Calcium in PDB 5jmo: X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14

Enzymatic activity of X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14

All present enzymatic activity of X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14, PDB code: 5jmo 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) 66.38 / 2.00
Space group P 21 2 21
Cell size a, b, c (Å), α, β, γ (°) 169.775, 50.039, 144.244, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 19.7

Other elements in 5jmo:

The structure of X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14 (pdb code 5jmo). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14, PDB code: 5jmo:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5jmo

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Calcium binding site 1 out of 6 in the X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14


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 Inhibitory Antibody NB14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:17.2
occ:1.00
 OD2 A:ASP174 2.3 14.7 1.0
O A:ASP181 2.4 14.4 1.0
O A:HOH769 2.5 16.8 1.0
O A:HOH859 2.5 19.1 1.0
O A:HOH1008 2.5 17.9 1.0
OD1 A:ASP179 2.5 19.0 1.0
OD2 A:ASP179 2.6 22.3 1.0
CG A:ASP179 2.9 18.8 1.0
CG A:ASP174 3.3 16.3 1.0
C A:ASP181 3.6 16.3 1.0
CB A:ASP174 3.6 15.2 1.0
CB A:ASP181 4.1 16.7 1.0
CA A:ASP181 4.2 16.7 1.0
CB A:ASP179 4.4 15.7 1.0
OD1 A:ASP174 4.4 15.7 1.0
O A:HOH1016 4.5 35.9 1.0
N A:ASP181 4.5 20.7 1.0
NH2 A:ARG225 4.5 14.2 1.0
CB A:ASP177 4.6 17.6 1.0
N A:PRO182 4.6 14.2 1.0
O A:HOH1022 4.6 33.2 1.0
CG A:ASP181 4.6 20.2 1.0
OD2 A:ASP177 4.7 25.6 1.0
O A:HOH891 4.8 39.6 1.0
O A:GLN183 4.9 13.5 1.0
N A:GLN183 4.9 13.7 1.0
CA A:PRO182 4.9 13.9 1.0

Calcium binding site 2 out of 6 in 5jmo

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Calcium binding site 2 out of 6 in the X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14


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 Inhibitory Antibody NB14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:18.9
occ:1.00
 O A:VAL210 2.3 20.0 1.0
O A:VAL205 2.3 18.0 1.0
O A:GLY212 2.4 18.7 1.0
OD2 A:ASP115 2.4 21.1 1.0
OD1 A:ASP162 2.5 18.2 1.0
OD2 A:ASP162 2.6 19.9 1.0
OD1 A:ASN208 2.6 21.5 1.0
CG A:ASP162 2.9 17.2 1.0
CG A:ASP115 3.5 18.6 1.0
C A:VAL210 3.5 21.1 1.0
C A:VAL205 3.5 18.0 1.0
C A:GLY212 3.6 16.1 1.0
CG A:ASN208 3.6 16.6 1.0
ND2 A:ASN208 3.9 18.7 1.0
N A:GLY212 4.1 19.2 1.0
CB A:ASP115 4.1 16.6 1.0
N A:VAL210 4.2 20.6 1.0
CA A:VAL210 4.2 18.1 1.0
C A:CYS211 4.3 24.7 1.0
CA A:GLY212 4.3 14.0 1.0
N A:ALA206 4.4 21.1 1.0
CB A:ASP162 4.4 14.4 1.0
CA A:ALA206 4.4 19.3 1.0
CA A:VAL205 4.4 16.0 1.0
N A:VAL205 4.4 15.9 1.0
OD1 A:ASP115 4.4 20.6 1.0
CB A:VAL210 4.4 20.8 1.0
N A:CYS211 4.5 21.4 1.0
N A:VAL213 4.6 14.4 1.0
O A:CYS211 4.6 24.6 1.0
O A:HOH910 4.7 21.0 1.0
CA A:CYS211 4.7 20.7 1.0
CA A:VAL213 4.7 15.2 1.0
CG1 A:VAL213 4.8 20.2 1.0
CB A:CYS211 4.8 21.6 1.0
N A:ASN208 4.8 20.3 1.0
CB A:VAL205 4.8 19.4 1.0
C A:ALA206 4.8 17.9 1.0
C A:ALA204 4.9 15.7 1.0
CB A:ASN208 4.9 20.4 1.0
N A:ASN207 4.9 21.4 1.0
CB A:ALA204 5.0 12.4 1.0

Calcium binding site 3 out of 6 in 5jmo

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Calcium binding site 3 out of 6 in the X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14


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 Inhibitory Antibody NB14 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:14.8
occ:1.00
 O A:HOH808 2.3 12.4 1.0
OD2 A:ASP301 2.3 16.1 1.0
OD1 A:ASP258 2.4 13.8 1.0
OE1 A:GLU331 2.4 15.1 1.0
O A:HOH955 2.4 15.3 1.0
O A:HOH948 2.6 14.8 1.0
OE2 A:GLU331 2.6 11.3 1.0
CD A:GLU331 2.8 16.0 1.0
CG A:ASP301 3.3 17.6 1.0
CG A:ASP258 3.5 15.2 1.0
NH2 G:AR75 3.9 15.4 1.0
OD1 A:ASP301 4.0 16.8 1.0
CB A:ASP301 4.1 13.9 1.0
CB A:ASP258 4.1 12.7 1.0
CA A:ASP258 4.1 18.4 1.0
O A:HOH953 4.2 17.5 1.0
CG A:GLU331 4.3 14.9 1.0
OD2 A:ASP258 4.4 16.9 1.0
CA A:GLY294 4.4 11.8 1.0
O A:SER293 4.5 14.1 1.0
OD2 A:ASP306 4.6 18.1 1.0
O A:HOH901 4.6 17.2 1.0
CB A:ASP306 4.6 15.3 1.0
CZ G:AR75 4.6 18.2 1.0
O A:GLU257 4.7 16.6 1.0
O A:SER302 4.7 18.1 1.0
CA A:CYS303 4.8 16.1 1.0
O A:PRO256 4.8 17.0 1.0
N A:GLY296 4.9 15.4 1.0
N A:ASP258 4.9 16.1 1.0
C A:SER302 5.0 16.9 1.0

Calcium binding site 4 out of 6 in 5jmo

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Calcium binding site 4 out of 6 in the X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:14.3
occ:1.00
 OD2 B:ASP174 2.3 14.9 1.0
O B:HOH1029 2.3 18.5 1.0
O B:ASP181 2.4 14.4 1.0
O B:HOH934 2.4 16.0 1.0
O B:HOH757 2.5 15.8 1.0
OD1 B:ASP179 2.5 16.0 1.0
OD2 B:ASP179 2.6 19.6 1.0
CG B:ASP179 2.9 17.8 1.0
CG B:ASP174 3.3 15.8 1.0
C B:ASP181 3.5 14.1 1.0
CB B:ASP174 3.6 15.4 1.0
CB B:ASP181 4.1 18.8 1.0
CA B:ASP181 4.2 15.9 1.0
CB B:ASP179 4.4 15.4 1.0
OD1 B:ASP174 4.4 13.3 1.0
N B:ASP181 4.5 15.0 1.0
NH2 B:ARG225 4.5 16.1 1.0
CB B:ASP177 4.6 17.9 1.0
CG B:ASP181 4.6 21.6 1.0
N B:PRO182 4.6 12.0 1.0
OD2 B:ASP177 4.8 28.1 1.0
O B:GLN183 4.9 12.7 1.0
N B:GLN183 4.9 11.0 1.0
CA B:PRO182 4.9 12.2 1.0
OD1 B:ASP181 4.9 15.7 1.0

Calcium binding site 5 out of 6 in 5jmo

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Calcium binding site 5 out of 6 in the X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:12.9
occ:1.00
 O B:VAL205 2.3 9.1 1.0
OD2 B:ASP115 2.4 13.9 1.0
O B:VAL210 2.4 12.7 1.0
O B:GLY212 2.4 11.8 1.0
OD1 B:ASP162 2.5 13.0 1.0
OD2 B:ASP162 2.6 12.4 1.0
OD1 B:ASN208 2.6 9.8 1.0
CG B:ASP162 2.9 11.8 1.0
CG B:ASP115 3.5 12.7 1.0
C B:VAL210 3.5 12.7 1.0
C B:VAL205 3.5 10.8 1.0
C B:GLY212 3.6 11.3 1.0
CG B:ASN208 3.6 9.9 1.0
ND2 B:ASN208 4.0 10.7 1.0
N B:GLY212 4.1 9.7 1.0
CB B:ASP115 4.1 10.0 1.0
CA B:VAL210 4.2 11.3 1.0
N B:VAL210 4.2 13.2 1.0
C B:CYS211 4.3 12.6 1.0
CB B:VAL210 4.3 12.4 1.0
CA B:GLY212 4.3 11.8 1.0
CA B:ALA206 4.3 10.2 1.0
N B:ALA206 4.4 10.2 1.0
CB B:ASP162 4.4 13.6 1.0
OD1 B:ASP115 4.5 11.6 1.0
CA B:VAL205 4.5 9.7 1.0
N B:CYS211 4.6 10.7 1.0
O B:CYS211 4.6 12.4 1.0
N B:VAL213 4.6 11.2 1.0
N B:VAL205 4.6 10.2 1.0
O B:HOH900 4.7 14.5 1.0
C B:ALA206 4.7 13.8 1.0
CA B:VAL213 4.7 11.9 1.0
CA B:CYS211 4.8 13.4 1.0
CB B:VAL205 4.8 12.1 1.0
CG1 B:VAL213 4.8 11.4 1.0
CB B:CYS211 4.9 12.0 1.0
N B:ASN208 4.9 10.4 1.0
N B:ASN207 4.9 11.2 1.0
CB B:ASN208 4.9 12.4 1.0
CG1 B:VAL210 5.0 12.3 1.0
C B:ALA204 5.0 9.5 1.0

Calcium binding site 6 out of 6 in 5jmo

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Calcium binding site 6 out of 6 in the X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of Furin in Complex with the Inhibitory Antibody NB14 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:16.3
occ:1.00
 OD2 B:ASP301 2.3 15.2 1.0
OD1 B:ASP258 2.4 14.3 1.0
OE1 B:GLU331 2.4 14.5 1.0
O B:HOH750 2.4 10.1 1.0
O B:HOH795 2.5 15.4 1.0
OE2 B:GLU331 2.5 18.0 1.0
O B:HOH923 2.5 14.4 1.0
CD B:GLU331 2.8 16.4 1.0
CG B:ASP301 3.3 17.9 1.0
CG B:ASP258 3.4 15.7 1.0
NH1 H:AR76 3.9 13.6 1.0
OD1 B:ASP301 4.0 18.2 1.0
CA B:ASP258 4.1 15.4 1.0
CB B:ASP258 4.1 15.6 1.0
CB B:ASP301 4.2 17.4 1.0
O B:HOH933 4.3 20.4 1.0
CG B:GLU331 4.3 14.3 1.0
OD2 B:ASP258 4.3 15.8 1.0
CA B:GLY294 4.5 12.7 1.0
O B:SER302 4.5 18.2 1.0
O B:HOH915 4.5 17.6 1.0
OD2 B:ASP306 4.6 19.7 1.0
O B:SER293 4.6 15.2 1.0
CB B:ASP306 4.6 15.5 1.0
CZ H:AR76 4.7 13.7 1.0
O B:GLU257 4.7 16.3 1.0
O B:PRO256 4.8 12.2 1.0
CA B:CYS303 4.8 16.6 1.0
C B:SER302 4.9 14.2 1.0
N B:GLY296 4.9 13.8 1.0
N B:ASP258 4.9 14.3 1.0

Reference:

S.O.Dahms, J.W.Creemers, Y.Schaub, G.P.Bourenkov, T.Zogg, H.Brandstetter, M.E.Than. The Structure of A Furin-Antibody Complex Explains Non-Competitive Inhibition By Steric Exclusion of Substrate Conformers. Sci Rep V. 6 34303 2016.
ISSN: ESSN 2045-2322
PubMed: 27670069
DOI: 10.1038/SREP34303
Page generated: Sat Dec 12 05:32:00 2020

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