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Sodium in PDB 8b4x: X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- R-Tle-K-6-(Aminomethyl)-3-Amino-Isoindol

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

All present enzymatic activity of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- R-Tle-K-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- R-Tle-K-6-(Aminomethyl)-3-Amino-Isoindol, PDB code: 8b4x 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) 46.06 / 1.60
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.049, 132.049, 155.492, 90, 90, 120
R / Rfree (%) 15.8 / 17

Other elements in 8b4x:

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

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

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- R-Tle-K-6-(Aminomethyl)-3-Amino-Isoindol (pdb code 8b4x). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- R-Tle-K-6-(Aminomethyl)-3-Amino-Isoindol, PDB code: 8b4x:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 8b4x

Go back to Sodium Binding Sites List in 8b4x
Sodium binding site 1 out of 4 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- R-Tle-K-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- R-Tle-K-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:19.0
occ:1.00
 O A:SER311 2.3 18.5 1.0
O A:THR309 2.3 19.1 1.0
O A:HOH863 2.4 18.2 1.0
OG1 A:THR314 2.4 18.5 1.0
O A:THR314 2.4 18.9 1.0
HG1 A:THR314 2.8 22.3 1.0
HB2 A:SER316 3.1 23.7 1.0
C A:THR314 3.3 19.5 1.0
H A:THR314 3.3 21.0 1.0
C A:THR309 3.4 19.8 1.0
H A:SER316 3.4 23.6 1.0
C A:SER311 3.5 19.1 1.0
CB A:THR314 3.6 18.1 1.0
HA A:THR309 3.7 21.2 1.0
HE1 A:MET534 3.8 24.0 1.0
CA A:THR314 3.8 17.9 1.0
O A:HOH800 3.8 28.9 1.0
H A:SER311 3.8 22.0 1.0
N A:SER311 3.9 18.3 1.0
HE3 A:MET534 3.9 24.0 1.0
N A:SER316 3.9 19.6 1.0
N A:THR314 3.9 17.5 1.0
CB A:SER316 3.9 19.7 1.0
HB3 A:SER316 3.9 23.7 1.0
HE2 A:MET534 4.0 24.0 1.0
HB3 A:SER311 4.0 24.0 1.0
HB A:THR314 4.1 21.8 1.0
CE A:MET534 4.1 19.9 1.0
O A:TYR308 4.2 20.6 1.0
CA A:SER311 4.2 17.7 1.0
CA A:THR309 4.2 17.6 1.0
C A:ASN310 4.2 18.2 1.0
HA A:ILE312 4.2 20.2 1.0
HA A:LEU315 4.3 26.3 1.0
N A:LEU315 4.3 19.1 1.0
N A:ASN310 4.3 18.7 1.0
HB2 A:SER335 4.3 22.5 1.0
HA A:ASN310 4.4 22.8 1.0
CA A:SER316 4.5 17.9 1.0
O A:SER335 4.5 19.5 1.0
C A:LEU315 4.6 22.2 1.0
N A:ILE312 4.6 17.0 1.0
CA A:ASN310 4.6 18.9 1.0
CA A:LEU315 4.6 21.8 1.0
CB A:SER311 4.6 19.9 1.0
HG23 A:THR314 4.7 22.8 1.0
O A:ASN310 4.7 20.9 1.0
CG2 A:THR314 4.7 18.9 1.0
HA A:THR314 4.7 21.6 1.0
CA A:ILE312 4.7 16.8 1.0
C A:ILE312 4.8 19.1 1.0
HA A:SER316 4.8 21.5 1.0
HG21 A:THR314 5.0 22.8 1.0

Sodium binding site 2 out of 4 in 8b4x

Go back to Sodium Binding Sites List in 8b4x
Sodium binding site 2 out of 4 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- R-Tle-K-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- R-Tle-K-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:32.1
occ:1.00
 O A:HOH1064 2.3 40.7 1.0
O A:SER279 2.4 25.2 1.0
O A:HOH839 2.4 27.5 1.0
O A:HOH1105 2.4 46.1 1.0
O A:GLY284 2.6 25.6 1.0
HA2 A:GLY284 3.3 31.8 1.0
HA A:SER279 3.4 24.4 1.0
C A:SER279 3.5 25.7 1.0
C A:GLY284 3.5 22.5 1.0
HA3 A:GLY284 3.8 31.8 1.0
CA A:GLY284 3.8 26.5 1.0
CA A:SER279 3.9 20.2 1.0
O A:HOH1068 4.1 35.4 1.0
O A:VAL278 4.3 22.1 1.0
O A:HOH1073 4.4 41.2 1.0
O A:HOH1094 4.4 40.1 1.0
HA A:GLN280 4.4 30.4 1.0
O A:HOH771 4.5 36.6 1.0
HB3 A:SER279 4.5 29.9 1.0
N A:GLN280 4.6 25.1 1.0
N A:LEU285 4.7 21.8 1.0
CB A:SER279 4.8 24.8 1.0
HA A:LEU285 4.9 28.3 1.0

Sodium binding site 3 out of 4 in 8b4x

Go back to Sodium Binding Sites List in 8b4x
Sodium binding site 3 out of 4 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- R-Tle-K-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- R-Tle-K-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:26.8
occ:0.32
 O A:SER544 2.1 22.3 1.0
O A:HOH911 2.3 22.9 1.0
C A:SER544 3.1 22.8 1.0
HA3 A:GLY545 3.2 27.9 1.0
HB3 A:SER544 3.3 29.3 1.0
HB3 A:PRO508 3.5 29.5 1.0
HG A:SER544 3.6 37.2 1.0
HB2 A:PRO508 3.6 29.5 1.0
N A:GLY545 3.9 23.4 1.0
CA A:GLY545 3.9 23.2 1.0
CB A:SER544 3.9 24.4 1.0
CA A:SER544 4.0 21.0 1.0
CB A:PRO508 4.0 24.5 1.0
OG A:SER544 4.2 30.9 1.0
HA2 A:GLY545 4.2 27.9 1.0
H A:SER544 4.3 27.6 1.0
N A:SER544 4.3 22.9 1.0
HG2 A:PRO508 4.5 26.6 1.0
HB3 A:ASP542 4.6 25.0 1.0
O A:ASP542 4.6 23.2 1.0
H A:GLY545 4.7 28.1 1.0
HA A:SER544 4.8 25.2 1.0
HB2 A:SER544 4.8 29.3 1.0
CG A:PRO508 4.8 22.1 1.0
OD1 A:ASP542 4.8 22.7 1.0
HG3 A:MET509 4.9 29.7 0.4
CG A:ASP542 5.0 24.8 1.0

Sodium binding site 4 out of 4 in 8b4x

Go back to Sodium Binding Sites List in 8b4x
Sodium binding site 4 out of 4 in the X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- R-Tle-K-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 4 of X-Ray Structure of Furin (PCSK3) in Complex with Guanidinomethyl-Phac- R-Tle-K-6-(Aminomethyl)-3-Amino-Isoindol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:33.6
occ:0.28
 O A:HOH1022 2.4 37.1 1.0
O A:HOH1057 2.4 37.7 1.0
OE1 A:GLU546 2.5 41.9 1.0
CD A:GLU546 3.8 49.2 1.0
HB3 A:GLU546 3.9 28.8 1.0
O A:HOH855 4.2 40.8 1.0
O A:HOH1122 4.2 37.0 1.0
O A:HOH1085 4.4 43.3 1.0
O A:HOH712 4.5 30.1 1.0
OE2 A:GLU546 4.5 47.3 1.0
O A:HOH1076 4.6 53.4 1.0
CB A:GLU546 4.6 24.0 1.0
O A:HOH884 4.6 30.6 1.0
HB2 A:GLU546 4.6 28.8 1.0
CG A:GLU546 4.8 27.5 1.0

Reference:

S.O.Dahms, H.Brandstetter. Aminoisoindol-Based Furin Inhibitors To Be Published.
Page generated: Thu Dec 28 11:32:54 2023

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