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

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

All present enzymatic activity of X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Lys]-Lys-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-Lys]-Lys-4-Amba, PDB code: 6hzb 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) 43.08 / 1.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.616, 131.616, 155.565, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 18.2

Other elements in 6hzb:

The structure of X-Ray Structure of Furin in Complex with the Cyclic Inhibitor C[Glutaryl-Arg-Arg-Lys]-Lys-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-Lys]-Lys-4-Amba (pdb code 6hzb). 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-Lys]-Lys-4-Amba, PDB code: 6hzb:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 6hzb

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

b:20.6
occ:1.00
 O A:THR309 2.3 19.9 1.0
O A:SER311 2.3 18.2 1.0
O A:HOH860 2.4 18.3 1.0
OG1 A:THR314 2.4 19.0 1.0
O A:THR314 2.5 18.7 1.0
C A:THR314 3.3 19.4 1.0
C A:THR309 3.4 21.5 1.0
C A:SER311 3.5 19.9 1.0
CB A:THR314 3.6 19.3 1.0
CA A:THR314 3.8 19.1 1.0
N A:SER311 3.8 19.1 1.0
O A:HOH842 3.8 27.7 1.0
N A:SER316 3.9 18.9 1.0
N A:THR314 3.9 19.6 1.0
CB A:SER316 3.9 20.5 1.0
O A:TYR308 4.0 20.0 1.0
CA A:THR309 4.1 20.7 1.0
CE A:MET534 4.1 19.4 1.0
C A:ASN310 4.1 22.1 1.0
CA A:SER311 4.2 18.1 1.0
N A:LEU315 4.3 18.8 1.0
N A:ASN310 4.3 17.5 1.0
CA A:SER316 4.5 21.3 1.0
O A:SER335 4.5 19.1 1.0
C A:LEU315 4.5 21.6 1.0
N A:ILE312 4.6 17.8 1.0
CA A:ASN310 4.6 19.2 1.0
CA A:LEU315 4.6 20.7 1.0
CB A:SER311 4.6 20.6 1.0
O A:ASN310 4.6 21.2 1.0
CG2 A:THR314 4.7 19.0 1.0
CA A:ILE312 4.7 17.9 1.0
C A:ILE312 4.8 20.6 1.0
C A:TYR308 4.9 20.2 1.0

Sodium binding site 2 out of 3 in 6hzb

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

b:32.3
occ:1.00
 O A:SER279 2.4 25.0 1.0
O A:HOH815 2.4 26.3 1.0
O A:HOH1065 2.5 37.0 1.0
O A:HOH1076 2.5 35.2 1.0
O A:GLY284 2.5 24.7 1.0
O A:HOH827 3.1 39.2 1.0
C A:SER279 3.4 24.6 1.0
C A:GLY284 3.4 26.5 1.0
CA A:GLY284 3.7 26.9 1.0
CA A:SER279 3.9 24.2 1.0
O A:HOH1043 4.0 32.0 1.0
O A:VAL278 4.3 20.4 1.0
O A:HOH775 4.4 31.3 1.0
O A:HOH1062 4.5 40.5 1.0
O A:HOH1080 4.5 32.1 1.0
N A:GLN280 4.6 24.6 1.0
N A:LEU285 4.7 22.5 1.0
CB A:SER279 4.8 21.2 1.0

Sodium binding site 3 out of 3 in 6hzb

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

b:33.7
occ:0.50
 O A:SER544 2.2 22.1 1.0
O A:HOH847 2.4 22.6 1.0
C A:SER544 3.2 22.1 1.0
CA A:GLY545 3.9 23.9 1.0
N A:GLY545 3.9 23.9 1.0
CB A:PRO508 4.0 22.4 1.0
CA A:SER544 4.1 20.7 1.0
CB A:SER544 4.2 23.9 1.0
OG A:SER544 4.2 28.1 1.0
N A:SER544 4.5 21.0 1.0
O A:ASP542 4.6 22.4 1.0
CG A:PRO508 4.9 23.2 1.0
OD1 A:ASP542 5.0 24.2 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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