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Calcium in PDB 1r64: The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor

Enzymatic activity of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor

All present enzymatic activity of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor:
3.4.21.61;

Protein crystallography data

The structure of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor, PDB code: 1r64 was solved by T.Holyoak, C.A.Kettner, G.A.Petsko, R.S.Fuller, D.Ringe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.20
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 113.541, 113.541, 364.971, 90.00, 90.00, 120.00
R / Rfree (%) 19.7 / 23.4

Other elements in 1r64:

The structure of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor also contains other interesting chemical elements:

Potassium (K) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor (pdb code 1r64). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor, PDB code: 1r64:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1r64

Go back to Calcium Binding Sites List in 1r64
Calcium binding site 1 out of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca700

b:18.7
occ:1.00
 OE1 A:GLU350 2.3 15.5 1.0
OD2 A:ASP320 2.4 16.9 1.0
OD2 A:ASP277 2.4 21.1 1.0
O A:HOH1128 2.4 10.6 1.0
O A:HOH1129 2.4 10.7 1.0
OE2 A:GLU350 2.5 17.2 1.0
O A:HOH1130 2.6 21.5 1.0
CD A:GLU350 2.7 15.7 1.0
CG A:ASP320 3.2 17.5 1.0
CG A:ASP277 3.4 20.9 1.0
OD1 A:ASP320 3.8 17.5 1.0
NH2 C:BOR5 3.8 17.1 1.0
CB A:ASP277 4.1 18.6 1.0
CA A:ASP277 4.2 18.4 1.0
CB A:ASP320 4.2 18.6 1.0
CG A:GLU350 4.2 14.9 1.0
OD1 A:ASP277 4.2 21.4 1.0
CA A:GLY313 4.4 18.5 1.0
O A:SER312 4.4 19.4 1.0
CZ C:BOR5 4.5 17.8 1.0
O A:ASN321 4.6 16.2 1.0
OD1 A:ASP325 4.7 17.8 1.0
CB A:ASP325 4.7 17.3 1.0
O A:HOH958 4.7 14.5 1.0
O A:HOH986 4.7 22.0 1.0
O A:PRO275 4.8 19.5 1.0
O A:ALA276 4.8 17.5 1.0
C A:ASN321 4.9 18.4 1.0
CB A:GLU350 4.9 14.3 1.0
N A:ASP277 5.0 17.8 1.0
CA A:CYS322 5.0 18.4 1.0
NE C:BOR5 5.0 19.3 1.0
N A:GLY315 5.0 17.2 1.0

Calcium binding site 2 out of 6 in 1r64

Go back to Calcium Binding Sites List in 1r64
Calcium binding site 2 out of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:24.6
occ:1.00
 O A:LYS224 2.3 24.6 1.0
O A:PHE229 2.3 30.5 1.0
OD1 A:ASP135 2.3 24.6 1.0
O A:GLY231 2.4 24.0 1.0
OD1 A:ASP184 2.4 23.8 1.0
OD1 A:ASN227 2.5 30.0 1.0
OD2 A:ASP184 2.7 25.3 1.0
CG A:ASP184 2.9 24.0 1.0
CG A:ASP135 3.4 25.5 1.0
C A:LYS224 3.5 24.9 1.0
C A:PHE229 3.5 31.0 1.0
CG A:ASN227 3.6 28.6 1.0
C A:GLY231 3.6 24.6 1.0
ND2 A:ASN227 4.0 30.4 1.0
CB A:ASP135 4.1 25.9 1.0
N A:PHE229 4.2 32.1 1.0
N A:GLY231 4.2 27.7 1.0
CA A:PHE229 4.2 30.8 1.0
C A:CYS230 4.2 28.8 1.0
CB A:PHE229 4.3 30.3 1.0
OD2 A:ASP135 4.3 25.0 1.0
CA A:GLY231 4.4 25.9 1.0
CA A:LYS224 4.4 24.5 1.0
O A:CYS230 4.4 28.1 1.0
N A:LYS225 4.4 25.6 1.0
CB A:ASP184 4.4 22.9 1.0
CA A:LYS225 4.4 26.9 1.0
N A:LYS224 4.5 24.8 1.0
N A:CYS230 4.5 30.0 1.0
CB A:LYS224 4.6 25.3 1.0
N A:VAL232 4.7 23.1 1.0
N A:ASN227 4.7 30.8 1.0
CA A:CYS230 4.8 29.6 1.0
CB A:ASN227 4.9 29.8 1.0
CA A:VAL232 4.9 22.8 1.0
C A:LYS225 4.9 28.9 1.0
C A:ALA223 4.9 24.7 1.0
CG2 A:VAL232 4.9 25.5 1.0
N A:GLY226 4.9 30.4 1.0
CD2 A:PHE229 5.0 29.1 1.0
O A:HOH978 5.0 23.1 1.0

Calcium binding site 3 out of 6 in 1r64

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Calcium binding site 3 out of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:23.1
occ:1.00
 O A:HOH959 2.6 16.3 1.0
O A:SER333 2.6 16.8 1.0
O A:SER330 2.7 17.9 1.0
O A:THR328 2.7 17.1 1.0
OG A:SER333 2.9 19.0 1.0
OG1 A:THR335 2.9 18.1 1.0
C A:SER333 3.4 17.1 1.0
C A:THR328 3.7 16.8 1.0
O A:HOH913 3.7 9.3 1.0
N A:THR335 3.7 15.1 1.0
CE A:MET555 3.8 11.4 1.0
C A:SER330 3.9 19.4 1.0
CB A:THR335 3.9 16.6 1.0
CB A:SER333 4.0 17.6 1.0
N A:SER330 4.0 17.7 1.0
CA A:SER333 4.1 15.9 1.0
N A:ILE334 4.1 15.8 1.0
O A:ALA354 4.3 19.2 1.0
C A:ILE334 4.3 16.2 1.0
N A:SER333 4.3 16.3 1.0
CA A:ILE334 4.3 15.8 1.0
CA A:THR335 4.4 16.1 1.0
O A:TYR327 4.4 16.9 1.0
CA A:THR328 4.4 16.6 1.0
N A:ASN329 4.5 16.5 1.0
C A:ASN329 4.5 16.9 1.0
CA A:ASN329 4.5 17.5 1.0
CA A:SER330 4.6 18.2 1.0
N A:ILE331 4.9 18.3 1.0
CB A:ALA354 4.9 18.0 1.0
CA A:ILE331 4.9 18.3 1.0

Calcium binding site 4 out of 6 in 1r64

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Calcium binding site 4 out of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca700

b:17.9
occ:1.00
 O B:HOH1950 2.3 14.2 1.0
OD2 B:ASP277 2.3 22.7 1.0
O B:HOH2029 2.3 21.4 1.0
OE1 B:GLU350 2.4 22.5 1.0
OD2 B:ASP320 2.4 22.2 1.0
OE2 B:GLU350 2.4 22.0 1.0
O B:HOH2003 2.4 15.7 1.0
CD B:GLU350 2.7 20.2 1.0
CG B:ASP277 3.3 21.4 1.0
CG B:ASP320 3.3 20.7 1.0
NH2 D:BOR5 3.7 19.9 1.0
OD1 B:ASP320 3.9 17.8 1.0
CB B:ASP277 4.0 19.6 1.0
CA B:ASP277 4.1 18.3 1.0
OD1 B:ASP277 4.1 21.2 1.0
CG B:GLU350 4.2 19.8 1.0
O B:HOH1919 4.2 19.6 1.0
O B:SER312 4.3 19.4 1.0
CB B:ASP320 4.3 18.4 1.0
CA B:GLY313 4.4 18.7 1.0
CZ D:BOR5 4.5 18.8 1.0
OD1 B:ASP325 4.6 19.2 1.0
O B:PRO275 4.7 21.0 1.0
O B:ASN321 4.7 19.9 1.0
CB B:ASP325 4.7 18.3 1.0
O B:HOH2001 4.8 31.4 1.0
O B:ALA276 4.8 19.1 1.0
N B:ASP277 4.9 18.2 1.0
NE D:BOR5 4.9 19.9 1.0
N B:GLY315 4.9 16.7 1.0
CB B:GLU350 4.9 16.7 1.0
C B:ASN321 5.0 19.3 1.0
CA B:CYS322 5.0 18.6 1.0

Calcium binding site 5 out of 6 in 1r64

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Calcium binding site 5 out of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:37.2
occ:1.00
 OD1 B:ASP135 2.3 32.3 1.0
O B:LYS224 2.3 33.9 1.0
OD1 B:ASP184 2.3 35.0 1.0
O B:PHE229 2.3 39.6 1.0
O B:GLY231 2.4 36.4 1.0
OD1 B:ASN227 2.5 31.8 1.0
OD2 B:ASP184 2.6 36.4 1.0
CG B:ASP184 2.8 36.7 1.0
CG B:ASP135 3.4 33.9 1.0
C B:PHE229 3.4 40.0 1.0
C B:LYS224 3.5 34.3 1.0
CG B:ASN227 3.5 35.2 1.0
C B:GLY231 3.6 36.2 1.0
ND2 B:ASN227 3.9 33.1 1.0
N B:GLY231 4.1 37.2 1.0
CB B:ASP135 4.1 35.3 1.0
N B:PHE229 4.1 41.0 1.0
CA B:PHE229 4.1 40.1 1.0
CB B:PHE229 4.2 38.7 1.0
C B:CYS230 4.3 37.1 1.0
CA B:GLY231 4.3 36.5 1.0
OD2 B:ASP135 4.3 33.8 1.0
CB B:ASP184 4.3 35.5 1.0
CA B:LYS224 4.4 33.8 1.0
N B:LYS225 4.4 34.3 1.0
CA B:LYS225 4.5 35.0 1.0
N B:CYS230 4.5 39.2 1.0
N B:LYS224 4.5 34.0 1.0
O B:CYS230 4.6 36.3 1.0
CB B:LYS224 4.6 34.7 1.0
N B:VAL232 4.7 35.3 1.0
O B:HOH2040 4.7 30.6 1.0
N B:ASN227 4.7 37.4 1.0
CA B:CYS230 4.8 37.5 1.0
CB B:ASN227 4.9 35.5 1.0
C B:LYS225 4.9 34.6 1.0
CD2 B:PHE229 4.9 38.6 1.0
C B:ALA223 4.9 34.5 1.0
CA B:VAL232 4.9 34.4 1.0
CG2 B:VAL232 5.0 37.5 1.0
N B:GLY226 5.0 34.2 1.0
CB B:CYS230 5.0 36.5 1.0

Calcium binding site 6 out of 6 in 1r64

Go back to Calcium Binding Sites List in 1r64
Calcium binding site 6 out of 6 in the The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The 2.2 A Crystal Structure of KEX2 Protease in Complex with Ac-Arg- Glu-Lys-Boroarg Peptidyl Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:20.3
occ:1.00
 O B:SER330 2.6 16.6 1.0
O B:SER333 2.6 19.0 1.0
O B:THR328 2.8 16.7 1.0
O B:HOH1911 2.8 15.9 1.0
OG B:SER333 2.9 18.7 1.0
OG1 B:THR335 2.9 19.2 1.0
C B:SER333 3.4 19.9 1.0
C B:THR328 3.6 16.3 1.0
O B:HOH1991 3.7 24.8 1.0
CE B:MET555 3.8 14.8 1.0
C B:SER330 3.8 17.7 1.0
N B:THR335 3.8 23.0 1.0
CB B:THR335 4.0 19.6 1.0
N B:SER330 4.0 18.5 1.0
CB B:SER333 4.0 18.6 1.0
CA B:SER333 4.1 19.7 1.0
N B:ILE334 4.2 20.8 1.0
N B:SER333 4.2 20.0 1.0
O B:TYR327 4.3 19.7 1.0
O B:ALA354 4.3 22.4 1.0
C B:ASN329 4.4 19.1 1.0
C B:ILE334 4.4 22.9 1.0
CA B:THR328 4.4 16.2 1.0
CA B:ILE334 4.4 20.9 1.0
N B:ASN329 4.4 15.4 1.0
CA B:THR335 4.4 19.9 1.0
CA B:ASN329 4.5 17.4 1.0
CA B:SER330 4.5 17.7 1.0
N B:ILE331 4.8 17.9 1.0
CA B:ILE331 4.9 19.0 1.0
CB B:ALA354 4.9 20.8 1.0

Reference:

T.Holyoak, C.A.Kettner, G.A.Petsko, R.S.Fuller, D.Ringe. Structural Basis For Differences in Substrate Selectivity in KEX2 and Furin Protein Convertases Biochemistry V. 43 2412 2004.
ISSN: ISSN 0006-2960
PubMed: 14992578
DOI: 10.1021/BI035849H
Page generated: Thu Jul 11 22:03:45 2024

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