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Sodium in PDB 6eqw: X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba

Enzymatic activity of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba

All present enzymatic activity of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-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 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba, PDB code: 6eqw 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 / 1.99
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.713, 131.713, 155.393, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 18.4

Other elements in 6eqw:

The structure of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-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 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba (pdb code 6eqw). 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 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba, PDB code: 6eqw:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 6eqw

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

b:16.2
occ:1.00
 O A:SER311 2.2 13.9 1.0
O A:THR309 2.3 16.3 1.0
O A:HOH798 2.4 15.4 1.0
OG1 A:THR314 2.4 13.9 1.0
O A:THR314 2.4 12.7 1.0
C A:THR314 3.2 15.3 1.0
C A:THR309 3.4 15.3 1.0
C A:SER311 3.4 15.8 1.0
CB A:THR314 3.6 15.9 1.0
N A:SER311 3.7 15.8 1.0
O A:HOH863 3.7 23.8 1.0
CA A:THR314 3.8 16.2 1.0
N A:SER316 3.9 16.9 1.0
N A:THR314 3.9 14.3 1.0
CB A:SER316 4.0 16.4 1.0
O A:TYR308 4.1 16.2 1.0
CA A:SER311 4.1 15.9 1.0
CE A:MET534 4.1 16.3 1.0
C A:ASN310 4.1 18.5 1.0
CA A:THR309 4.2 15.6 1.0
N A:LEU315 4.2 14.6 1.0
N A:ASN310 4.3 13.9 1.0
N A:ILE312 4.5 13.2 1.0
CA A:SER316 4.5 18.1 1.0
O A:SER335 4.5 15.0 1.0
C A:LEU315 4.5 18.1 1.0
CA A:LEU315 4.6 16.9 1.0
CA A:ASN310 4.6 15.7 1.0
CB A:SER311 4.6 16.7 1.0
O A:ASN310 4.7 16.5 1.0
CA A:ILE312 4.7 12.8 1.0
CG2 A:THR314 4.7 13.1 1.0
C A:ILE312 4.8 15.7 1.0

Sodium binding site 2 out of 4 in 6eqw

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

b:27.2
occ:1.00
 O A:HOH1088 2.4 31.7 1.0
O A:SER279 2.4 21.7 1.0
O A:HOH1107 2.5 34.3 1.0
O A:HOH778 2.5 22.3 1.0
O A:GLY284 2.5 21.8 1.0
C A:SER279 3.5 23.8 1.0
C A:GLY284 3.5 22.5 1.0
CA A:GLY284 3.7 22.9 1.0
CA A:SER279 3.9 20.9 1.0
O A:HOH1087 4.0 30.3 1.0
O A:HOH1086 4.3 32.8 1.0
O A:VAL278 4.3 17.0 1.0
O A:HOH843 4.3 30.3 1.0
O A:HOH1113 4.5 31.4 1.0
N A:GLN280 4.6 21.1 1.0
N A:LEU285 4.7 18.4 1.0
CB A:SER279 4.8 18.1 1.0
O A:HOH1053 4.9 39.6 1.0
N A:SER279 5.0 15.9 1.0

Sodium binding site 3 out of 4 in 6eqw

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

b:33.3
occ:0.50
 O A:SER544 2.2 18.4 1.0
O A:HOH761 2.4 17.6 1.0
C A:SER544 3.1 17.1 1.0
N A:GLY545 3.9 18.9 1.0
CA A:GLY545 4.0 19.8 1.0
CB A:SER544 4.0 18.9 1.0
CB A:PRO508 4.0 17.6 1.0
CA A:SER544 4.0 17.8 1.0
OG A:SER544 4.0 27.5 1.0
N A:SER544 4.4 17.5 1.0
O A:ASP542 4.7 19.3 1.0
CG A:PRO508 4.9 19.3 1.0
OD1 A:ASP542 4.9 18.8 1.0
CG A:ASP542 5.0 22.2 1.0

Sodium binding site 4 out of 4 in 6eqw

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

b:36.7
occ:0.50
 O A:HOH1043 2.4 30.2 1.0
O A:HOH1064 2.5 27.6 1.0
OE2 A:GLU546 2.5 36.0 1.0
CD A:GLU546 3.7 34.6 1.0
O A:HOH823 4.2 30.4 1.0
O A:HOH1140 4.2 25.8 1.0
O A:HOH1095 4.3 28.9 1.0
OE1 A:GLU546 4.4 31.7 1.0
O A:HOH753 4.5 22.6 1.0
O A:HOH826 4.5 26.8 1.0
CB A:GLU546 4.5 18.4 1.0
O A:HOH1079 4.6 39.0 1.0
CG A:GLU546 4.7 20.9 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 Dec 15 12:12:03 2020

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