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Calcium in PDB 5mim: Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N

Enzymatic activity of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N

All present enzymatic activity of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N:
3.4.21.75;

Protein crystallography data

The structure of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N, PDB code: 5mim was solved by S.O.Dahms, J.Guan-Sheng, M.E.Than, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.69 / 1.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 132.204, 132.204, 155.727, 90.00, 90.00, 120.00
R / Rfree (%) 16.5 / 18.4

Other elements in 5mim:

The structure of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N 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 Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N (pdb code 5mim). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N, PDB code: 5mim:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 5mim

Go back to Calcium Binding Sites List in 5mim
Calcium binding site 1 out of 3 in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:22.5
occ:1.00
 O A:ASP181 2.3 20.2 1.0
OD2 A:ASP174 2.3 18.4 1.0
O A:HOH762 2.4 20.7 1.0
O A:HOH1071 2.5 24.2 1.0
O A:HOH736 2.5 22.9 1.0
OD1 A:ASP179 2.5 26.3 1.0
OD2 A:ASP179 2.6 28.6 1.0
CG A:ASP179 2.9 25.2 1.0
CG A:ASP174 3.3 21.1 1.0
C A:ASP181 3.5 18.5 1.0
CB A:ASP174 3.6 20.2 1.0
O A:HOH1107 3.9 39.6 1.0
CB A:ASP181 4.1 24.6 1.0
CA A:ASP181 4.2 19.1 1.0
N A:ASP181 4.4 21.2 1.0
CB A:ASP179 4.4 21.2 1.0
NH2 A:ARG225 4.4 23.2 1.0
OD1 A:ASP174 4.5 17.2 1.0
CB A:ASP177 4.5 18.5 1.0
CG A:ASP181 4.5 35.9 1.0
N A:PRO182 4.6 20.4 1.0
OD2 A:ASP177 4.6 35.9 1.0
N A:GLN183 4.8 21.2 1.0
O A:GLN183 4.8 18.9 1.0
CA A:PRO182 4.8 21.0 1.0
OD2 A:ASP181 4.9 33.1 1.0
O A:HOH1103 4.9 44.2 1.0

Calcium binding site 2 out of 3 in 5mim

Go back to Calcium Binding Sites List in 5mim
Calcium binding site 2 out of 3 in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:22.6
occ:1.00
 O A:VAL210 2.3 20.7 1.0
O A:VAL205 2.3 22.1 1.0
OD2 A:ASP115 2.4 21.3 1.0
OD1 A:ASP162 2.4 23.5 1.0
O A:GLY212 2.5 23.0 1.0
OD1 A:ASN208 2.5 22.7 1.0
OD2 A:ASP162 2.6 24.0 1.0
CG A:ASP162 2.9 22.6 1.0
CG A:ASP115 3.5 20.1 1.0
C A:VAL210 3.5 27.7 1.0
C A:VAL205 3.5 23.8 1.0
CG A:ASN208 3.6 23.8 1.0
C A:GLY212 3.7 23.5 1.0
ND2 A:ASN208 3.9 19.3 1.0
CB A:ASP115 4.1 22.4 1.0
N A:GLY212 4.2 24.2 1.0
CA A:VAL210 4.2 24.2 1.0
N A:VAL210 4.2 23.0 1.0
CB A:VAL210 4.3 26.3 1.0
C A:CYS211 4.3 28.0 1.0
CA A:ALA206 4.4 18.2 1.0
CB A:ASP162 4.4 22.3 1.0
N A:ALA206 4.4 19.0 1.0
OD1 A:ASP115 4.4 20.9 1.0
CA A:VAL205 4.4 20.8 1.0
CA A:GLY212 4.5 18.2 1.0
N A:VAL205 4.5 23.0 1.0
N A:CYS211 4.5 25.7 1.0
O A:CYS211 4.7 21.1 1.0
N A:VAL213 4.7 20.9 1.0
O A:HOH851 4.7 19.3 1.0
C A:ALA206 4.7 24.8 1.0
CA A:VAL213 4.7 15.1 1.0
CG1 A:VAL213 4.8 22.1 1.0
CB A:VAL205 4.8 26.5 1.0
N A:ASN208 4.8 26.1 1.0
CA A:CYS211 4.8 25.6 1.0
CB A:CYS211 4.8 30.0 1.0
CB A:ASN208 4.9 26.5 1.0
N A:ASN207 4.9 24.7 1.0
CG1 A:VAL210 4.9 30.1 1.0
C A:ALA204 4.9 19.6 1.0

Calcium binding site 3 out of 3 in 5mim

Go back to Calcium Binding Sites List in 5mim
Calcium binding site 3 out of 3 in the Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Xray Structure of Human Furin Bound with the 2,5-Dideoxystreptamine Derived Small Molecule Inhibitor 1N within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:15.1
occ:1.00
 OD2 A:ASP301 2.4 14.9 1.0
O A:HOH825 2.4 13.4 1.0
OE1 A:GLU331 2.4 15.5 1.0
OD1 A:ASP258 2.4 17.2 1.0
OE2 A:GLU331 2.5 13.8 1.0
O A:HOH932 2.5 15.7 1.0
O A:HOH1023 2.5 15.9 1.0
CD A:GLU331 2.8 14.8 1.0
CG A:ASP301 3.2 14.4 1.0
CG A:ASP258 3.5 21.8 1.0
OD1 A:ASP301 3.9 16.2 1.0
CB A:ASP301 4.1 12.5 1.0
CA A:ASP258 4.1 18.4 1.0
CB A:ASP258 4.1 21.0 1.0
O A:HOH940 4.3 35.4 1.0
CG A:GLU331 4.3 14.6 1.0
OD2 A:ASP258 4.4 19.0 1.0
O A:HOH859 4.4 15.1 1.0
O A:HOH903 4.5 14.5 1.0
CB A:ASP306 4.5 14.5 1.0
O A:SER293 4.6 18.9 1.0
OD2 A:ASP306 4.6 18.1 1.0
CA A:GLY294 4.6 13.2 1.0
CA A:CYS303 4.8 13.9 1.0
O A:PRO256 4.8 16.7 1.0
O A:GLU257 4.8 17.7 1.0
N A:GLY296 4.9 17.1 1.0
N A:ASP258 4.9 16.3 1.0

Reference:

S.O.Dahms, G.S.Jiao, M.E.Than. Structural Studies Revealed Active Site Distortions of Human Furin By A Small Molecule Inhibitor. Acs Chem. Biol. V. 12 1211 2017.
ISSN: ESSN 1554-8937
PubMed: 28402100
DOI: 10.1021/ACSCHEMBIO.6B01110
Page generated: Mon Jul 15 08:26:20 2024

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