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Calcium 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:

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

Calcium binding site 1 out of 3 in 6hlb

Go back to Calcium Binding Sites List in 6hlb
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)4-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 Peptide C[Succinyl-Phe-2-Nal-(Arg)4-Lys]-Arg-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:38.6
occ:1.00
 O A:HOH785 2.3 38.1 1.0
O A:HOH864 2.4 36.8 1.0
O A:ASP181 2.4 36.8 1.0
OD2 A:ASP174 2.4 34.7 1.0
O A:HOH954 2.5 44.7 1.0
OD2 A:ASP179 2.6 43.8 1.0
OD1 A:ASP179 2.6 40.3 1.0
CG A:ASP179 3.0 43.1 1.0
CG A:ASP174 3.4 35.8 1.0
C A:ASP181 3.6 35.8 1.0
CB A:ASP174 3.7 36.3 1.0
CB A:ASP181 4.1 43.2 1.0
CA A:ASP181 4.2 37.7 1.0
N A:ASP181 4.4 38.3 1.0
NH2 A:ARG225 4.4 39.4 1.0
CB A:ASP179 4.5 40.4 1.0
OD1 A:ASP174 4.5 37.1 1.0
CG A:ASP181 4.6 47.0 1.0
O A:HOH1023 4.6 52.8 1.0
N A:PRO182 4.7 35.9 1.0
CB A:ASP177 4.7 42.2 1.0
N A:GLN183 4.8 35.6 1.0
OD2 A:ASP181 4.9 52.3 1.0
O A:GLN183 4.9 31.7 1.0
CA A:PRO182 4.9 37.5 1.0
OD2 A:ASP177 4.9 53.1 1.0

Calcium binding site 2 out of 3 in 6hlb

Go back to Calcium Binding Sites List in 6hlb
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)4-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 Peptide C[Succinyl-Phe-2-Nal-(Arg)4-Lys]-Arg-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:36.1
occ:1.00
 O A:VAL210 2.3 37.0 1.0
O A:VAL205 2.4 37.2 1.0
OD2 A:ASP115 2.4 37.2 1.0
OD1 A:ASP162 2.4 39.3 1.0
O A:GLY212 2.4 35.5 1.0
OD2 A:ASP162 2.6 36.7 1.0
OD1 A:ASN208 2.7 39.5 1.0
CG A:ASP162 2.8 38.7 1.0
CG A:ASP115 3.5 34.7 1.0
C A:VAL210 3.5 40.4 1.0
C A:VAL205 3.6 36.9 1.0
CG A:ASN208 3.7 41.2 1.0
C A:GLY212 3.7 37.9 1.0
ND2 A:ASN208 4.0 36.8 1.0
N A:GLY212 4.2 38.7 1.0
CB A:ASP115 4.2 39.7 1.0
CA A:VAL210 4.3 38.3 1.0
N A:VAL210 4.3 38.9 1.0
C A:CYS211 4.3 40.5 1.0
CB A:ASP162 4.4 34.7 1.0
CB A:VAL210 4.4 39.5 1.0
CA A:GLY212 4.4 35.3 1.0
N A:ALA206 4.4 35.4 1.0
OD1 A:ASP115 4.5 38.6 1.0
CA A:ALA206 4.5 37.1 1.0
N A:VAL205 4.5 38.4 1.0
CA A:VAL205 4.5 36.3 1.0
N A:CYS211 4.5 38.4 1.0
O A:CYS211 4.6 38.2 1.0
N A:VAL213 4.7 33.3 1.0
O A:HOH826 4.7 34.6 1.0
CA A:VAL213 4.8 33.1 1.0
CG1 A:VAL213 4.8 39.4 1.0
CA A:CYS211 4.8 40.5 1.0
C A:ALA206 4.8 41.8 1.0
CB A:VAL205 4.9 43.4 1.0
CG1 A:VAL210 4.9 36.5 1.0
N A:ASN208 4.9 41.0 1.0
CB A:CYS211 4.9 37.7 1.0
C A:ALA204 4.9 31.7 1.0
N A:ASN207 4.9 42.6 1.0
CB A:ASN208 5.0 46.1 1.0

Calcium binding site 3 out of 3 in 6hlb

Go back to Calcium Binding Sites List in 6hlb
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)4-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 Peptide C[Succinyl-Phe-2-Nal-(Arg)4-Lys]-Arg-4-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:29.2
occ:1.00
 O A:HOH793 2.4 26.8 1.0
OD1 A:ASP258 2.4 32.9 1.0
OD2 A:ASP301 2.4 27.2 1.0
O A:HOH741 2.5 29.6 1.0
O A:HOH836 2.5 28.2 1.0
OE2 A:GLU331 2.5 28.0 1.0
OE1 A:GLU331 2.5 29.8 1.0
CD A:GLU331 2.9 33.1 1.0
CG A:ASP301 3.3 33.8 1.0
CG A:ASP258 3.5 35.7 1.0
OD1 A:ASP301 4.1 30.2 1.0
CB A:ASP301 4.2 28.8 1.0
N35 B:00S7 4.2 26.7 1.0
CB A:ASP258 4.2 33.6 1.0
CA A:ASP258 4.3 34.4 1.0
O A:HOH838 4.3 32.6 1.0
OD2 A:ASP258 4.4 33.6 1.0
CG A:GLU331 4.4 27.2 1.0
O A:SER302 4.5 30.4 1.0
OD2 A:ASP306 4.6 30.8 1.0
O A:HOH865 4.6 31.0 1.0
O A:GLU257 4.6 29.4 1.0
O A:SER293 4.7 24.9 1.0
CB A:ASP306 4.7 27.5 1.0
CA A:GLY294 4.7 27.2 1.0
CA A:CYS303 4.9 28.0 1.0
C27 B:00S7 4.9 28.5 1.0
N A:GLY296 4.9 28.4 1.0
C A:SER302 5.0 34.3 1.0
N A:ASP258 5.0 32.6 1.0
O A:PRO256 5.0 29.3 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 Jul 16 08:26:19 2024

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