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Sodium in PDB 6eqv: X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba

Enzymatic activity of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba

All present enzymatic activity of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba, PDB code: 6eqv 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) 45.98 / 1.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.601, 131.601, 155.638, 90.00, 90.00, 120.00
R / Rfree (%) 16.4 / 18.2

Other elements in 6eqv:

The structure of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba 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 X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba (pdb code 6eqv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba, PDB code: 6eqv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6eqv

Go back to Sodium Binding Sites List in 6eqv
Sodium binding site 1 out of 4 in the X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-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 the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:15.5
occ:1.00
 O A:SER311 2.3 14.0 1.0
O A:THR309 2.4 15.8 1.0
O A:HOH808 2.4 14.8 1.0
O A:THR314 2.4 13.8 1.0
OG1 A:THR314 2.5 14.4 1.0
C A:THR314 3.2 14.9 1.0
C A:THR309 3.4 14.6 1.0
C A:SER311 3.5 14.1 1.0
CB A:THR314 3.6 14.2 1.0
O A:HOH884 3.7 24.4 1.0
CA A:THR314 3.8 15.4 1.0
N A:SER311 3.8 13.3 1.0
N A:SER316 3.9 15.7 1.0
N A:THR314 3.9 14.3 1.0
CB A:SER316 3.9 17.6 1.0
CE A:MET534 4.1 13.4 1.0
C A:ASN310 4.2 14.8 1.0
CA A:SER311 4.2 15.1 1.0
O A:TYR308 4.2 16.8 1.0
CA A:THR309 4.2 14.4 1.0
N A:LEU315 4.2 12.2 1.0
N A:ASN310 4.3 13.8 1.0
O A:SER335 4.5 14.3 1.0
CA A:SER316 4.5 15.1 1.0
C A:LEU315 4.5 19.9 1.0
CA A:LEU315 4.5 18.1 1.0
N A:ILE312 4.6 13.6 1.0
CA A:ASN310 4.6 13.2 1.0
CB A:SER311 4.6 16.0 1.0
O A:ASN310 4.7 16.6 1.0
CA A:ILE312 4.8 12.1 1.0
CG2 A:THR314 4.8 15.0 1.0
C A:ILE312 4.8 15.4 1.0

Sodium binding site 2 out of 4 in 6eqv

Go back to Sodium Binding Sites List in 6eqv
Sodium binding site 2 out of 4 in the X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-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 the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:24.5
occ:1.00
 O A:HOH1122 2.4 28.4 1.0
O A:SER279 2.4 19.8 1.0
O A:HOH800 2.4 20.2 1.0
O A:HOH1141 2.4 31.4 1.0
O A:GLY284 2.5 21.3 1.0
C A:SER279 3.5 21.5 1.0
C A:GLY284 3.5 21.9 1.0
CA A:GLY284 3.7 21.7 1.0
CA A:SER279 3.9 19.7 1.0
O A:HOH1104 4.1 29.6 1.0
O A:HOH713 4.3 29.6 1.0
O A:VAL278 4.3 15.9 1.0
O A:HOH1124 4.4 32.0 1.0
O A:HOH1154 4.6 27.4 1.0
N A:GLN280 4.6 22.7 1.0
N A:LEU285 4.7 19.0 1.0
CB A:SER279 4.8 18.7 1.0

Sodium binding site 3 out of 4 in 6eqv

Go back to Sodium Binding Sites List in 6eqv
Sodium binding site 3 out of 4 in the X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-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 the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:32.4
occ:0.50
 O A:SER544 2.2 17.1 1.0
O A:HOH774 2.3 17.8 1.0
C A:SER544 3.1 15.3 1.0
CB A:SER544 3.9 19.8 1.0
OG A:SER544 3.9 26.1 1.0
CA A:SER544 3.9 16.1 1.0
N A:GLY545 4.0 17.4 1.0
CA A:GLY545 4.1 16.3 1.0
CB A:PRO508 4.2 19.0 1.0
N A:SER544 4.3 14.6 1.0
O A:ASP542 4.6 16.7 1.0
OD1 A:ASP542 4.7 20.1 1.0
CG A:ASP542 4.8 23.5 1.0
CG A:PRO508 5.0 18.5 1.0

Sodium binding site 4 out of 4 in 6eqv

Go back to Sodium Binding Sites List in 6eqv
Sodium binding site 4 out of 4 in the X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-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 the Proprotein Convertase Furin Bound with the Competitive Inhibitor Phac-Cit-Val-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na607

b:27.0
occ:0.50
 OE2 A:GLU546 2.4 30.1 1.0
O A:HOH1097 2.4 24.0 1.0
O A:HOH1091 2.5 25.1 1.0
CD A:GLU546 3.6 32.4 1.0
O A:HOH765 4.0 29.8 1.0
O A:HOH1169 4.2 21.9 1.0
O A:HOH1131 4.3 28.9 1.0
OE1 A:GLU546 4.4 30.9 1.0
O A:HOH1095 4.5 37.8 1.0
O A:HOH726 4.5 23.0 1.0
CB A:GLU546 4.5 20.1 1.0
O A:HOH858 4.6 22.9 1.0
CG A:GLU546 4.7 22.2 1.0

Reference:

S.O.Dahms, K.Hardes, T.Steinmetzer, M.E.Than. X-Ray Structures of the Proprotein Convertase Furin Bound with Substrate Analogue Inhibitors Reveal Substrate Specificity Determinants Beyond the S4 Pocket. Biochemistry V. 57 925 2018.
ISSN: ISSN 1520-4995
PubMed: 29314830
DOI: 10.1021/ACS.BIOCHEM.7B01124
Page generated: Tue Oct 8 08:28:13 2024

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