Atomistry » Sodium » PDB 5jiq-5kc1 » 5jxj
Atomistry »
  Sodium »
    PDB 5jiq-5kc1 »
      5jxj »

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

Go back to Sodium Binding Sites List in 5jxj
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

Go back to Sodium Binding Sites List in 5jxj
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

Go back to Sodium Binding Sites List in 5jxj
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

Go back to Sodium Binding Sites List in 5jxj
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy