1.0
O A:HOH1013 2.5 49.4 1.0
O A:HOH815 2.5 34.9 1.0
O A:GLY284 2.6 33.0 1.0
HA A:SER279 3.3 36.8 1.0
HA2 A:GLY284 3.3 42.3 1.0
C A:SER279 3.4 31.7 1.0
C A:GLY284 3.5 34.4 1.0
CA A:GLY284 3.7 35.2 1.0
HA3 A:GLY284 3.7 42.3 1.0
CA A:SER279 3.9 30.6 1.0
O A:HOH987 4.1 37.4 1.0
O A:VAL278 4.3 29.6 1.0
HA A:GLN280 4.3 40.5 1.0
HB3 A:SER279 4.4 37.3 1.0
O A:HOH1010 4.4 41.1 1.0
O A:HOH820 4.4 38.8 1.0
O A:HOH1000 4.4 45.1 1.0
N A:GLN280 4.6 32.5 1.0
N A:LEU285 4.7 33.9 1.0
CB A:SER279 4.7 31.0 1.0
HA A:LEU285 4.9 39.8 1.0
N A:SER279 5.0 27.8 1.0
CA A:GLN280 5.0 33.7 1.0

Sodium binding site 3 out of 3 in 8oyh

Go back to Sodium Binding Sites List in 8oyh
Sodium binding site 3 out of 3 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- Can-Tle-Can-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:31.2
occ:0.35
 O A:SER544 2.1 31.8 1.0
O A:HOH823 2.3 31.7 1.0
C A:SER544 3.1 29.8 1.0
HA3 A:GLY545 3.2 38.0 1.0
HB3 A:PRO508 3.5 38.6 1.0
HB2 A:PRO508 3.5 38.6 1.0
HB3 A:SER544 3.5 37.8 1.0
HG A:SER544 3.6 43.6 1.0
N A:GLY545 3.9 30.4 1.0
CA A:GLY545 3.9 31.6 1.0
CB A:PRO508 3.9 32.1 1.0
CA A:SER544 4.0 29.1 1.0
CB A:SER544 4.0 31.5 1.0
HA2 A:GLY545 4.2 38.0 1.0
OG A:SER544 4.2 36.3 1.0
H A:SER544 4.3 33.1 1.0
N A:SER544 4.4 27.6 1.0
HG2 A:PRO508 4.4 34.8 1.0
HB3 A:ASP542 4.5 36.4 1.0
O A:ASP542 4.5 29.4 1.0
H A:GLY545 4.7 36.5 1.0
CG A:PRO508 4.7 28.9 1.0
HA A:SER544 4.9 35.0 1.0
OD1 A:ASP542 4.9 30.8 1.0
HB2 A:SER544 5.0 37.8 1.0

Reference:

R.W.Lange, K.Bloch, M.R.Heindl, J.Wollenhaupt, M.S.Weiss, H.Brandstetter, G.Klebe, F.H.Falcone, E.Bottcher-Friebertshauser, S.O.Dahms, T.Steinmetzer. Fragment-Based Design, Synthesis, and Characterization of Aminoisoindole-Derived Furin Inhibitors. Chemmedchem 00057 2024.
ISSN: ESSN 1860-7187
PubMed: 38385828
DOI: 10.1002/CMDC.202400057
Page generated: Wed Oct 9 12:51:20 2024

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