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

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

All present enzymatic activity of X-Ray Structure of Furin in Complex with the Cyclic Peptide C[Succinyl-Phe-2-Nal-(Arg)4-Lys]-Arg-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)4-Lys]-Arg-4-Amba, PDB code: 6hlb 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) 46.53 / 2.00
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 133.255, 133.255, 157.351, 90.00, 90.00, 120.00
R / Rfree (%) 16.9 / 18.7

Other elements in 6hlb:

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

Sodium binding site 1 out of 3 in 6hlb

Go back to Sodium Binding Sites List in 6hlb
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)4-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 Peptide C[Succinyl-Phe-2-Nal-(Arg)4-Lys]-Arg-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na604

b:27.5
occ:1.00
 O A:SER311 2.4 23.5 1.0
O A:THR314 2.4 25.3 1.0
O A:HOH815 2.4 25.2 1.0
OG1 A:THR314 2.5 24.7 1.0
O A:THR309 2.5 26.5 1.0
C A:THR314 3.2 25.6 1.0
C A:THR309 3.5 30.1 1.0
C A:SER311 3.6 28.0 1.0
CB A:THR314 3.6 27.3 1.0
CA A:THR314 3.8 25.9 1.0
O A:HOH781 3.8 38.4 1.0
N A:THR314 3.9 26.8 1.0
N A:SER311 3.9 26.3 1.0
N A:SER316 4.0 26.6 1.0
CB A:SER316 4.0 28.6 1.0
N A:LEU315 4.2 26.8 1.0
CE A:MET534 4.2 27.8 1.0
O A:TYR308 4.2 30.2 1.0
CA A:SER311 4.3 26.2 1.0
C A:ASN310 4.3 29.4 1.0
CA A:THR309 4.3 27.2 1.0
N A:ASN310 4.5 26.6 1.0
CA A:LEU315 4.5 30.9 1.0
C A:LEU315 4.6 30.4 1.0
CA A:SER316 4.6 31.7 1.0
O A:SER335 4.6 26.2 1.0
N A:ILE312 4.6 26.0 1.0
CA A:ASN310 4.7 27.5 1.0
CB A:SER311 4.7 26.4 1.0
O A:ASN310 4.8 31.5 1.0
CA A:ILE312 4.8 26.8 1.0
C A:ILE312 4.8 28.1 1.0
CG2 A:THR314 4.8 24.4 1.0

Sodium binding site 2 out of 3 in 6hlb

Go back to Sodium Binding Sites List in 6hlb
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)4-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 Peptide C[Succinyl-Phe-2-Nal-(Arg)4-Lys]-Arg-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na605

b:37.5
occ:1.00
 O A:HOH777 2.4 31.3 1.0
O A:SER279 2.4 33.7 1.0
O A:HOH1000 2.6 45.8 1.0
O A:GLY284 2.6 33.6 1.0
O A:HOH990 2.6 43.2 1.0
C A:SER279 3.5 33.6 1.0
C A:GLY284 3.5 34.5 1.0
CA A:GLY284 3.8 33.6 1.0
CA A:SER279 3.9 32.1 1.0
O A:HOH948 4.0 36.0 1.0
O A:HOH759 4.3 37.9 1.0
O A:VAL278 4.3 28.4 1.0
O A:HOH976 4.4 49.1 1.0
O A:HOH1005 4.5 33.5 1.0
N A:GLN280 4.6 32.1 1.0
N A:LEU285 4.7 30.8 1.0
CB A:SER279 4.8 31.1 1.0

Sodium binding site 3 out of 3 in 6hlb

Go back to Sodium Binding Sites List in 6hlb
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)4-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 Peptide C[Succinyl-Phe-2-Nal-(Arg)4-Lys]-Arg-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na606

b:40.5
occ:0.50
 O A:SER544 2.2 29.7 1.0
O A:HOH802 2.5 32.4 1.0
C A:SER544 3.2 29.0 1.0
CA A:GLY545 3.9 31.8 1.0
N A:GLY545 4.0 33.0 1.0
CB A:PRO508 4.0 28.0 1.0
CA A:SER544 4.2 29.9 1.0
CB A:SER544 4.2 30.1 1.0
OG A:SER544 4.3 39.0 1.0
N A:SER544 4.5 28.3 1.0
O A:ASP542 4.7 29.7 1.0
O A:HOH724 4.7 38.3 1.0
CG A:PRO508 4.9 31.3 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 09:20:55 2024

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