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Sodium in PDB 5jxi: Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta.

Enzymatic activity of Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta.

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

Protein crystallography data

The structure of Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta., PDB code: 5jxi 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) 43.35 / 2.00
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.448, 132.448, 155.673, 90.00, 90.00, 120.00
R / Rfree (%) 15.8 / 18.5

Other elements in 5jxi:

The structure of Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta. also contains other interesting chemical elements:

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

Sodium Binding Sites:

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

Sodium binding site 1 out of 7 in 5jxi

Go back to Sodium Binding Sites List in 5jxi
Sodium binding site 1 out of 7 in the Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta.


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 in Presence of Edta. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:14.0
occ:1.00
 O A:THR309 2.4 13.2 1.0
O A:THR314 2.4 12.6 1.0
OG1 A:THR314 2.4 11.2 1.0
O A:SER311 2.5 10.3 1.0
O A:HOH889 2.5 12.8 1.0
OG A:SER316 2.5 14.2 1.0
C A:THR314 3.2 13.4 1.0
C A:THR309 3.4 15.1 1.0
CB A:THR314 3.5 14.6 1.0
CB A:SER316 3.6 13.4 1.0
C A:SER311 3.6 11.9 1.0
CA A:THR314 3.7 11.7 1.0
O A:HOH864 3.8 12.9 1.0
N A:SER316 4.0 12.8 1.0
N A:THR314 4.0 8.8 1.0
N A:SER311 4.0 12.2 1.0
CA A:THR309 4.1 14.1 1.0
N A:LEU315 4.2 12.1 1.0
CA A:SER311 4.3 10.9 1.0
C A:ASN310 4.3 12.5 1.0
CA A:SER316 4.4 12.3 1.0
O A:TYR308 4.4 12.5 1.0
CE A:MET534 4.4 11.6 1.0
O A:SER335 4.4 11.8 1.0
N A:ASN310 4.4 11.1 1.0
OG1 A:THR309 4.5 13.4 1.0
C A:LEU315 4.6 16.5 1.0
CA A:LEU315 4.6 11.7 1.0
CA A:ASN310 4.7 10.7 1.0
N A:ILE312 4.7 11.6 1.0
CB A:SER311 4.8 10.3 1.0
CG2 A:THR314 4.8 9.7 1.0
O A:ASN310 4.8 15.2 1.0
CA A:ILE312 4.9 9.1 1.0
C A:ILE312 4.9 12.8 1.0

Sodium binding site 2 out of 7 in 5jxi

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Sodium binding site 2 out of 7 in the Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta.


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 in Presence of Edta. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:26.8
occ:1.00
 O A:HOH1171 2.4 36.9 1.0
O A:HOH820 2.4 23.4 1.0
O A:SER279 2.5 19.6 1.0
O A:HOH1134 2.5 34.9 1.0
O A:GLY284 2.6 17.4 1.0
C A:SER279 3.5 19.2 1.0
C A:GLY284 3.6 18.8 1.0
CA A:SER279 3.9 18.3 1.0
CA A:GLY284 3.9 18.4 1.0
O A:HOH1101 3.9 27.4 1.0
O A:VAL278 4.3 16.0 1.0
O A:HOH1149 4.4 35.6 1.0
O A:HOH757 4.4 30.8 1.0
O A:HOH1165 4.5 36.1 1.0
N A:GLN280 4.7 20.2 1.0
CB A:SER279 4.7 16.6 1.0
N A:LEU285 4.8 17.2 1.0
O A:HOH1055 5.0 30.6 1.0

Sodium binding site 3 out of 7 in 5jxi

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Sodium binding site 3 out of 7 in the Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta.


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 in Presence of Edta. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:28.9
occ:0.50
 O A:SER544 2.2 17.6 1.0
O A:HOH828 2.5 18.5 1.0
C A:SER544 3.2 12.4 1.0
CB A:PRO508 3.9 15.8 1.0
CA A:GLY545 4.0 15.4 1.0
N A:GLY545 4.0 14.3 1.0
CB A:SER544 4.1 18.1 1.0
CA A:SER544 4.1 15.3 1.0
OG A:SER544 4.2 20.4 1.0
N A:SER544 4.4 15.7 1.0
O A:ASP542 4.6 16.2 1.0
CG A:PRO508 4.7 18.5 1.0
O A:HOH718 4.9 21.6 1.0
OD1 A:ASP542 4.9 16.1 1.0

Sodium binding site 4 out of 7 in 5jxi

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Sodium binding site 4 out of 7 in the Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta.


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 in Presence of Edta. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:35.4
occ:1.00
 O A:HOH727 2.2 27.7 1.0
O A:HOH1094 2.5 29.5 1.0
O A:GLY265 2.5 16.5 1.0
O A:HOH1115 2.6 38.4 1.0
O A:HOH1173 2.6 26.3 1.0
OD1 A:ASP264 2.8 29.2 1.0
OD2 A:ASP264 3.3 43.4 1.0
CG A:ASP264 3.4 29.2 1.0
C A:GLY265 3.7 19.5 1.0
N A:ALA267 3.9 13.6 1.0
OH A:TYR308 4.0 15.1 1.0
C A:PRO266 4.3 16.7 1.0
O A:HOH783 4.4 13.5 1.0
N A:GLY265 4.4 15.9 1.0
CB A:ALA267 4.4 14.8 1.0
O A:HOH1020 4.5 33.0 1.0
CA A:PRO266 4.5 13.8 1.0
N A:PRO266 4.6 18.2 1.0
O A:HOH1089 4.6 25.9 1.0
CA A:ALA267 4.6 14.3 1.0
CA A:GLY265 4.6 16.6 1.0
O A:HOH1135 4.7 42.9 1.0
CB A:ASP264 4.9 18.2 1.0
CZ A:TYR308 4.9 16.1 1.0

Sodium binding site 5 out of 7 in 5jxi

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Sodium binding site 5 out of 7 in the Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta.


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 in Presence of Edta. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:30.6
occ:1.00
 O A:ASP181 2.4 24.5 1.0
O A:HOH729 2.4 27.6 1.0
O A:HOH913 2.4 35.2 1.0
OD2 A:ASP174 2.4 24.1 1.0
O A:HOH897 2.7 46.5 1.0
OD1 A:ASP179 2.9 38.2 1.0
CG A:ASP174 3.3 24.2 1.0
OD2 A:ASP179 3.4 49.0 1.0
CB A:ASP174 3.5 19.8 1.0
C A:ASP181 3.5 19.8 1.0
CG A:ASP179 3.5 42.7 1.0
CB A:ASP181 4.0 24.0 1.0
O A:HOH1158 4.1 39.2 1.0
CA A:ASP181 4.2 20.7 1.0
OD2 A:ASP177 4.4 41.1 1.0
CG A:ASP181 4.4 35.3 1.0
N A:ASP181 4.5 22.2 1.0
CB A:ASP177 4.5 23.5 1.0
OD1 A:ASP174 4.5 22.4 1.0
N A:PRO182 4.6 19.3 1.0
NH2 A:ARG225 4.6 22.0 1.0
O A:GLN183 4.7 19.6 1.0
OD2 A:ASP181 4.7 29.1 1.0
N A:GLN183 4.7 18.9 1.0
CD A:ARG225 4.8 15.8 1.0
CA A:PRO182 4.8 21.3 1.0
CG A:ASP177 4.9 37.7 1.0
O A:HOH1176 4.9 53.6 1.0
CA A:ASP174 5.0 20.0 1.0

Sodium binding site 6 out of 7 in 5jxi

Go back to Sodium Binding Sites List in 5jxi
Sodium binding site 6 out of 7 in the Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta.


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 in Presence of Edta. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:33.3
occ:1.00
 O A:HOH824 2.4 22.9 1.0
O A:HOH853 2.4 40.6 1.0
O A:SER253 2.5 25.3 1.0
O A:HOH989 2.5 30.4 1.0
O A:HOH733 2.5 21.4 1.0
O A:TRP254 2.8 30.5 1.0
C A:TRP254 3.2 27.6 1.0
NA A:NA608 3.2 33.7 1.0
C A:SER253 3.3 23.8 1.0
CA A:TRP254 3.6 24.3 1.0
N A:TRP254 3.8 20.4 1.0
OD2 A:ASP306 3.9 18.8 1.0
N A:GLY255 3.9 27.4 1.0
OD2 A:ASP258 4.2 27.0 1.0
CA A:GLY255 4.2 25.8 1.0
O A:PRO256 4.3 20.8 1.0
CA A:SER253 4.3 16.9 1.0
C A:GLY255 4.5 27.8 1.0
NE1 A:TRP291 4.6 15.3 1.0
OD1 A:ASP258 4.7 26.8 1.0
O A:HOH1155 4.7 9.1 1.0
O A:HOH799 4.7 18.1 1.0
O A:GLY255 4.8 26.5 1.0
O A:ALA292 4.8 14.2 1.0
CB A:SER253 4.9 18.6 1.0
CG A:ASP258 4.9 25.6 1.0
O A:HOH1092 4.9 30.0 1.0
O A:HOH1147 4.9 39.1 1.0
CA A:GLY294 4.9 13.4 1.0
O A:HOH1143 5.0 22.3 1.0
CG A:ASP306 5.0 21.9 1.0

Sodium binding site 7 out of 7 in 5jxi

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Sodium binding site 7 out of 7 in the Structure of the Unliganded Form of the Proprotein Convertase Furin in Presence of Edta.


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 in Presence of Edta. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na608

b:33.7
occ:1.00
 O A:HOH1147 2.4 39.1 1.0
O A:HOH1143 2.4 22.3 1.0
O A:HOH1092 2.5 30.0 1.0
O A:SER253 2.5 25.3 1.0
O A:HOH989 2.6 30.4 1.0
O A:HOH824 2.6 22.9 1.0
NA A:NA607 3.2 33.3 1.0
C A:SER253 3.6 23.8 1.0
O A:HOH1125 3.8 40.4 1.0
CA A:TRP254 3.9 24.3 1.0
O A:HOH998 4.1 34.1 1.0
N A:TRP254 4.2 20.4 1.0
CB A:SER253 4.5 18.6 1.0
OG A:SER253 4.5 21.4 1.0
O A:HOH1152 4.5 39.0 1.0
O A:HOH1155 4.5 9.1 1.0
O A:HOH941 4.5 36.5 1.0
C A:TRP254 4.6 27.6 1.0
OD1 A:ASN295 4.6 33.3 1.0
CA A:SER253 4.7 16.9 1.0
OD2 A:ASP258 4.8 27.0 1.0
O A:TRP254 5.0 30.5 1.0
O A:HOH733 5.0 21.4 1.0
CB A:TRP254 5.0 24.1 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 21:58:05 2024

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