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Sodium in PDB 5jxg: Structure of the Unliganded Form of the Proprotein Convertase Furin.

Enzymatic activity of Structure of the Unliganded Form of the Proprotein Convertase Furin.

All present enzymatic activity of Structure of the Unliganded Form of the Proprotein Convertase Furin.:
3.4.21.75;

Protein crystallography data

The structure of Structure of the Unliganded Form of the Proprotein Convertase Furin., PDB code: 5jxg was solved by S.O.Dahms, M.Arciniega, T.Steinmetzer, R.Huber, M.E.Than, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.06 / 1.80
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.957, 131.957, 155.634, 90.00, 90.00, 120.00
R / Rfree (%) 15.4 / 17.3

Other elements in 5jxg:

The structure of Structure of the Unliganded Form of the Proprotein Convertase Furin. 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 Structure of the Unliganded Form of the Proprotein Convertase Furin. (pdb code 5jxg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Structure of the Unliganded Form of the Proprotein Convertase Furin., PDB code: 5jxg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 5jxg

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Sodium binding site 1 out of 8 in the Structure of the Unliganded Form of the Proprotein Convertase Furin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of the Unliganded Form of the Proprotein Convertase Furin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:11.3
occ:1.00
 O A:THR309 2.4 10.3 1.0
O A:THR314 2.4 11.3 1.0
OG1 A:THR314 2.4 10.4 1.0
O A:HOH871 2.5 13.8 1.0
O A:SER311 2.5 11.1 1.0
OG A:SER316 2.5 13.4 1.0
C A:THR314 3.2 12.4 1.0
C A:THR309 3.4 15.0 1.0
CB A:THR314 3.6 11.2 1.0
CB A:SER316 3.6 10.9 1.0
C A:SER311 3.7 10.6 1.0
O A:HOH972 3.7 15.1 1.0
CA A:THR314 3.8 11.5 1.0
N A:SER316 3.9 11.5 1.0
N A:SER311 4.0 11.2 1.0
N A:THR314 4.0 11.5 1.0
CA A:THR309 4.1 10.2 1.0
N A:LEU315 4.2 10.7 1.0
C A:ASN310 4.3 13.4 1.0
CA A:SER311 4.3 12.3 1.0
CE A:MET534 4.3 11.9 1.0
CA A:SER316 4.4 11.9 1.0
O A:TYR308 4.4 13.4 1.0
N A:ASN310 4.4 10.8 1.0
O A:SER335 4.4 11.9 1.0
C A:LEU315 4.6 12.0 1.0
CA A:LEU315 4.6 10.2 1.0
OG1 A:THR309 4.6 13.7 1.0
CA A:ASN310 4.6 9.0 1.0
N A:ILE312 4.7 9.7 1.0
CB A:SER311 4.8 11.2 1.0
CG2 A:THR314 4.8 10.7 1.0
O A:ASN310 4.8 13.4 1.0
CA A:ILE312 4.9 9.8 1.0
C A:ILE312 4.9 10.2 1.0

Sodium binding site 2 out of 8 in 5jxg

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Sodium binding site 2 out of 8 in the Structure of the Unliganded Form of the Proprotein Convertase Furin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of the Unliganded Form of the Proprotein Convertase Furin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:25.4
occ:1.00
 O A:HOH874 2.2 18.7 1.0
O A:HOH824 2.4 23.3 1.0
O A:HOH1175 2.4 24.5 1.0
O A:GLY265 2.5 12.9 1.0
OD1 A:ASP264 2.5 17.3 1.0
O A:HOH1242 2.5 21.8 1.0
NA A:NA606 3.2 28.7 1.0
CG A:ASP264 3.3 21.6 1.0
OD2 A:ASP264 3.5 28.7 1.0
NA A:NA610 3.6 32.7 1.0
C A:GLY265 3.7 15.3 1.0
N A:GLY265 4.1 13.2 1.0
O A:HOH1239 4.1 37.8 1.0
N A:ALA267 4.1 12.4 1.0
OH A:TYR308 4.3 13.7 1.0
O A:HOH1336 4.3 48.1 1.0
CB A:ALA267 4.4 16.7 1.0
C A:PRO266 4.4 15.5 1.0
CA A:GLY265 4.5 13.6 1.0
O A:HOH1168 4.5 23.3 1.0
O A:HOH747 4.5 13.6 1.0
CB A:ASP264 4.6 12.5 1.0
N A:PRO266 4.6 14.8 1.0
CA A:PRO266 4.6 12.9 1.0
CA A:ALA267 4.7 13.8 1.0
O A:HOH1167 4.7 19.5 1.0
O A:HOH1327 4.7 38.3 1.0
O A:HOH1278 4.8 28.0 1.0
C A:ASP264 5.0 15.0 1.0

Sodium binding site 3 out of 8 in 5jxg

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Sodium binding site 3 out of 8 in the Structure of the Unliganded Form of the Proprotein Convertase Furin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of the Unliganded Form of the Proprotein Convertase Furin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:28.7
occ:1.00
 O A:HOH928 2.3 23.1 1.0
O A:HOH1278 2.4 28.0 1.0
O A:HOH1242 2.4 21.8 1.0
O A:HOH874 2.5 18.7 1.0
O A:HOH1304 2.5 29.2 1.0
O A:HOH824 2.6 23.3 1.0
NA A:NA605 3.2 25.4 1.0
O A:HOH1167 4.2 19.5 1.0
O A:HOH1006 4.3 41.2 1.0
O A:HOH1331 4.4 54.8 1.0
OD2 A:ASP264 4.4 28.7 1.0
OE2 A:GLU236 4.4 17.1 1.0
O A:HOH1054 4.5 39.5 1.0
O A:HOH1336 4.5 48.1 1.0
OH A:TYR308 4.5 13.7 1.0
O A:HOH747 4.6 13.6 1.0
O A:HOH753 4.7 25.5 1.0
O A:VAL231 4.8 17.6 1.0
OD1 A:ASP264 5.0 17.3 1.0
O A:HOH1163 5.0 8.8 1.0
CG A:ASP264 5.0 21.6 1.0

Sodium binding site 4 out of 8 in 5jxg

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Sodium binding site 4 out of 8 in the Structure of the Unliganded Form of the Proprotein Convertase Furin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of the Unliganded Form of the Proprotein Convertase Furin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:23.4
occ:1.00
 O A:HOH1244 2.4 33.2 1.0
O A:HOH1213 2.4 30.8 1.0
O A:SER279 2.4 17.0 1.0
O A:HOH765 2.5 21.1 1.0
O A:GLY284 2.5 17.3 1.0
O A:HOH1008 3.0 39.9 1.0
C A:GLY284 3.5 17.8 1.0
C A:SER279 3.5 17.3 1.0
CA A:GLY284 3.8 17.8 1.0
CA A:SER279 3.9 15.3 1.0
O A:HOH1201 4.1 26.5 1.0
O A:VAL278 4.3 12.8 1.0
O A:HOH1218 4.4 34.2 1.0
O A:HOH733 4.5 29.5 1.0
O A:HOH1247 4.5 34.3 1.0
N A:GLN280 4.7 18.4 1.0
N A:LEU285 4.7 15.1 1.0
CB A:SER279 4.8 17.2 1.0

Sodium binding site 5 out of 8 in 5jxg

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Sodium binding site 5 out of 8 in the Structure of the Unliganded Form of the Proprotein Convertase Furin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of the Unliganded Form of the Proprotein Convertase Furin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na608

b:29.6
occ:0.50
 O A:SER544 2.2 15.0 1.0
O A:HOH823 2.4 13.9 1.0
C A:SER544 3.1 13.2 1.0
N A:GLY545 3.9 15.1 1.0
CA A:GLY545 4.0 15.7 1.0
CB A:SER544 4.0 17.5 1.0
CB A:PRO508 4.0 14.9 1.0
CA A:SER544 4.0 12.3 1.0
OG A:SER544 4.0 21.2 1.0
N A:SER544 4.4 13.3 1.0
O A:ASP542 4.6 14.0 1.0
CG A:PRO508 4.8 14.8 1.0
OD1 A:ASP542 4.9 15.6 1.0
CG A:ASP542 5.0 18.6 1.0

Sodium binding site 6 out of 8 in 5jxg

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Sodium binding site 6 out of 8 in the Structure of the Unliganded Form of the Proprotein Convertase Furin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of the Unliganded Form of the Proprotein Convertase Furin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na609

b:31.1
occ:0.50
 O A:HOH1063 2.4 25.4 1.0
OE2 A:GLU546 2.4 28.3 1.0
O A:HOH1177 2.5 24.4 1.0
CD A:GLU546 3.7 30.5 1.0
O A:HOH756 4.1 30.2 1.0
O A:HOH1293 4.2 20.7 1.0
O A:HOH1197 4.2 27.0 1.0
OE1 A:GLU546 4.4 28.7 1.0
O A:HOH737 4.4 18.9 1.0
O A:HOH977 4.5 20.9 1.0
O A:HOH1193 4.5 35.6 1.0
CB A:GLU546 4.5 16.5 1.0
CG A:GLU546 4.7 18.4 1.0

Sodium binding site 7 out of 8 in 5jxg

Go back to Sodium Binding Sites List in 5jxg
Sodium binding site 7 out of 8 in the Structure of the Unliganded Form of the Proprotein Convertase Furin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Structure of the Unliganded Form of the Proprotein Convertase Furin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na610

b:32.7
occ:1.00
 OD1 A:ASP264 2.4 17.3 1.0
O A:HOH1168 2.4 23.3 1.0
O A:HOH850 2.5 29.8 1.0
O A:HOH1239 2.5 37.8 1.0
O A:HOH1175 2.6 24.5 1.0
CG A:ASP264 3.3 21.6 1.0
NA A:NA605 3.6 25.4 1.0
OD2 A:ASP264 3.8 28.7 1.0
O A:HOH824 4.0 23.3 1.0
O A:HOH1327 4.1 38.3 1.0
CA A:ASP264 4.2 13.8 1.0
CB A:ASP264 4.3 12.5 1.0
O A:HOH1315 4.3 43.7 1.0
N A:GLY265 4.4 13.2 1.0
O A:HOH1195 4.5 44.3 1.0
O A:GLY265 4.6 12.9 1.0
O A:VAL263 4.6 16.4 1.0
O A:HOH1174 4.6 37.7 1.0
O A:HOH1336 4.7 48.1 1.0
C A:ASP264 4.9 15.0 1.0

Sodium binding site 8 out of 8 in 5jxg

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Sodium binding site 8 out of 8 in the Structure of the Unliganded Form of the Proprotein Convertase Furin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Structure of the Unliganded Form of the Proprotein Convertase Furin. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na611

b:39.7
occ:1.00
 O A:HOH1173 2.3 42.7 1.0
O A:HOH947 2.3 40.9 1.0
O A:HOH840 2.3 28.0 1.0
O A:HOH1289 2.4 46.9 1.0
O A:THR413 2.4 16.2 1.0
O A:HOH907 2.5 14.6 1.0
O A:HOH866 3.3 32.0 1.0
C A:THR413 3.6 16.2 1.0
O A:HOH1140 3.9 28.8 1.0
O A:HOH1131 4.2 41.9 1.0
O A:HOH1319 4.2 45.7 1.0
O A:ASN414 4.2 14.5 1.0
O A:HOH1123 4.3 28.1 1.0
C A:ASN414 4.4 20.2 1.0
CA A:ASN414 4.4 14.4 1.0
N A:ASN414 4.5 13.4 1.0
O A:GLY510 4.5 15.2 1.0
CA A:THR413 4.6 12.6 1.0
O A:MET509 4.7 18.2 0.5
N A:THR413 4.7 14.2 1.0
O A:MET509 4.7 18.1 0.5
CB A:THR413 4.8 22.4 1.0
C A:GLY510 4.9 16.8 1.0
OG1 A:THR511 4.9 14.8 1.0
O A:HOH1074 4.9 19.1 1.0

Reference:

S.O.Dahms, M.Arciniega, T.Steinmetzer, R.Huber, M.E.Than. Structure of the Unliganded Form of the Proprotein Convertase Furin Suggests Activation By A Substrate-Induced Mechanism. Proc.Natl.Acad.Sci.Usa V. 113 11196 2016.
ISSN: ESSN 1091-6490
PubMed: 27647913
DOI: 10.1073/PNAS.1613630113
Page generated: Mon Oct 7 21:58:00 2024

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