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Sodium in PDB 5jxj: Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta

Enzymatic activity of Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta

All present enzymatic activity of Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta:
3.4.21.75;

Protein crystallography data

The structure of Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta, PDB code: 5jxj 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) 43.23 / 2.00
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.080, 132.080, 155.642, 90.00, 90.00, 120.00
R / Rfree (%) 16.7 / 18.9

Other elements in 5jxj:

The structure of Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba 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 Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta (pdb code 5jxj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta, PDB code: 5jxj:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5jxj

Go back to Sodium Binding Sites List in 5jxj
Sodium binding site 1 out of 6 in the Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba 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 Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na602

b:16.2
occ:1.00
 O A:SER311 2.3 16.2 1.0
O A:HOH798 2.3 13.9 1.0
O A:THR309 2.4 16.8 1.0
O A:THR314 2.4 15.4 1.0
OG1 A:THR314 2.5 13.4 1.0
C A:THR314 3.2 16.0 1.0
C A:THR309 3.4 16.3 1.0
C A:SER311 3.5 14.8 1.0
CB A:THR314 3.6 17.4 1.0
O A:HOH833 3.7 22.5 1.0
CA A:THR314 3.8 15.9 1.0
N A:SER311 3.8 15.0 1.0
N A:SER316 3.9 17.5 1.0
CB A:SER316 3.9 16.0 1.0
N A:THR314 3.9 12.6 1.0
CA A:SER311 4.1 15.9 1.0
CA A:THR309 4.2 15.5 1.0
O A:TYR308 4.2 17.0 1.0
C A:ASN310 4.2 16.9 1.0
CE A:MET534 4.2 16.0 1.0
N A:LEU315 4.2 15.6 1.0
N A:ASN310 4.4 13.4 1.0
CA A:SER316 4.5 16.5 1.0
O A:SER335 4.5 14.6 1.0
C A:LEU315 4.5 23.2 1.0
N A:ILE312 4.5 14.8 1.0
CA A:LEU315 4.5 18.3 1.0
CB A:SER311 4.6 12.7 1.0
CA A:ASN310 4.7 11.4 1.0
O A:ASN310 4.7 16.6 1.0
CA A:ILE312 4.7 14.4 1.0
CG2 A:THR314 4.8 14.3 1.0
C A:ILE312 4.8 16.3 1.0

Sodium binding site 2 out of 6 in 5jxj

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Sodium binding site 2 out of 6 in the Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba 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 Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na603

b:20.6
occ:0.50
 O A:HOH1146 2.4 45.1 1.0
O A:HOH1087 2.4 25.6 1.0
O A:HOH971 2.4 33.8 1.0
OD1 A:ASP264 2.5 24.4 1.0
O A:HOH956 2.5 32.7 1.0
O A:HOH778 2.5 35.3 1.0
CG A:ASP264 3.4 25.2 1.0
O H:HOH103 4.0 22.4 1.0
CA A:ASP264 4.0 17.6 1.0
O A:HOH1117 4.1 36.1 1.0
N A:GLY265 4.1 21.1 1.0
O A:GLY265 4.2 18.5 1.0
OD2 A:ASP264 4.2 27.1 1.0
CB A:ASP264 4.2 18.5 1.0
O A:VAL263 4.4 21.0 1.0
C A:ASP264 4.6 19.4 1.0
O A:HOH1122 4.7 47.1 1.0
O A:HOH982 4.8 28.6 1.0
O A:HOH1152 4.9 36.7 1.0
NH1 H:ARG2 5.0 17.5 1.0

Sodium binding site 3 out of 6 in 5jxj

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Sodium binding site 3 out of 6 in the Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba 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 Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:49.6
occ:0.50
 O A:HOH1032 2.4 38.8 1.0
O A:HOH1073 2.5 37.6 1.0
OE2 A:GLU546 2.6 51.0 1.0
CD A:GLU546 3.8 42.0 1.0
O A:HOH1134 4.1 40.5 1.0
O A:HOH718 4.2 25.5 1.0
O A:HOH1091 4.3 39.2 1.0
CB A:GLU546 4.4 19.1 1.0
O A:HOH818 4.5 28.1 1.0
OE1 A:GLU546 4.6 42.7 1.0
NH2 A:ARG468 4.7 41.8 1.0
CG A:GLU546 4.7 24.1 1.0

Sodium binding site 4 out of 6 in 5jxj

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Sodium binding site 4 out of 6 in the Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba 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 Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:29.8
occ:1.00
 O A:ASP181 2.2 23.9 1.0
OD2 A:ASP174 2.4 27.1 1.0
O A:HOH776 2.5 29.1 1.0
O A:HOH714 2.5 27.5 1.0
O A:HOH805 2.8 39.2 1.0
OD1 A:ASP179 2.8 30.8 1.0
CG A:ASP174 3.3 24.2 1.0
OD2 A:ASP179 3.3 42.1 1.0
C A:ASP181 3.4 20.8 1.0
CG A:ASP179 3.4 33.2 1.0
CB A:ASP174 3.5 22.8 1.0
CB A:ASP181 4.0 29.2 1.0
CA A:ASP181 4.1 21.0 1.0
CG A:ASP181 4.3 32.5 1.0
N A:ASP181 4.4 26.4 1.0
NH2 A:ARG225 4.4 26.6 1.0
N A:PRO182 4.5 21.2 1.0
OD1 A:ASP174 4.5 24.6 1.0
OD2 A:ASP177 4.5 37.1 1.0
OD2 A:ASP181 4.5 28.3 1.0
N A:GLN183 4.6 21.6 1.0
O A:GLN183 4.6 19.6 1.0
CB A:ASP177 4.6 28.0 1.0
CA A:PRO182 4.7 23.2 1.0
CD A:ARG225 4.8 22.1 1.0
C A:PRO182 4.9 27.1 1.0
OD1 A:ASP181 4.9 30.3 1.0
CB A:ASP179 4.9 21.9 1.0
CA A:ASP174 5.0 22.7 1.0

Sodium binding site 5 out of 6 in 5jxj

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Sodium binding site 5 out of 6 in the Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba 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 Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:28.6
occ:0.50
 O A:SER544 2.2 17.4 1.0
O A:HOH738 2.4 17.6 1.0
O A:HOH1077 2.6 36.0 0.5
C A:SER544 3.2 15.6 1.0
CB A:PRO508 3.9 18.0 1.0
N A:GLY545 4.0 16.8 1.0
CA A:GLY545 4.0 20.1 1.0
CB A:SER544 4.1 18.5 1.0
CA A:SER544 4.1 19.7 1.0
OG A:SER544 4.1 24.0 1.0
N A:SER544 4.4 18.8 1.0
O A:ASP542 4.6 17.9 1.0
CG A:PRO508 4.8 19.3 1.0
OD1 A:ASP542 4.9 20.7 1.0
O A:HOH718 5.0 25.5 1.0

Sodium binding site 6 out of 6 in 5jxj

Go back to Sodium Binding Sites List in 5jxj
Sodium binding site 6 out of 6 in the Structure of the Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba 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 Proprotein Convertase Furin Complexed to Meta- Guanidinomethyl-Phac-Rvr-Amba in Presence of Edta within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:26.4
occ:1.00
 O A:HOH1098 2.3 33.0 1.0
O A:HOH756 2.4 19.5 1.0
O A:SER279 2.4 22.3 1.0
O A:HOH1097 2.5 33.4 1.0
O A:GLY284 2.6 24.6 1.0
C A:SER279 3.4 21.0 1.0
C A:GLY284 3.5 20.4 1.0
CA A:GLY284 3.7 24.3 1.0
O A:HOH1034 3.9 28.6 1.0
CA A:SER279 3.9 20.1 1.0
O A:HOH866 4.2 41.7 1.0
O A:VAL278 4.3 17.8 1.0
O A:HOH1085 4.4 36.8 1.0
O A:HOH1108 4.5 33.8 1.0
N A:GLN280 4.6 19.9 1.0
N A:LEU285 4.7 17.4 1.0
CB A:SER279 4.7 19.8 1.0
N A:SER279 5.0 15.1 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 21:58:23 2024

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