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Sodium in PDB 6hzd: X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba

Enzymatic activity of X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba

All present enzymatic activity of X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba, PDB code: 6hzd was solved by S.O.Dahms, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.94 / 1.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.564, 131.564, 155.338, 90.00, 90.00, 120.00
R / Rfree (%) 16.4 / 18.3

Other elements in 6hzd:

The structure of X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba also contains other interesting chemical elements:

Calcium (Ca) 3 atoms
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba (pdb code 6hzd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba, PDB code: 6hzd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6hzd

Go back to Sodium Binding Sites List in 6hzd
Sodium binding site 1 out of 3 in the X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-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 Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:23.7
occ:1.00
 O A:THR309 2.3 20.4 1.0
O A:SER311 2.3 21.0 1.0
O A:HOH858 2.4 20.8 1.0
OG1 A:THR314 2.4 22.3 1.0
O A:THR314 2.5 22.5 1.0
C A:THR314 3.3 23.6 1.0
C A:THR309 3.4 26.0 1.0
C A:SER311 3.5 23.8 1.0
CB A:THR314 3.6 21.4 1.0
N A:SER311 3.8 21.4 1.0
O A:HOH844 3.8 33.0 1.0
CA A:THR314 3.8 22.1 1.0
CB A:SER316 3.9 22.8 1.0
N A:SER316 3.9 21.9 1.0
N A:THR314 3.9 22.9 1.0
O A:TYR308 4.1 24.1 1.0
CE A:MET534 4.1 23.7 1.0
CA A:THR309 4.1 22.8 1.0
C A:ASN310 4.1 23.7 1.0
CA A:SER311 4.2 22.4 1.0
N A:LEU315 4.3 20.4 1.0
N A:ASN310 4.3 20.1 1.0
CA A:SER316 4.5 22.9 1.0
O A:SER335 4.5 21.6 1.0
CA A:ASN310 4.5 20.4 1.0
N A:ILE312 4.6 22.4 1.0
C A:LEU315 4.6 23.5 1.0
CB A:SER311 4.6 22.7 1.0
CA A:LEU315 4.6 23.5 1.0
O A:ASN310 4.7 24.6 1.0
CG2 A:THR314 4.7 21.5 1.0
CA A:ILE312 4.8 21.9 1.0
C A:ILE312 4.8 24.1 1.0
C A:TYR308 5.0 23.7 1.0

Sodium binding site 2 out of 3 in 6hzd

Go back to Sodium Binding Sites List in 6hzd
Sodium binding site 2 out of 3 in the X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-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 Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:34.5
occ:1.00
 O A:SER279 2.4 27.0 1.0
O A:HOH784 2.4 28.2 1.0
O A:HOH1071 2.4 39.3 1.0
O A:HOH1054 2.5 39.3 1.0
O A:GLY284 2.6 29.1 1.0
O A:HOH825 3.0 44.5 1.0
C A:SER279 3.4 28.5 1.0
C A:GLY284 3.5 29.9 1.0
CA A:GLY284 3.7 28.9 1.0
CA A:SER279 3.9 29.0 1.0
O A:HOH1017 3.9 32.9 1.0
O A:VAL278 4.3 25.6 1.0
O A:HOH830 4.3 35.1 1.0
O A:HOH1076 4.5 35.4 1.0
O A:HOH1060 4.6 40.2 1.0
N A:GLN280 4.6 30.3 1.0
N A:LEU285 4.7 27.0 1.0
CB A:SER279 4.8 26.0 1.0
N A:SER279 5.0 23.6 1.0
O A:HOH1103 5.0 48.0 1.0
CA A:GLN280 5.0 30.0 1.0

Sodium binding site 3 out of 3 in 6hzd

Go back to Sodium Binding Sites List in 6hzd
Sodium binding site 3 out of 3 in the X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-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 Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:37.9
occ:0.50
 O A:SER544 2.2 25.4 1.0
O A:HOH792 2.4 26.3 1.0
C A:SER544 3.2 24.6 1.0
CA A:GLY545 3.9 28.6 1.0
CB A:PRO508 3.9 25.6 1.0
N A:GLY545 3.9 27.5 1.0
CB A:SER544 4.1 25.4 1.0
CA A:SER544 4.1 25.8 1.0
OG A:SER544 4.3 31.0 1.0
N A:SER544 4.5 25.7 1.0
O A:ASP542 4.6 25.9 1.0
CG A:PRO508 4.7 26.2 1.0
O A:HOH721 4.9 36.0 1.0

Reference:

T.Van Lam Van, T.Ivanova, K.Hardes, M.R.Heindl, R.E.Morty, E.Bottcher-Friebertshauser, I.Lindberg, M.E.Than, S.O.Dahms, T.Steinmetzer. Design, Synthesis, and Characterization of Macrocyclic Inhibitors of the Proprotein Convertase Furin. Chemmedchem V. 14 673 2019.
ISSN: ESSN 1860-7187
PubMed: 30680958
DOI: 10.1002/CMDC.201800807
Page generated: Tue Oct 8 09:29:33 2024

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