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

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

All present enzymatic activity of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor Arg-Arg-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 Arg-Arg-Arg-Val-Arg-Amba, PDB code: 6eqx 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) 47.16 / 1.99
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.805, 131.805, 155.347, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 18.4

Other elements in 6eqx:

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

Sodium binding site 1 out of 4 in 6eqx

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

b:14.9
occ:1.00
 O A:SER311 2.3 13.2 1.0
O A:HOH781 2.3 14.1 1.0
O A:THR309 2.4 15.8 1.0
O A:THR314 2.4 11.4 1.0
OG1 A:THR314 2.5 13.2 1.0
C A:THR314 3.3 13.2 1.0
C A:SER311 3.4 13.3 1.0
C A:THR309 3.5 15.6 1.0
O A:HOH880 3.7 24.8 1.0
CB A:THR314 3.7 13.9 1.0
N A:SER311 3.8 12.6 1.0
CA A:THR314 3.8 12.0 1.0
N A:SER316 3.9 14.8 1.0
N A:THR314 3.9 12.0 1.0
CB A:SER316 4.0 15.2 1.0
CE A:MET534 4.0 13.2 1.0
CA A:SER311 4.1 12.2 1.0
O A:TYR308 4.1 15.4 1.0
C A:ASN310 4.2 15.9 1.0
CA A:THR309 4.2 16.1 1.0
N A:LEU315 4.3 13.2 1.0
O A:SER335 4.4 13.6 1.0
N A:ASN310 4.4 13.6 1.0
N A:ILE312 4.5 12.1 1.0
CA A:SER316 4.5 14.8 1.0
CA A:LEU315 4.5 14.3 1.0
C A:LEU315 4.6 17.3 1.0
CB A:SER311 4.6 13.8 1.0
CA A:ASN310 4.7 15.7 1.0
O A:ASN310 4.7 15.5 1.0
CA A:ILE312 4.7 11.7 1.0
C A:ILE312 4.8 13.3 1.0
CG2 A:THR314 4.8 12.2 1.0

Sodium binding site 2 out of 4 in 6eqx

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

b:26.6
occ:1.00
 O A:HOH1091 2.3 30.6 1.0
O A:HOH1102 2.4 36.2 1.0
O A:SER279 2.4 18.3 1.0
O A:HOH794 2.4 20.3 1.0
O A:GLY284 2.5 19.2 1.0
C A:GLY284 3.5 20.1 1.0
C A:SER279 3.5 21.0 1.0
CA A:GLY284 3.7 19.8 1.0
CA A:SER279 3.9 18.2 1.0
O A:HOH1069 3.9 26.5 1.0
O A:HOH1088 4.3 29.4 1.0
O A:VAL278 4.3 14.2 1.0
O A:HOH840 4.4 27.3 1.0
O A:HOH1113 4.5 29.5 1.0
N A:GLN280 4.7 18.2 1.0
N A:LEU285 4.7 17.1 1.0
CB A:SER279 4.8 15.3 1.0
O A:HOH1144 4.9 48.2 1.0
O A:HOH1007 4.9 34.4 1.0

Sodium binding site 3 out of 4 in 6eqx

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

b:31.8
occ:0.50
 O A:SER544 2.2 16.7 1.0
O A:HOH784 2.4 16.9 1.0
C A:SER544 3.1 14.5 1.0
N A:GLY545 3.9 14.8 1.0
CA A:GLY545 4.0 16.4 1.0
CB A:SER544 4.0 17.5 1.0
OG A:SER544 4.0 27.4 1.0
CB A:PRO508 4.0 16.7 1.0
CA A:SER544 4.0 14.8 1.0
N A:SER544 4.4 14.9 1.0
O A:ASP542 4.6 17.0 1.0
CG A:PRO508 4.9 17.6 1.0
OD1 A:ASP542 4.9 16.9 1.0
CG A:ASP542 5.0 21.1 1.0

Sodium binding site 4 out of 4 in 6eqx

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

b:32.0
occ:0.50
 O A:HOH1055 2.4 27.8 1.0
O A:HOH1077 2.4 27.9 1.0
OE2 A:GLU546 2.5 34.3 1.0
CD A:GLU546 3.7 34.6 1.0
O A:HOH777 4.1 30.5 1.0
O A:HOH1134 4.2 26.6 1.0
O A:HOH1106 4.4 30.1 1.0
OE1 A:GLU546 4.4 30.0 1.0
O A:HOH721 4.5 23.1 1.0
O A:HOH857 4.5 24.0 1.0
CB A:GLU546 4.5 16.1 1.0
O A:HOH1090 4.6 42.9 1.0
CG A:GLU546 4.7 19.5 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 08:31:42 2024

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