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Calcium in PDB 1ot5: The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor

Enzymatic activity of The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor

All present enzymatic activity of The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor:
3.4.21.61;

Protein crystallography data

The structure of The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor, PDB code: 1ot5 was solved by T.Holyoak, M.A.Wilson, T.D.Fenn, 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) 49.30 / 2.40
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 113.844, 113.844, 370.218, 90.00, 90.00, 120.00
R / Rfree (%) 20.9 / 24.5

Calcium Binding Sites:

The binding sites of Calcium atom in the The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor (pdb code 1ot5). 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 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor, PDB code: 1ot5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1ot5

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Calcium binding site 1 out of 6 in the The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A 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 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca600

b:19.5
occ:1.00
 OE2 A:GLU350 2.3 15.4 1.0
OD2 A:ASP277 2.3 26.5 1.0
OD2 A:ASP320 2.4 19.6 1.0
O A:HOH618 2.5 28.9 1.0
OE1 A:GLU350 2.5 15.4 1.0
O A:HOH607 2.5 30.8 1.0
O A:HOH623 2.6 32.1 1.0
CD A:GLU350 2.7 16.7 1.0
CG A:ASP320 3.1 20.9 1.0
CG A:ASP277 3.3 27.2 1.0
OD1 A:ASP320 3.7 19.1 1.0
CB A:ASP277 4.0 25.9 1.0
CA A:ASP277 4.0 24.5 1.0
CB A:ASP320 4.0 20.6 1.0
NH2 C:BOR4 4.1 23.3 1.0
OD1 A:ASP277 4.2 28.8 1.0
CG A:GLU350 4.2 17.6 1.0
O A:HOH617 4.3 25.7 1.0
O A:ASN321 4.4 26.8 1.0
O A:HOH741 4.4 37.4 1.0
CA A:GLY313 4.5 19.4 1.0
O A:SER312 4.6 21.6 1.0
CB A:ASP325 4.6 22.5 1.0
O A:PRO275 4.6 18.1 1.0
O A:ALA276 4.7 22.4 1.0
OD1 A:ASP325 4.7 22.7 1.0
CZ C:BOR4 4.8 22.5 1.0
C A:ASN321 4.9 25.8 1.0
N A:ASP277 4.9 22.1 1.0
N A:GLY315 5.0 18.5 1.0

Calcium binding site 2 out of 6 in 1ot5

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Calcium binding site 2 out of 6 in the The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A 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 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca601

b:28.3
occ:1.00
 O A:LYS224 2.3 35.4 1.0
O A:PHE229 2.3 39.0 1.0
O A:GLY231 2.3 29.8 1.0
OD1 A:ASP135 2.4 32.4 1.0
OD1 A:ASP184 2.5 44.7 1.0
OD2 A:ASP184 2.6 44.6 1.0
ND2 A:ASN227 2.8 37.4 1.0
CG A:ASP184 2.9 42.0 1.0
C A:PHE229 3.5 40.6 1.0
C A:LYS224 3.5 37.0 1.0
CG A:ASP135 3.5 34.1 1.0
C A:GLY231 3.5 30.1 1.0
CG A:ASN227 3.7 38.3 1.0
OD1 A:ASN227 3.8 40.5 1.0
N A:GLY231 4.1 34.5 1.0
CA A:PHE229 4.2 40.9 1.0
C A:CYS230 4.2 37.8 1.0
N A:PHE229 4.2 41.5 1.0
CB A:ASP135 4.3 35.9 1.0
CA A:GLY231 4.3 32.1 1.0
CA A:LYS224 4.3 37.2 1.0
CB A:PHE229 4.3 38.7 1.0
CB A:ASP184 4.4 40.1 1.0
N A:LYS224 4.4 37.7 1.0
OD2 A:ASP135 4.4 32.6 1.0
N A:CYS230 4.5 39.6 1.0
N A:LYS225 4.5 38.6 1.0
CB A:LYS224 4.5 39.2 1.0
O A:CYS230 4.5 39.9 1.0
N A:VAL232 4.6 28.8 1.0
CA A:LYS225 4.6 39.1 1.0
O A:HOH697 4.7 35.7 1.0
C A:ALA223 4.7 36.0 1.0
CA A:VAL232 4.8 28.9 1.0
CA A:CYS230 4.8 39.6 1.0
N A:ASN227 4.8 40.0 1.0
CB A:ALA223 4.9 34.5 1.0
N A:GLY226 4.9 40.8 1.0
CD2 A:PHE229 5.0 40.7 1.0

Calcium binding site 3 out of 6 in 1ot5

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Calcium binding site 3 out of 6 in the The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A 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 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca602

b:45.8
occ:1.00
 O A:SER333 2.3 22.2 1.0
OG A:SER333 2.4 26.5 1.0
O A:SER330 2.4 22.1 1.0
O A:HOH609 2.5 33.4 1.0
O A:THR328 2.5 20.3 1.0
C A:SER333 3.0 22.7 1.0
OG1 A:THR335 3.2 19.0 1.0
CB A:SER333 3.5 22.1 1.0
C A:THR328 3.5 19.9 1.0
C A:SER330 3.5 19.0 1.0
CA A:SER333 3.6 22.7 1.0
N A:SER330 3.7 17.9 1.0
O A:HOH659 3.7 33.2 1.0
N A:SER333 3.7 22.2 1.0
N A:THR335 3.9 22.8 1.0
N A:ILE334 4.0 22.1 1.0
O A:TYR327 4.1 22.9 1.0
CE A:MET555 4.1 18.3 1.0
CB A:THR335 4.2 19.6 1.0
C A:ASN329 4.2 19.4 1.0
CA A:SER330 4.2 19.8 1.0
CA A:THR328 4.3 21.2 1.0
CA A:ILE334 4.4 20.5 1.0
N A:ASN329 4.4 20.0 1.0
CA A:ASN329 4.4 20.4 1.0
C A:ILE334 4.4 22.0 1.0
CB A:SER330 4.6 20.0 1.0
N A:ILE331 4.6 20.6 1.0
CA A:THR335 4.6 20.9 1.0
CA A:ILE331 4.7 21.2 1.0
C A:ILE331 4.8 20.1 1.0
O A:ALA354 4.9 26.4 1.0
O A:ASN329 5.0 20.3 1.0
C A:TYR332 5.0 21.9 1.0
N A:TYR332 5.0 18.9 1.0

Calcium binding site 4 out of 6 in 1ot5

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Calcium binding site 4 out of 6 in the The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A 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 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca600

b:19.7
occ:1.00
 O B:HOH633 2.4 32.6 1.0
OE2 B:GLU350 2.4 15.4 1.0
OD2 B:ASP277 2.4 26.5 1.0
O B:HOH615 2.4 29.6 1.0
O B:HOH610 2.5 27.4 1.0
OE1 B:GLU350 2.5 15.4 1.0
OD2 B:ASP320 2.6 19.6 1.0
CD B:GLU350 2.8 16.7 1.0
CG B:ASP320 3.3 20.9 1.0
CG B:ASP277 3.4 27.2 1.0
OD1 B:ASP320 3.8 19.1 1.0
NH2 D:BOR4 4.0 19.8 1.0
CA B:ASP277 4.0 24.5 1.0
CB B:ASP277 4.1 25.9 1.0
O B:HOH674 4.2 33.7 1.0
CB B:ASP320 4.2 20.6 1.0
OD1 B:ASP277 4.3 28.8 1.0
O B:HOH648 4.3 30.6 1.0
CG B:GLU350 4.3 17.6 1.0
O B:SER312 4.3 21.6 1.0
CA B:GLY313 4.5 19.4 1.0
O B:ASN321 4.5 26.8 1.0
OD1 B:ASP325 4.6 22.7 1.0
O B:ALA276 4.6 22.4 1.0
O B:PRO275 4.7 18.1 1.0
CB B:ASP325 4.7 22.5 1.0
CZ D:BOR4 4.8 22.6 1.0
N B:ASP277 4.8 22.1 1.0
C B:ASN321 4.9 25.8 1.0
CA B:CYS322 5.0 25.3 1.0
N B:GLY315 5.0 18.5 1.0

Calcium binding site 5 out of 6 in 1ot5

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Calcium binding site 5 out of 6 in the The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A 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 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:29.5
occ:1.00
 O B:LYS224 2.3 35.4 1.0
OD2 B:ASP184 2.4 44.6 1.0
O B:GLY231 2.4 29.8 1.0
OD1 B:ASP184 2.4 44.7 1.0
O B:PHE229 2.5 39.0 1.0
OD1 B:ASP135 2.5 32.4 1.0
ND2 B:ASN227 2.6 37.4 1.0
CG B:ASP184 2.7 42.0 1.0
C B:LYS224 3.5 37.0 1.0
CG B:ASN227 3.6 38.3 1.0
C B:GLY231 3.6 30.1 1.0
CG B:ASP135 3.6 34.1 1.0
C B:PHE229 3.6 40.6 1.0
OD1 B:ASN227 3.8 40.5 1.0
N B:GLY231 4.2 34.5 1.0
CB B:ASP184 4.2 40.1 1.0
CB B:ASP135 4.2 35.9 1.0
N B:PHE229 4.3 41.5 1.0
CA B:PHE229 4.3 40.9 1.0
CA B:GLY231 4.4 32.1 1.0
CA B:LYS224 4.4 37.2 1.0
CB B:PHE229 4.4 38.7 1.0
N B:LYS224 4.4 37.7 1.0
C B:CYS230 4.5 37.8 1.0
N B:LYS225 4.5 38.6 1.0
OD2 B:ASP135 4.6 32.6 1.0
CB B:LYS224 4.6 39.2 1.0
CA B:LYS225 4.6 39.1 1.0
N B:VAL232 4.6 28.8 1.0
N B:CYS230 4.7 39.6 1.0
O B:CYS230 4.8 39.9 1.0
CA B:VAL232 4.8 28.9 1.0
N B:ASN227 4.8 40.0 1.0
C B:ALA223 4.8 36.0 1.0
CA B:ASP184 4.9 40.4 1.0
N B:GLY226 4.9 40.8 1.0
CB B:ASN227 4.9 38.6 1.0
CB B:ALA223 5.0 34.5 1.0

Calcium binding site 6 out of 6 in 1ot5

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Calcium binding site 6 out of 6 in the The 2.4 Angstrom Crystal Structure of KEX2 in Complex with A 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 2.4 Angstrom Crystal Structure of KEX2 in Complex with A Peptidyl- Boronic Acid Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:39.0
occ:1.00
 O B:SER333 2.4 22.2 1.0
O B:HOH606 2.4 30.6 1.0
O B:SER330 2.5 22.1 1.0
OG B:SER333 2.5 26.5 1.0
O B:THR328 2.6 20.3 1.0
OG1 B:THR335 3.1 19.0 1.0
C B:SER333 3.1 22.7 1.0
C B:THR328 3.5 19.9 1.0
CB B:SER333 3.6 22.1 1.0
C B:SER330 3.7 19.0 1.0
O B:HOH618 3.7 28.4 1.0
CA B:SER333 3.7 22.7 1.0
N B:SER333 3.8 22.2 1.0
N B:THR335 3.9 22.8 1.0
N B:SER330 3.9 17.9 1.0
CE B:MET555 4.0 18.3 1.0
N B:ILE334 4.0 22.1 1.0
CB B:THR335 4.2 19.6 1.0
C B:ASN329 4.2 19.4 1.0
O B:TYR327 4.3 22.9 1.0
CA B:THR328 4.3 21.2 1.0
N B:ASN329 4.4 20.0 1.0
CA B:ASN329 4.4 20.4 1.0
CA B:ILE334 4.4 20.5 1.0
C B:ILE334 4.4 22.0 1.0
CA B:SER330 4.4 19.8 1.0
CA B:THR335 4.6 20.9 1.0
O B:ALA354 4.6 26.4 1.0
N B:ILE331 4.7 20.6 1.0
CA B:ILE331 4.8 21.2 1.0
C B:ILE331 4.8 20.1 1.0
O B:ASN329 4.8 20.3 1.0
CB B:SER330 4.9 20.0 1.0
O B:ILE331 4.9 22.4 1.0

Reference:

T.Holyoak, M.A.Wilson, T.D.Fenn, C.A.Kettner, G.A.Petsko, R.S.Fuller, D.Ringe. 2.4 A Resolution Crystal Structure of the Prototypical Hormone-Processing Protease KEX2 in Complex with An Ala-Lys-Arg Boronic Acid Inhibitor Biochemistry V. 42 6709 2003.
ISSN: ISSN 0006-2960
PubMed: 12779325
DOI: 10.1021/BI034434T
Page generated: Thu Jul 11 13:30:29 2024

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