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Sodium in PDB 4omd: X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba

Enzymatic activity of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba

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

Protein crystallography data

The structure of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba, PDB code: 4omd 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 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.616, 152.612, 168.538, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 21.8

Other elements in 4omd:

The structure of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-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 Phac-Rvr-Amba (pdb code 4omd). 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 Phac-Rvr-Amba, PDB code: 4omd:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 4omd

Go back to Sodium Binding Sites List in 4omd
Sodium binding site 1 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-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 Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:11.7
occ:1.00
 O A:SER311 2.1 17.7 1.0
O A:THR309 2.2 22.8 1.0
O A:THR314 2.4 13.9 1.0
O A:HOH764 2.4 26.4 1.0
OG1 A:THR314 2.5 13.1 1.0
C A:THR314 3.2 14.8 1.0
C A:THR309 3.2 20.9 1.0
C A:SER311 3.3 18.8 1.0
N A:SER311 3.6 20.7 1.0
CB A:THR314 3.7 15.1 1.0
CA A:THR314 3.8 15.3 1.0
N A:THR314 3.8 16.2 1.0
O A:TYR308 3.9 19.9 1.0
CA A:SER311 4.0 19.0 1.0
C A:ASN310 4.0 20.9 1.0
N A:SER316 4.0 12.3 1.0
CA A:THR309 4.0 18.6 1.0
CE A:MET534 4.1 16.4 1.0
N A:ASN310 4.2 21.2 1.0
CB A:SER316 4.2 14.2 1.0
N A:LEU315 4.3 13.5 1.0
N A:ILE312 4.4 17.1 1.0
CA A:ASN310 4.4 19.8 1.0
O A:ASN310 4.5 18.6 1.0
CB A:SER311 4.5 20.6 1.0
CA A:ILE312 4.6 15.8 1.0
CG2 A:THR314 4.6 17.5 1.0
O A:SER335 4.6 14.7 1.0
CA A:LEU315 4.7 11.3 1.0
C A:LEU315 4.7 12.9 1.0
CA A:SER316 4.7 12.7 1.0
C A:ILE312 4.8 18.1 1.0
C A:TYR308 4.8 18.0 1.0
N A:THR309 4.9 17.9 1.0
N A:TYR313 5.0 18.9 1.0

Sodium binding site 2 out of 6 in 4omd

Go back to Sodium Binding Sites List in 4omd
Sodium binding site 2 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-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 Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na606

b:20.9
occ:1.00
 O B:THR314 2.2 14.7 1.0
O B:THR309 2.3 15.0 1.0
O B:SER311 2.5 22.6 1.0
OG1 B:THR314 2.5 9.9 1.0
O B:HOH703 2.5 11.7 1.0
C B:THR314 3.1 14.4 1.0
C B:THR309 3.3 14.7 1.0
CB B:THR314 3.6 12.5 1.0
C B:SER311 3.6 19.5 1.0
N B:SER316 3.7 14.7 1.0
CA B:THR314 3.7 15.3 1.0
CB B:SER316 3.9 16.0 1.0
N B:THR314 3.9 15.0 1.0
N B:SER311 4.0 17.6 1.0
CA B:THR309 4.1 15.5 1.0
N B:LEU315 4.1 15.0 1.0
O B:TYR308 4.1 16.2 1.0
CE B:MET534 4.2 22.3 1.0
C B:ASN310 4.3 17.7 1.0
CA B:SER311 4.3 18.7 1.0
CA B:SER316 4.3 14.4 1.0
N B:ASN310 4.3 16.0 1.0
C B:LEU315 4.4 16.0 1.0
CA B:LEU315 4.4 15.8 1.0
O B:SER335 4.5 19.1 1.0
CA B:ASN310 4.7 17.0 1.0
N B:ILE312 4.7 18.7 1.0
O B:ASN310 4.8 18.7 1.0
CG2 B:THR314 4.8 11.5 1.0
CA B:ILE312 4.8 18.8 1.0
CB B:SER311 4.8 16.3 1.0
OG B:SER316 4.9 21.2 1.0
C B:ILE312 4.9 18.9 1.0
C B:TYR308 5.0 16.1 1.0

Sodium binding site 3 out of 6 in 4omd

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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 Phac-Rvr-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 Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na606

b:21.6
occ:1.00
 OG1 C:THR314 2.2 19.9 1.0
O C:SER311 2.3 22.1 1.0
O C:THR314 2.3 21.1 1.0
O C:THR309 2.3 14.8 1.0
O C:HOH718 2.5 15.0 1.0
C C:THR314 3.1 20.9 1.0
C C:THR309 3.3 15.2 1.0
CB C:THR314 3.4 19.5 1.0
C C:SER311 3.4 18.9 1.0
CA C:THR314 3.6 20.1 1.0
N C:THR314 3.7 20.2 1.0
N C:SER311 3.8 17.9 1.0
O C:TYR308 3.8 18.5 1.0
N C:SER316 3.9 15.3 1.0
CA C:THR309 4.0 15.6 1.0
CA C:SER311 4.1 18.3 1.0
N C:LEU315 4.1 20.8 1.0
CB C:SER316 4.1 14.9 1.0
C C:ASN310 4.2 16.3 1.0
N C:ASN310 4.3 15.7 1.0
CE C:MET534 4.4 19.9 1.0
CG2 C:THR314 4.5 18.7 1.0
C C:LEU315 4.5 15.7 1.0
N C:ILE312 4.5 18.6 1.0
CA C:LEU315 4.5 17.6 1.0
CA C:SER316 4.5 16.2 1.0
CB C:SER311 4.5 15.2 1.0
CA C:ASN310 4.6 15.9 1.0
O C:ASN310 4.7 16.6 1.0
CA C:ILE312 4.7 19.0 1.0
C C:TYR308 4.7 18.6 1.0
C C:ILE312 4.8 21.1 1.0
O C:SER335 4.8 21.4 1.0
N C:THR309 4.9 17.2 1.0
N C:TYR313 5.0 20.4 1.0
C C:TYR313 5.0 20.4 1.0

Sodium binding site 4 out of 6 in 4omd

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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 Phac-Rvr-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 Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na606

b:21.1
occ:1.00
 O D:THR314 2.2 14.7 1.0
O D:SER311 2.2 19.2 1.0
O D:THR309 2.4 19.3 1.0
OG1 D:THR314 2.5 19.3 1.0
O D:HOH721 2.6 17.9 1.0
C D:THR314 3.1 16.1 1.0
C D:SER311 3.4 17.9 1.0
C D:THR309 3.4 19.1 1.0
CB D:THR314 3.6 17.8 1.0
CA D:THR314 3.6 16.9 1.0
N D:THR314 3.8 17.8 1.0
O D:HOH733 3.8 28.2 1.0
N D:SER316 3.9 16.1 1.0
N D:SER311 3.9 20.1 1.0
CE D:MET534 4.1 18.3 1.0
N D:LEU315 4.1 15.2 1.0
CB D:SER316 4.1 15.4 1.0
O D:TYR308 4.1 19.4 1.0
CA D:SER311 4.2 17.1 1.0
CA D:THR309 4.2 18.6 1.0
C D:ASN310 4.2 21.1 1.0
N D:ASN310 4.4 20.2 1.0
CA D:LEU315 4.4 15.6 1.0
N D:ILE312 4.5 16.4 1.0
C D:LEU315 4.5 16.1 1.0
CA D:SER316 4.5 16.6 1.0
CA D:ILE312 4.6 16.1 1.0
O D:SER335 4.6 19.0 1.0
CA D:ASN310 4.7 20.4 1.0
CB D:SER311 4.7 16.1 1.0
O D:ASN310 4.7 20.6 1.0
C D:ILE312 4.7 17.5 1.0
CG2 D:THR314 4.8 19.8 1.0
N D:TYR313 5.0 16.4 1.0

Sodium binding site 5 out of 6 in 4omd

Go back to Sodium Binding Sites List in 4omd
Sodium binding site 5 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-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 Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na606

b:17.0
occ:1.00
 O E:SER311 2.1 19.1 1.0
O E:THR309 2.3 19.9 1.0
OG1 E:THR314 2.4 13.4 1.0
O E:THR314 2.4 20.1 1.0
O E:HOH704 2.7 9.8 1.0
C E:THR314 3.2 16.7 1.0
C E:THR309 3.2 19.3 1.0
C E:SER311 3.3 19.3 1.0
CB E:THR314 3.5 16.2 1.0
N E:SER311 3.6 19.0 1.0
CA E:THR314 3.7 16.9 1.0
N E:THR314 3.7 15.0 1.0
O E:TYR308 3.8 16.6 1.0
CA E:SER311 3.9 17.4 1.0
C E:ASN310 4.0 19.0 1.0
CA E:THR309 4.0 18.9 1.0
N E:SER316 4.1 12.5 1.0
N E:ASN310 4.2 20.9 1.0
CB E:SER316 4.2 10.1 1.0
N E:LEU315 4.3 14.6 1.0
CE E:MET534 4.3 11.3 1.0
N E:ILE312 4.3 18.1 1.0
CB E:SER311 4.4 14.2 1.0
CA E:ASN310 4.5 20.2 1.0
CG2 E:THR314 4.5 15.6 1.0
O E:ASN310 4.5 19.2 1.0
CA E:ILE312 4.6 17.5 1.0
CA E:LEU315 4.7 15.1 1.0
C E:LEU315 4.7 16.0 1.0
CA E:SER316 4.7 11.3 1.0
C E:TYR308 4.7 16.5 1.0
C E:ILE312 4.7 18.9 1.0
O E:SER335 4.8 18.6 1.0
N E:THR309 4.9 17.2 1.0
N E:TYR313 4.9 20.1 1.0

Sodium binding site 6 out of 6 in 4omd

Go back to Sodium Binding Sites List in 4omd
Sodium binding site 6 out of 6 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-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 Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na606

b:25.1
occ:1.00
 O F:HOH715 2.3 20.1 1.0
O F:THR309 2.3 17.7 1.0
O F:THR314 2.3 23.5 1.0
O F:SER311 2.3 20.1 1.0
OG1 F:THR314 2.3 13.2 1.0
C F:THR314 3.1 21.0 1.0
C F:THR309 3.3 16.3 1.0
CB F:THR314 3.5 18.0 1.0
C F:SER311 3.5 20.2 1.0
CA F:THR314 3.6 18.6 1.0
N F:THR314 3.8 15.8 1.0
N F:SER311 3.8 20.2 1.0
N F:SER316 3.8 18.7 1.0
O F:TYR308 3.9 19.2 1.0
CA F:THR309 4.0 15.0 1.0
CB F:SER316 4.0 17.3 1.0
N F:LEU315 4.1 19.6 1.0
CA F:SER311 4.1 20.0 1.0
C F:ASN310 4.2 19.0 1.0
N F:ASN310 4.2 17.3 1.0
CE F:MET534 4.4 14.9 1.0
C F:LEU315 4.4 20.3 1.0
CA F:SER316 4.5 17.3 1.0
CA F:LEU315 4.5 19.8 1.0
N F:ILE312 4.6 20.9 1.0
CA F:ASN310 4.6 18.3 1.0
CB F:SER311 4.6 19.4 1.0
CG2 F:THR314 4.6 20.2 1.0
O F:ASN310 4.7 18.7 1.0
O F:SER335 4.8 19.5 1.0
C F:TYR308 4.8 17.2 1.0
CA F:ILE312 4.8 18.6 1.0
N F:THR309 4.9 16.0 1.0
C F:ILE312 4.9 20.3 1.0
OG F:SER316 4.9 26.6 1.0

Reference:

S.O.Dahms, K.Hardes, G.L.Becker, T.Steinmetzer, H.Brandstetter, M.E.Than. X-Ray Structures of Human Furin in Complex with Competitive Inhibitors. Acs Chem.Biol. V. 9 1113 2014.
ISSN: ISSN 1554-8929
PubMed: 24666235
DOI: 10.1021/CB500087X
Page generated: Tue Dec 15 06:57:02 2020

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