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Sodium in PDB 4ryd: X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba

Enzymatic activity of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba

All present enzymatic activity of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba, PDB code: 4ryd was solved by S.O.Dahms, M.E.Than, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.652, 152.701, 168.398, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.9

Other elements in 4ryd:

The structure of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba also contains other interesting chemical elements:

Calcium (Ca) 18 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba (pdb code 4ryd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba, PDB code: 4ryd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4ryd

Go back to Sodium Binding Sites List in 4ryd
Sodium binding site 1 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba


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 Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:16.3
occ:1.00
 O A:SER311 2.2 15.2 1.0
O A:THR309 2.3 18.1 1.0
O A:THR314 2.5 19.1 1.0
OG1 A:THR314 2.5 12.7 1.0
O A:HOH784 2.5 16.3 1.0
C A:THR314 3.3 20.2 1.0
C A:THR309 3.4 19.4 1.0
C A:SER311 3.4 18.9 1.0
O A:HOH776 3.6 25.7 1.0
CB A:THR314 3.7 18.0 1.0
N A:SER311 3.8 18.8 1.0
CA A:THR314 3.8 17.2 1.0
N A:THR314 3.9 17.2 1.0
N A:SER316 4.0 17.4 1.0
CB A:SER316 4.0 16.9 1.0
CE A:MET534 4.1 13.4 1.0
O A:TYR308 4.1 19.7 1.0
C A:ASN310 4.1 21.9 1.0
CA A:SER311 4.1 18.9 1.0
CA A:THR309 4.2 21.1 1.0
N A:ASN310 4.3 20.5 1.0
N A:LEU315 4.3 18.6 1.0
N A:ILE312 4.5 17.4 1.0
O A:SER335 4.5 14.7 1.0
CA A:ASN310 4.5 20.9 1.0
O A:ASN310 4.6 21.2 1.0
CA A:SER316 4.6 15.4 1.0
C A:LEU315 4.6 18.0 1.0
CA A:ILE312 4.6 17.3 1.0
CA A:LEU315 4.6 18.4 1.0
CB A:SER311 4.6 17.3 1.0
C A:ILE312 4.7 16.3 1.0
CG2 A:THR314 4.7 12.9 1.0

Sodium binding site 2 out of 6 in 4ryd

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Sodium binding site 2 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba


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 Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na607

b:16.8
occ:1.00
 O B:THR309 2.3 16.8 1.0
O B:SER311 2.4 18.0 1.0
OG1 B:THR314 2.4 14.0 1.0
O B:HOH703 2.4 14.9 1.0
O B:THR314 2.4 17.5 1.0
C B:THR314 3.2 17.4 1.0
C B:THR309 3.4 18.2 1.0
O B:HOH794 3.5 21.3 1.0
C B:SER311 3.5 18.6 1.0
CB B:THR314 3.6 16.9 1.0
CA B:THR314 3.8 17.9 1.0
N B:SER316 3.8 19.3 1.0
N B:SER311 3.9 17.9 1.0
CB B:SER316 3.9 16.3 1.0
N B:THR314 3.9 16.9 1.0
CE B:MET534 4.0 14.9 1.0
O B:TYR308 4.1 18.1 1.0
CA B:THR309 4.2 17.8 1.0
C B:ASN310 4.2 20.1 1.0
N B:LEU315 4.2 18.8 1.0
CA B:SER311 4.2 17.1 1.0
N B:ASN310 4.3 17.6 1.0
CA B:SER316 4.4 17.8 1.0
O B:SER335 4.5 18.9 1.0
C B:LEU315 4.5 19.3 1.0
CA B:LEU315 4.5 19.0 1.0
N B:ILE312 4.6 18.2 1.0
CA B:ASN310 4.6 20.0 1.0
O B:ASN310 4.7 17.0 1.0
CG2 B:THR314 4.7 13.9 1.0
CA B:ILE312 4.7 18.8 1.0
CB B:SER311 4.7 14.3 1.0
C B:ILE312 4.8 17.1 1.0
OG B:SER316 5.0 23.4 1.0

Sodium binding site 3 out of 6 in 4ryd

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Sodium binding site 3 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba


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 Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na607

b:18.2
occ:1.00
 O C:THR314 2.3 16.5 1.0
O C:SER311 2.3 18.2 1.0
OG1 C:THR314 2.3 15.4 1.0
O C:HOH721 2.4 14.2 1.0
O C:THR309 2.4 16.3 1.0
C C:THR314 3.1 18.3 1.0
C C:THR309 3.4 17.5 1.0
C C:SER311 3.5 17.6 1.0
CB C:THR314 3.5 16.6 1.0
CA C:THR314 3.7 18.0 1.0
O C:HOH788 3.8 23.4 1.0
N C:THR314 3.8 18.5 1.0
N C:SER316 3.8 14.8 1.0
N C:SER311 3.9 17.8 1.0
CB C:SER316 4.0 15.0 1.0
O C:TYR308 4.0 19.1 1.0
N C:LEU315 4.1 18.4 1.0
CA C:SER311 4.2 17.5 1.0
CA C:THR309 4.2 17.0 1.0
C C:ASN310 4.2 19.0 1.0
CE C:MET534 4.2 17.3 1.0
N C:ASN310 4.4 19.0 1.0
C C:LEU315 4.4 16.1 1.0
CA C:SER316 4.5 17.1 1.0
CA C:LEU315 4.5 17.8 1.0
N C:ILE312 4.5 16.5 1.0
CG2 C:THR314 4.6 16.1 1.0
O C:SER335 4.6 19.3 1.0
CA C:ASN310 4.7 18.2 1.0
CB C:SER311 4.7 15.3 1.0
O C:ASN310 4.7 18.5 1.0
CA C:ILE312 4.7 16.8 1.0
C C:ILE312 4.8 16.8 1.0
C C:TYR308 5.0 18.0 1.0
O C:ILE312 5.0 14.4 1.0

Sodium binding site 4 out of 6 in 4ryd

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Sodium binding site 4 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba


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 Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na607

b:16.6
occ:1.00
 O D:SER311 2.3 15.3 1.0
O D:THR314 2.4 16.8 1.0
O D:HOH723 2.4 15.7 1.0
O D:THR309 2.4 18.7 1.0
OG1 D:THR314 2.5 14.7 1.0
C D:THR314 3.2 16.8 1.0
C D:SER311 3.5 19.6 1.0
C D:THR309 3.5 21.0 1.0
CB D:THR314 3.6 15.5 1.0
O D:HOH736 3.6 23.7 1.0
CA D:THR314 3.8 16.4 1.0
N D:SER316 3.9 18.2 1.0
N D:THR314 3.9 15.5 1.0
CE D:MET534 3.9 13.7 1.0
N D:SER311 3.9 20.1 1.0
CB D:SER316 4.0 16.5 1.0
C D:ASN310 4.2 23.7 1.0
N D:LEU315 4.2 16.5 1.0
CA D:SER311 4.2 20.2 1.0
O D:TYR308 4.2 21.1 1.0
CA D:THR309 4.3 18.3 1.0
N D:ASN310 4.4 22.1 1.0
O D:SER335 4.4 20.3 1.0
N D:ILE312 4.5 17.2 1.0
CA D:LEU315 4.5 19.4 1.0
CA D:SER316 4.5 19.0 1.0
C D:LEU315 4.5 18.6 1.0
CA D:ILE312 4.6 16.9 1.0
O D:ASN310 4.6 25.5 1.0
CA D:ASN310 4.6 23.5 1.0
C D:ILE312 4.7 18.4 1.0
CB D:SER311 4.8 18.1 1.0
CG2 D:THR314 4.8 10.8 1.0
O D:ILE312 5.0 18.4 1.0

Sodium binding site 5 out of 6 in 4ryd

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Sodium binding site 5 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na607

b:20.6
occ:1.00
 O E:SER311 2.2 19.4 1.0
O E:THR314 2.4 17.9 1.0
O E:THR309 2.4 18.4 1.0
OG1 E:THR314 2.4 19.0 1.0
O E:HOH704 2.4 11.2 1.0
C E:THR314 3.2 18.0 1.0
C E:SER311 3.4 19.5 1.0
C E:THR309 3.5 18.5 1.0
CB E:THR314 3.6 18.6 1.0
CA E:THR314 3.7 17.6 1.0
O E:HOH769 3.8 27.6 1.0
N E:THR314 3.8 15.4 1.0
N E:SER311 3.8 17.0 1.0
N E:SER316 3.9 17.2 1.0
CE E:MET534 4.0 15.3 1.0
CB E:SER316 4.1 14.6 1.0
CA E:SER311 4.1 15.9 1.0
O E:TYR308 4.1 19.7 1.0
C E:ASN310 4.2 19.4 1.0
N E:LEU315 4.2 15.6 1.0
CA E:THR309 4.3 16.8 1.0
N E:ASN310 4.4 16.9 1.0
N E:ILE312 4.4 16.0 1.0
CA E:LEU315 4.5 19.6 1.0
O E:SER335 4.5 15.1 1.0
C E:LEU315 4.5 19.2 1.0
CA E:SER316 4.6 16.4 1.0
CA E:ILE312 4.6 17.4 1.0
CB E:SER311 4.6 13.5 1.0
CA E:ASN310 4.6 18.5 1.0
O E:ASN310 4.6 17.2 1.0
C E:ILE312 4.6 18.7 1.0
CG2 E:THR314 4.7 17.4 1.0
O E:ILE312 4.9 17.9 1.0
N E:TYR313 5.0 16.8 1.0

Sodium binding site 6 out of 6 in 4ryd

Go back to Sodium Binding Sites List in 4ryd
Sodium binding site 6 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Para-Guanidinomethyl-Phac-R-Tle-R-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na607

b:18.5
occ:1.00
 O F:SER311 2.2 16.4 1.0
O F:THR309 2.4 17.7 1.0
O F:HOH716 2.4 19.9 1.0
O F:THR314 2.4 21.1 1.0
OG1 F:THR314 2.4 17.6 1.0
C F:THR314 3.2 19.7 1.0
C F:THR309 3.4 19.9 1.0
C F:SER311 3.4 18.0 1.0
O F:HOH782 3.6 23.4 1.0
CB F:THR314 3.6 18.1 1.0
CA F:THR314 3.7 18.6 1.0
N F:SER311 3.8 19.0 1.0
N F:THR314 3.8 16.8 1.0
N F:SER316 3.9 18.1 1.0
CB F:SER316 4.0 16.6 1.0
O F:TYR308 4.1 17.9 1.0
CA F:SER311 4.1 18.1 1.0
C F:ASN310 4.1 20.4 1.0
CE F:MET534 4.1 18.5 1.0
CA F:THR309 4.2 19.2 1.0
N F:LEU315 4.2 17.4 1.0
N F:ASN310 4.3 17.8 1.0
N F:ILE312 4.5 17.7 1.0
C F:LEU315 4.6 20.7 1.0
CA F:ASN310 4.6 21.0 1.0
CA F:SER316 4.6 18.3 1.0
CA F:LEU315 4.6 21.0 1.0
O F:SER335 4.6 17.9 1.0
O F:ASN310 4.6 21.5 1.0
CB F:SER311 4.6 18.5 1.0
CA F:ILE312 4.6 17.8 1.0
CG2 F:THR314 4.7 16.1 1.0
C F:ILE312 4.7 19.2 1.0
C F:TYR308 5.0 17.9 1.0

Reference:

K.Hardes, G.L.Becker, Y.Lu, S.O.Dahms, S.Kohler, W.Beyer, K.Sandvig, H.Yamamoto, I.Lindberg, L.Walz, V.Von Messling, M.E.Than, W.Garten, T.Steinmetzer. Novel Furin Inhibitors with Potent Anti-Infectious Activity. Chemmedchem 2015.
ISSN: ESSN 1860-7187
PubMed: 25974265
DOI: 10.1002/CMDC.201500103
Page generated: Mon Oct 7 18:22:59 2024

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