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Calcium 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:

Chlorine (Cl) 1 atom
Sodium (Na) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6hld

Go back to Calcium Binding Sites List in 6hld
Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:37.2
occ:1.00
 O A:HOH755 2.4 37.1 1.0
O A:HOH871 2.4 37.3 1.0
OD2 A:ASP174 2.5 35.0 1.0
O A:ASP181 2.5 38.0 1.0
O A:HOH959 2.5 44.4 1.0
OD2 A:ASP179 2.6 39.5 1.0
OD1 A:ASP179 2.7 39.4 1.0
CG A:ASP179 3.0 41.5 1.0
CG A:ASP174 3.4 35.0 1.0
CB A:ASP174 3.7 34.2 1.0
C A:ASP181 3.7 35.9 1.0
CB A:ASP181 4.1 40.3 1.0
CA A:ASP181 4.3 34.5 1.0
NH2 A:ARG225 4.5 39.6 1.0
N A:ASP181 4.5 34.7 1.0
CB A:ASP179 4.5 37.0 1.0
OD1 A:ASP174 4.6 33.5 1.0
O A:HOH1020 4.6 53.1 1.0
CG A:ASP181 4.6 46.4 1.0
CB A:ASP177 4.7 41.6 1.0
N A:PRO182 4.7 33.7 1.0
N A:GLN183 4.8 38.1 1.0
OD2 A:ASP177 4.8 49.8 1.0
O A:GLN183 4.8 33.7 1.0
CA A:PRO182 4.9 35.5 1.0
OD2 A:ASP181 4.9 52.7 1.0

Calcium binding site 2 out of 3 in 6hld

Go back to Calcium Binding Sites List in 6hld
Calcium 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 Calcium with other atoms in the Ca 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:Ca602

b:34.8
occ:1.00
 O A:VAL210 2.3 31.8 1.0
O A:VAL205 2.3 36.0 1.0
OD2 A:ASP115 2.4 31.4 1.0
O A:GLY212 2.4 35.5 1.0
OD1 A:ASP162 2.4 39.2 1.0
OD2 A:ASP162 2.6 36.6 1.0
OD1 A:ASN208 2.7 37.0 1.0
CG A:ASP162 2.9 41.1 1.0
CG A:ASP115 3.5 36.0 1.0
C A:VAL210 3.5 40.9 1.0
C A:VAL205 3.5 35.9 1.0
C A:GLY212 3.6 40.5 1.0
CG A:ASN208 3.6 38.0 1.0
ND2 A:ASN208 4.0 35.5 1.0
N A:GLY212 4.1 36.1 1.0
CB A:ASP115 4.2 37.1 1.0
C A:CYS211 4.3 40.8 1.0
CA A:VAL210 4.3 37.6 1.0
N A:VAL210 4.3 39.2 1.0
CA A:GLY212 4.4 31.9 1.0
CB A:ASP162 4.4 34.8 1.0
N A:ALA206 4.4 34.4 1.0
CA A:ALA206 4.4 37.2 1.0
CB A:VAL210 4.4 40.5 1.0
OD1 A:ASP115 4.5 33.9 1.0
N A:VAL205 4.5 38.6 1.0
CA A:VAL205 4.5 33.3 1.0
N A:CYS211 4.5 40.9 1.0
O A:CYS211 4.5 34.2 1.0
N A:VAL213 4.6 31.5 1.0
O A:HOH832 4.7 31.6 1.0
CG1 A:VAL213 4.7 35.6 1.0
CA A:VAL213 4.8 33.5 1.0
C A:ALA206 4.8 40.4 1.0
CA A:CYS211 4.8 41.0 1.0
CB A:VAL205 4.8 41.1 1.0
C A:ALA204 4.9 32.7 1.0
CG1 A:VAL210 4.9 37.4 1.0
N A:ASN208 4.9 36.0 1.0
N A:ASN207 4.9 40.6 1.0
CB A:CYS211 5.0 39.8 1.0
CB A:ASN208 5.0 43.9 1.0

Calcium binding site 3 out of 3 in 6hld

Go back to Calcium Binding Sites List in 6hld
Calcium 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 Calcium with other atoms in the Ca 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:Ca603

b:29.0
occ:1.00
 OD1 A:ASP258 2.4 33.5 1.0
O A:HOH770 2.4 25.5 1.0
OD2 A:ASP301 2.4 28.5 1.0
O A:HOH750 2.5 27.2 1.0
OE2 A:GLU331 2.5 29.3 1.0
O A:HOH866 2.5 27.1 1.0
OE1 A:GLU331 2.6 29.4 1.0
CD A:GLU331 2.9 31.4 1.0
CG A:ASP301 3.4 33.4 1.0
CG A:ASP258 3.5 34.8 1.0
OD1 A:ASP301 4.1 31.4 1.0
CB A:ASP258 4.2 32.5 1.0
CB A:ASP301 4.2 28.6 1.0
CA A:ASP258 4.2 32.1 1.0
N35 B:00S7 4.2 29.2 1.0
O A:HOH855 4.3 32.3 1.0
OD2 A:ASP258 4.4 38.1 1.0
CG A:GLU331 4.4 29.5 1.0
O A:SER302 4.5 28.5 1.0
O A:SER293 4.6 26.4 1.0
OD2 A:ASP306 4.6 29.2 1.0
O A:HOH861 4.7 26.8 1.0
O A:GLU257 4.7 26.1 1.0
CB A:ASP306 4.7 24.0 1.0
CA A:GLY294 4.8 29.3 1.0
CA A:CYS303 4.9 25.3 1.0
O A:PRO256 4.9 30.6 1.0
C A:SER302 4.9 31.1 1.0
N A:GLY296 4.9 29.1 1.0
C27 B:00S7 5.0 30.6 1.0
N A:ASP258 5.0 30.7 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: Wed Jul 9 14:38:38 2025

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