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Sodium in PDB 6hld: X-Ray Structure of Furin in Complex with the Cyclic Peptide C[Succinyl-Phe-2-Nal-(Arg)3-Lys]-Lys-4-Amba

Enzymatic activity of X-Ray Structure of Furin in Complex with the Cyclic Peptide C[Succinyl-Phe-2-Nal-(Arg)3-Lys]-Lys-4-Amba

All present enzymatic activity of X-Ray Structure of Furin in Complex with the Cyclic Peptide C[Succinyl-Phe-2-Nal-(Arg)3-Lys]-Lys-4-Amba:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of Furin in Complex with the Cyclic Peptide C[Succinyl-Phe-2-Nal-(Arg)3-Lys]-Lys-4-Amba, PDB code: 6hld 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) 46.56 / 2.10
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 133.395, 133.395, 157.375, 90.00, 90.00, 120.00
R / Rfree (%) 17 / 19.6

Other elements in 6hld:

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

Sodium binding site 1 out of 3 in 6hld

Go back to Sodium Binding Sites List in 6hld
Sodium binding site 1 out of 3 in the X-Ray Structure of Furin in Complex with the Cyclic Peptide C[Succinyl-Phe-2-Nal-(Arg)3-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 Peptide C[Succinyl-Phe-2-Nal-(Arg)3-Lys]-Lys-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:26.3
occ:1.00
 O A:SER311 2.3 23.0 1.0
O A:THR309 2.4 26.9 1.0
O A:THR314 2.5 25.3 1.0
O A:HOH809 2.5 24.0 1.0
OG1 A:THR314 2.6 26.2 1.0
C A:THR314 3.3 26.9 1.0
C A:THR309 3.5 28.5 1.0
C A:SER311 3.5 27.9 1.0
CB A:THR314 3.7 27.6 1.0
N A:SER311 3.8 25.9 1.0
CA A:THR314 3.8 26.6 1.0
O A:HOH760 3.9 34.7 1.0
N A:THR314 3.9 27.4 1.0
N A:SER316 3.9 23.8 1.0
CB A:SER316 4.0 27.9 1.0
CA A:SER311 4.2 26.2 1.0
C A:ASN310 4.2 27.2 1.0
O A:TYR308 4.2 28.2 1.0
CE A:MET534 4.2 26.1 1.0
CA A:THR309 4.2 27.4 1.0
N A:LEU315 4.3 27.8 1.0
N A:ASN310 4.4 24.2 1.0
O A:SER335 4.5 23.9 1.0
CA A:SER316 4.6 27.2 1.0
N A:ILE312 4.6 22.3 1.0
C A:LEU315 4.6 30.9 1.0
CA A:LEU315 4.6 29.9 1.0
CA A:ASN310 4.7 26.4 1.0
CB A:SER311 4.7 27.1 1.0
O A:ASN310 4.7 27.9 1.0
CA A:ILE312 4.8 23.2 1.0
C A:ILE312 4.8 29.0 1.0
CG2 A:THR314 4.9 24.2 1.0

Sodium binding site 2 out of 3 in 6hld

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

b:40.9
occ:1.00
 O A:SER279 2.4 36.0 1.0
O A:HOH769 2.5 31.8 1.0
O A:HOH996 2.6 42.5 1.0
O A:HOH1011 2.6 48.3 1.0
O A:GLY284 2.8 31.6 1.0
C A:SER279 3.5 30.2 1.0
C A:GLY284 3.7 35.7 1.0
CA A:SER279 3.9 33.7 1.0
CA A:GLY284 3.9 33.3 1.0
O A:HOH974 4.1 39.5 1.0
O A:HOH763 4.2 40.3 1.0
O A:VAL278 4.4 27.3 1.0
O A:HOH988 4.4 46.0 1.0
O A:HOH1015 4.5 35.4 1.0
N A:GLN280 4.7 34.2 1.0
CB A:SER279 4.7 30.5 1.0
N A:LEU285 4.9 31.2 1.0

Sodium binding site 3 out of 3 in 6hld

Go back to Sodium Binding Sites List in 6hld
Sodium binding site 3 out of 3 in the X-Ray Structure of Furin in Complex with the Cyclic Peptide C[Succinyl-Phe-2-Nal-(Arg)3-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 Peptide C[Succinyl-Phe-2-Nal-(Arg)3-Lys]-Lys-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:38.3
occ:0.50
 O A:SER544 2.2 29.0 1.0
O A:HOH787 2.4 30.6 1.0
C A:SER544 3.2 28.9 1.0
CA A:GLY545 3.9 28.7 1.0
N A:GLY545 4.0 29.8 1.0
CB A:PRO508 4.1 26.0 1.0
CA A:SER544 4.2 28.5 1.0
OG A:SER544 4.2 38.3 1.0
CB A:SER544 4.2 30.0 1.0
N A:SER544 4.5 28.2 1.0
O A:ASP542 4.7 28.9 1.0
O A:HOH724 4.8 34.9 1.0
CG A:PRO508 4.9 28.8 1.0
OD1 A:ASP542 5.0 29.4 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 09:21:38 2024

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