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Calcium in PDB 6eqw: X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba

Enzymatic activity of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba

All present enzymatic activity of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba, PDB code: 6eqw was solved by S.O.Dahms, M.E.Than, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.98 / 1.99
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 131.713, 131.713, 155.393, 90.00, 90.00, 120.00
R / Rfree (%) 16.2 / 18.4

Other elements in 6eqw:

The structure of X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba also contains other interesting chemical elements:

Chlorine (Cl) 1 atom
Sodium (Na) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba (pdb code 6eqw). 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 the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba, PDB code: 6eqw:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 6eqw

Go back to Calcium Binding Sites List in 6eqw
Calcium binding site 1 out of 3 in the X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-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 the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:25.9
occ:1.00
 OD2 A:ASP174 2.3 23.6 1.0
O A:ASP181 2.4 24.3 1.0
O A:HOH755 2.4 26.8 1.0
O A:HOH1084 2.4 28.0 1.0
O A:HOH777 2.5 26.3 1.0
OD1 A:ASP179 2.6 26.1 1.0
OD2 A:ASP179 2.6 29.9 1.0
CG A:ASP179 2.9 24.4 1.0
CG A:ASP174 3.3 23.9 1.0
CB A:ASP174 3.5 21.7 1.0
C A:ASP181 3.5 23.2 1.0
CB A:ASP181 4.0 26.5 1.0
CA A:ASP181 4.2 23.1 1.0
N A:ASP181 4.3 25.5 1.0
OD1 A:ASP174 4.4 20.0 1.0
CB A:ASP179 4.4 22.3 1.0
CB A:ASP177 4.6 25.3 1.0
CG A:ASP181 4.6 35.6 1.0
OD2 A:ASP177 4.6 37.7 1.0
NH2 A:ARG225 4.6 24.0 1.0
N A:PRO182 4.6 23.5 1.0
N A:GLN183 4.8 24.2 1.0
O A:GLN183 4.8 18.7 1.0
CA A:PRO182 4.8 21.6 1.0
O A:HOH1120 4.9 43.9 1.0
CD A:ARG225 5.0 17.1 1.0
OD1 A:ASP181 5.0 28.9 1.0

Calcium binding site 2 out of 3 in 6eqw

Go back to Calcium Binding Sites List in 6eqw
Calcium binding site 2 out of 3 in the X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-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 the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:24.2
occ:1.00
 O A:VAL205 2.3 25.4 1.0
O A:VAL210 2.3 23.6 1.0
OD2 A:ASP115 2.3 26.4 1.0
O A:GLY212 2.4 24.3 1.0
OD1 A:ASP162 2.4 25.0 1.0
OD1 A:ASN208 2.5 26.6 1.0
OD2 A:ASP162 2.5 28.6 1.0
CG A:ASP162 2.8 26.9 1.0
CG A:ASP115 3.4 23.8 1.0
C A:VAL205 3.4 23.5 1.0
C A:VAL210 3.5 29.9 1.0
CG A:ASN208 3.5 25.8 1.0
C A:GLY212 3.6 27.3 1.0
ND2 A:ASN208 3.9 23.6 1.0
CB A:ASP115 4.1 24.9 1.0
N A:GLY212 4.2 27.0 1.0
N A:VAL210 4.3 26.8 1.0
CA A:VAL210 4.3 26.8 1.0
C A:CYS211 4.3 30.9 1.0
N A:ALA206 4.3 25.5 1.0
CA A:ALA206 4.3 20.8 1.0
CB A:ASP162 4.4 23.4 1.0
CB A:VAL210 4.4 30.4 1.0
CA A:VAL205 4.4 23.1 1.0
OD1 A:ASP115 4.4 24.4 1.0
N A:VAL205 4.4 25.1 1.0
CA A:GLY212 4.4 22.1 1.0
O A:CYS211 4.5 26.8 1.0
N A:CYS211 4.5 28.2 1.0
N A:VAL213 4.6 22.5 1.0
CA A:VAL213 4.7 22.3 1.0
CG1 A:VAL213 4.7 27.3 1.0
O A:HOH880 4.7 22.5 1.0
C A:ALA206 4.7 27.7 1.0
CB A:VAL205 4.7 27.0 1.0
N A:ASN208 4.8 25.9 1.0
N A:ASN207 4.8 28.6 1.0
CA A:CYS211 4.8 27.3 1.0
CB A:ASN208 4.9 30.9 1.0
C A:ALA204 4.9 22.6 1.0
CG1 A:VAL210 4.9 33.0 1.0
CB A:CYS211 5.0 27.6 1.0

Calcium binding site 3 out of 3 in 6eqw

Go back to Calcium Binding Sites List in 6eqw
Calcium binding site 3 out of 3 in the X-Ray Structure of the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-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 the Proprotein Convertase Furin Bound with the Competitive Inhibitor 4-Aminomethyl-Phenylacetyl-Arg-Val-Arg-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:15.8
occ:1.00
 OD2 A:ASP301 2.4 16.2 1.0
O A:HOH825 2.4 16.2 1.0
OD1 A:ASP258 2.4 18.5 1.0
O A:HOH795 2.4 16.6 1.0
OE1 A:GLU331 2.4 17.0 1.0
O A:HOH923 2.4 16.5 1.0
OE2 A:GLU331 2.5 16.5 1.0
CD A:GLU331 2.8 17.5 1.0
CG A:ASP301 3.3 17.6 1.0
CG A:ASP258 3.5 20.4 1.0
N35 D:00S5 4.1 17.5 1.0
OD1 A:ASP301 4.1 18.1 1.0
CB A:ASP301 4.1 16.9 1.0
CB A:ASP258 4.2 18.2 1.0
O A:HOH935 4.2 21.2 1.0
CA A:ASP258 4.2 17.9 1.0
CG A:GLU331 4.3 18.1 1.0
OD2 A:ASP258 4.3 17.0 1.0
O A:HOH874 4.5 20.4 1.0
O A:SER302 4.5 18.7 1.0
OD2 A:ASP306 4.5 16.2 1.0
O A:SER293 4.5 17.7 1.0
CA A:GLY294 4.6 14.5 1.0
O A:GLU257 4.7 17.0 1.0
CB A:ASP306 4.7 16.7 1.0
CA A:CYS303 4.8 19.2 1.0
C27 D:00S5 4.8 19.1 1.0
O A:PRO256 4.8 17.8 1.0
N A:GLY296 4.8 18.0 1.0
C A:SER302 4.9 21.0 1.0
N A:ASP258 5.0 19.1 1.0

Reference:

S.O.Dahms, K.Hardes, T.Steinmetzer, M.E.Than. X-Ray Structures of the Proprotein Convertase Furin Bound with Substrate Analogue Inhibitors Reveal Substrate Specificity Determinants Beyond the S4 Pocket. Biochemistry V. 57 925 2018.
ISSN: ISSN 1520-4995
PubMed: 29314830
DOI: 10.1021/ACS.BIOCHEM.7B01124
Page generated: Mon Jul 15 18:35:18 2024

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