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Calcium in PDB 2id4: The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor.

Enzymatic activity of The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor.

All present enzymatic activity of The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor.:
3.4.21.61;

Protein crystallography data

The structure of The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor., PDB code: 2id4 was solved by J.L.Wheatley, T.Holyoak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.79 / 1.90
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 112.851, 112.851, 370.165, 90.00, 90.00, 120.00
R / Rfree (%) 17.7 / 20.6

Other elements in 2id4:

The structure of The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor. also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor. (pdb code 2id4). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor., PDB code: 2id4:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 2id4

Go back to Calcium Binding Sites List in 2id4
Calcium binding site 1 out of 4 in the The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:29.0
occ:1.00
 OD2 A:ASP277 2.3 25.1 1.0
O A:HOH912 2.4 25.8 1.0
O A:HOH945 2.4 27.2 1.0
OD2 A:ASP320 2.4 22.9 1.0
O A:HOH938 2.4 28.5 1.0
OE2 A:GLU350 2.5 30.3 1.0
OE1 A:GLU350 2.5 28.2 1.0
CD A:GLU350 2.8 30.0 1.0
CG A:ASP320 3.3 25.4 1.0
CG A:ASP277 3.4 24.7 1.0
OD1 A:ASP320 3.9 23.4 1.0
CA A:ASP277 4.0 26.7 1.0
CB A:ASP277 4.0 26.2 1.0
NZ C:LYK5 4.2 28.9 1.0
CB A:ASP320 4.2 26.2 1.0
O A:HOH927 4.3 35.6 1.0
CG A:GLU350 4.3 29.1 1.0
OD1 A:ASP277 4.4 23.5 1.0
CA A:GLY313 4.4 26.9 1.0
O A:SER312 4.4 27.7 1.0
O A:ASN321 4.5 26.6 1.0
OD1 A:ASP325 4.5 27.0 1.0
O A:HOH913 4.5 28.6 1.0
O A:ALA276 4.6 27.4 1.0
CB A:ASP325 4.6 26.1 1.0
O A:PRO275 4.7 28.0 1.0
N A:ASP277 4.8 26.9 1.0
C A:ASN321 4.9 26.8 1.0
C A:ALA276 5.0 27.6 1.0

Calcium binding site 2 out of 4 in 2id4

Go back to Calcium Binding Sites List in 2id4
Calcium binding site 2 out of 4 in the The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca906

b:39.5
occ:1.00
 O A:LYS224 2.3 27.6 1.0
OD1 A:ASP135 2.3 29.4 1.0
O A:PHE229 2.3 27.2 1.0
OD1 A:ASP184 2.4 29.9 1.0
O A:GLY231 2.4 27.3 1.0
OD1 A:ASN227 2.5 21.9 1.0
OD2 A:ASP184 2.7 28.8 1.0
CG A:ASP184 2.9 28.8 1.0
CG A:ASP135 3.4 29.0 1.0
C A:LYS224 3.5 28.1 1.0
CG A:ASN227 3.5 25.7 1.0
C A:PHE229 3.5 27.5 1.0
C A:GLY231 3.6 27.1 1.0
ND2 A:ASN227 4.0 25.4 1.0
CB A:ASP135 4.0 28.5 1.0
N A:GLY231 4.1 27.4 1.0
C A:CYS230 4.2 27.6 1.0
CA A:LYS224 4.3 28.2 1.0
N A:PHE229 4.3 27.3 1.0
N A:LYS224 4.3 28.1 1.0
CA A:GLY231 4.3 27.1 1.0
CA A:PHE229 4.3 27.5 1.0
CB A:ASP184 4.4 28.8 1.0
OD2 A:ASP135 4.5 27.8 1.0
N A:LYS225 4.5 28.2 1.0
O A:CYS230 4.5 27.4 1.0
CB A:LYS224 4.5 28.0 1.0
CB A:PHE229 4.6 27.4 1.0
N A:CYS230 4.6 27.7 1.0
N A:VAL232 4.6 27.1 1.0
CA A:LYS225 4.6 28.5 1.0
N A:ASN227 4.7 27.1 1.0
CA A:CYS230 4.8 27.9 1.0
CB A:ASN227 4.8 26.6 1.0
C A:ALA223 4.8 28.3 1.0
CA A:VAL232 4.9 27.1 1.0
N A:GLY226 4.9 28.0 1.0
CD2 A:PHE229 4.9 27.7 1.0
CB A:ALA223 5.0 27.8 1.0
C A:LYS225 5.0 28.3 1.0
O A:HOH998 5.0 39.1 1.0

Calcium binding site 3 out of 4 in 2id4

Go back to Calcium Binding Sites List in 2id4
Calcium binding site 3 out of 4 in the The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:30.5
occ:1.00
 O B:HOH914 2.3 30.0 1.0
O B:HOH942 2.3 29.5 1.0
OD2 B:ASP277 2.4 27.6 1.0
OD2 B:ASP320 2.4 26.0 1.0
OE2 B:GLU350 2.4 28.9 1.0
OE1 B:GLU350 2.5 28.1 1.0
O B:HOH923 2.5 32.1 1.0
CD B:GLU350 2.8 28.1 1.0
CG B:ASP320 3.3 26.9 1.0
CG B:ASP277 3.5 27.4 1.0
OD1 B:ASP320 3.9 26.2 1.0
CA B:ASP277 4.1 27.1 1.0
CB B:ASP277 4.1 27.1 1.0
NZ D:LYK5 4.2 34.1 1.0
O B:HOH917 4.3 33.3 1.0
CG B:GLU350 4.3 28.1 1.0
CB B:ASP320 4.3 27.7 1.0
O B:HOH949 4.4 34.7 1.0
O B:SER312 4.4 27.4 1.0
OD1 B:ASP277 4.4 27.6 1.0
O B:ASN321 4.5 28.1 1.0
OD1 B:ASP325 4.5 30.1 1.0
O B:ALA276 4.6 27.0 1.0
CA B:GLY313 4.6 27.2 1.0
CB B:ASP325 4.7 28.6 1.0
O B:PRO275 4.7 26.2 1.0
N B:ASP277 4.9 27.0 1.0
C B:ASN321 4.9 28.0 1.0
CA B:CYS322 5.0 28.8 1.0

Calcium binding site 4 out of 4 in 2id4

Go back to Calcium Binding Sites List in 2id4
Calcium binding site 4 out of 4 in the The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The 1.9 A Structure of KEX2 in Complex with An Ac-R-E-R-K-Chloromethyl Ketone Inhibitor. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca906

b:45.7
occ:1.00
 O B:LYS224 2.3 29.4 1.0
O B:PHE229 2.3 28.9 1.0
OD1 B:ASP135 2.4 26.6 1.0
OD1 B:ASP184 2.4 26.2 1.0
O B:GLY231 2.5 28.0 1.0
OD1 B:ASN227 2.6 27.6 1.0
OD2 B:ASP184 2.7 26.7 1.0
CG B:ASP184 2.9 27.5 1.0
CG B:ASP135 3.4 27.3 1.0
C B:PHE229 3.5 29.1 1.0
C B:LYS224 3.5 29.4 1.0
CG B:ASN227 3.6 28.1 1.0
C B:GLY231 3.7 28.2 1.0
ND2 B:ASN227 4.0 26.5 1.0
CB B:ASP135 4.0 27.6 1.0
N B:GLY231 4.1 28.6 1.0
N B:PHE229 4.2 29.3 1.0
CA B:PHE229 4.3 29.2 1.0
C B:CYS230 4.3 29.0 1.0
CA B:LYS224 4.4 29.4 1.0
CB B:ASP184 4.4 28.0 1.0
CA B:GLY231 4.4 28.3 1.0
N B:LYS224 4.4 29.4 1.0
OD2 B:ASP135 4.4 27.4 1.0
CB B:PHE229 4.4 29.3 1.0
N B:LYS225 4.5 29.4 1.0
N B:CYS230 4.5 29.1 1.0
O B:CYS230 4.6 28.9 1.0
CB B:LYS224 4.6 29.3 1.0
CA B:LYS225 4.7 29.4 1.0
N B:VAL232 4.7 28.0 1.0
N B:ASN227 4.8 29.2 1.0
CA B:CYS230 4.8 29.1 1.0
C B:ALA223 4.8 29.2 1.0
N B:GLY226 4.9 29.3 1.0
CA B:VAL232 4.9 28.1 1.0
CB B:ASN227 4.9 28.9 1.0
O B:HOH1012 5.0 42.2 1.0
CD2 B:PHE229 5.0 28.9 1.0
CG2 B:VAL232 5.0 28.5 1.0
CB B:CYS230 5.0 29.4 1.0

Reference:

J.L.Wheatley, T.Holyoak. Differential P1 Arginine and Lysine Recognition in the Prototypical Proprotein Convertase KEX2. Proc.Natl.Acad.Sci.Usa V. 104 6626 2007.
ISSN: ISSN 0027-8424
PubMed: 17426142
DOI: 10.1073/PNAS.0701983104
Page generated: Tue Jul 8 06:13:08 2025

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