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Calcium 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:

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 Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba (pdb code 6hzd). 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 Inhibitor C[Glutaryl-Arg-Arg-Arg-Lys]-Arg-4-Amba, PDB code: 6hzd:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6hzd

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Calcium 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 Calcium with other atoms in the Ca 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:Ca601

b:33.1
occ:1.00
 OD2 A:ASP174 2.4 29.5 1.0
O A:HOH854 2.4 33.4 1.0
O A:HOH849 2.4 34.0 1.0
O A:ASP181 2.4 32.0 1.0
O A:HOH1052 2.5 36.5 1.0
OD2 A:ASP179 2.5 37.8 1.0
OD1 A:ASP179 2.6 36.0 1.0
CG A:ASP179 2.9 34.8 1.0
CG A:ASP174 3.3 31.1 1.0
CB A:ASP174 3.6 32.5 1.0
C A:ASP181 3.6 30.9 1.0
CB A:ASP181 4.0 36.5 1.0
CA A:ASP181 4.2 31.7 1.0
N A:ASP181 4.4 32.6 1.0
NH2 A:ARG225 4.4 35.9 1.0
CB A:ASP179 4.4 33.8 1.0
OD1 A:ASP174 4.5 28.4 1.0
CB A:ASP177 4.5 35.8 1.0
O A:HOH1092 4.5 45.8 1.0
CG A:ASP181 4.5 40.8 1.0
N A:PRO182 4.7 32.3 1.0
OD2 A:ASP177 4.7 44.6 1.0
N A:GLN183 4.8 31.5 1.0
CA A:PRO182 4.9 29.7 1.0
O A:GLN183 4.9 28.6 1.0
OD2 A:ASP181 5.0 43.2 1.0
OD1 A:ASP181 5.0 35.4 1.0

Calcium binding site 2 out of 3 in 6hzd

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

b:32.3
occ:1.00
 O A:VAL210 2.3 29.6 1.0
O A:VAL205 2.3 32.7 1.0
OD2 A:ASP115 2.4 30.7 1.0
OD1 A:ASP162 2.4 32.9 1.0
O A:GLY212 2.4 32.0 1.0
OD1 A:ASN208 2.6 33.9 1.0
OD2 A:ASP162 2.6 31.9 1.0
CG A:ASP162 2.9 33.6 1.0
CG A:ASP115 3.5 29.6 1.0
C A:VAL210 3.5 33.3 1.0
C A:VAL205 3.5 28.9 1.0
CG A:ASN208 3.6 35.5 1.0
C A:GLY212 3.6 34.1 1.0
ND2 A:ASN208 4.0 32.3 1.0
CB A:ASP115 4.1 32.3 1.0
N A:GLY212 4.2 32.2 1.0
CA A:VAL210 4.2 33.3 1.0
N A:VAL210 4.2 32.8 1.0
C A:CYS211 4.3 35.6 1.0
CB A:VAL210 4.3 34.3 1.0
CB A:ASP162 4.4 31.5 1.0
N A:ALA206 4.4 30.3 1.0
CA A:ALA206 4.4 30.2 1.0
N A:VAL205 4.4 33.0 1.0
CA A:GLY212 4.4 30.3 1.0
CA A:VAL205 4.4 31.3 1.0
OD1 A:ASP115 4.4 33.0 1.0
N A:CYS211 4.5 31.6 1.0
O A:CYS211 4.5 32.6 1.0
N A:VAL213 4.6 27.9 1.0
O A:HOH841 4.7 29.7 1.0
CA A:VAL213 4.7 27.0 1.0
CG1 A:VAL213 4.7 32.2 1.0
C A:ALA206 4.8 33.9 1.0
CA A:CYS211 4.8 36.1 1.0
CB A:VAL205 4.8 37.1 1.0
N A:ASN208 4.8 32.0 1.0
C A:ALA204 4.9 29.5 1.0
N A:ASN207 4.9 35.3 1.0
CG1 A:VAL210 4.9 33.7 1.0
CB A:CYS211 4.9 33.9 1.0
CB A:ASN208 4.9 35.6 1.0

Calcium binding site 3 out of 3 in 6hzd

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

b:23.9
occ:1.00
 OD2 A:ASP301 2.4 22.9 1.0
O A:HOH808 2.4 22.5 1.0
OE1 A:GLU331 2.4 23.9 1.0
O A:HOH902 2.4 23.3 1.0
OD1 A:ASP258 2.4 26.9 1.0
OE2 A:GLU331 2.5 23.9 1.0
O A:HOH853 2.5 23.1 1.0
CD A:GLU331 2.8 24.6 1.0
CG A:ASP301 3.3 26.9 1.0
CG A:ASP258 3.5 28.8 1.0
OD1 A:ASP301 4.0 24.6 1.0
N35 B:00S6 4.1 24.9 1.0
CB A:ASP301 4.1 22.7 1.0
CB A:ASP258 4.2 30.3 1.0
CA A:ASP258 4.2 23.5 1.0
O A:HOH869 4.2 27.3 1.0
CG A:GLU331 4.3 23.6 1.0
OD2 A:ASP258 4.4 28.4 1.0
O A:HOH903 4.5 26.5 1.0
O A:SER302 4.5 22.8 1.0
O A:SER293 4.6 22.0 1.0
OD2 A:ASP306 4.6 25.6 1.0
CA A:GLY294 4.6 23.6 1.0
O A:GLU257 4.6 24.7 1.0
CB A:ASP306 4.6 23.9 1.0
CA A:CYS303 4.8 24.0 1.0
C27 B:00S6 4.8 25.0 1.0
N A:GLY296 4.9 25.3 1.0
O A:PRO256 4.9 23.7 1.0
C A:SER302 4.9 27.0 1.0
N A:ASP258 4.9 27.3 1.0
CA A:GLY296 5.0 25.1 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 Jul 16 08:36:12 2024

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