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Calcium in PDB 1mdw: Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation

Enzymatic activity of Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation

All present enzymatic activity of Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation:
3.4.22.17;

Protein crystallography data

The structure of Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation, PDB code: 1mdw was solved by T.Moldoveanu, C.M.Hosfield, D.Lim, Z.Jia, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.600, 80.600, 75.300, 90.00, 103.90, 90.00
R / Rfree (%) 20.7 / 24.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation (pdb code 1mdw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation, PDB code: 1mdw:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1mdw

Go back to Calcium Binding Sites List in 1mdw
Calcium binding site 1 out of 4 in the Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:26.8
occ:1.00
 O A:ILE89 2.4 27.6 1.0
OD2 A:ASP96 2.4 22.2 1.0
O A:HOH348 2.4 27.1 1.0
O A:GLY91 2.4 28.2 1.0
O A:HOH347 2.4 26.8 1.0
OE2 A:GLU175 2.5 27.6 1.0
OD1 A:ASP96 2.5 24.4 1.0
OE1 A:GLU175 2.5 23.7 1.0
CG A:ASP96 2.7 25.4 1.0
CD A:GLU175 2.8 24.6 1.0
C A:ILE89 3.6 28.7 1.0
C A:GLY91 3.7 28.8 1.0
O A:HOH462 4.1 39.5 1.0
O A:GLY90 4.1 29.5 1.0
C A:GLY90 4.2 29.6 1.0
CB A:ASP96 4.2 25.1 1.0
N A:ILE89 4.2 28.6 1.0
CG A:GLU175 4.3 25.5 1.0
N A:THR93 4.4 25.9 1.0
N A:GLY91 4.4 29.8 1.0
CA A:ILE89 4.4 28.4 1.0
NE1 A:TRP177 4.4 24.0 1.0
O A:HOH483 4.4 82.9 1.0
OG1 A:THR93 4.5 28.0 1.0
O A:HOH431 4.5 60.5 1.0
CA A:ALA92 4.5 27.1 1.0
N A:ALA92 4.5 27.6 1.0
N A:GLY90 4.6 29.1 1.0
OG A:SER170 4.6 27.2 1.0
CA A:GLY90 4.6 29.8 1.0
CA A:GLY91 4.6 29.0 1.0
CB A:ILE89 4.7 28.7 1.0
C A:ALA92 5.0 26.9 1.0

Calcium binding site 2 out of 4 in 1mdw

Go back to Calcium Binding Sites List in 1mdw
Calcium binding site 2 out of 4 in the Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:23.8
occ:1.00
 OD2 A:ASP299 2.2 25.3 1.0
O A:HOH349 2.3 45.8 1.0
O A:HOH444 2.3 45.8 1.0
O A:GLU323 2.3 23.4 1.0
O A:GLN319 2.4 24.0 1.0
OE1 A:GLU292 2.4 26.0 1.0
OD1 A:ASP321 2.6 23.1 1.0
OE2 A:GLU292 2.6 25.1 1.0
CD A:GLU292 2.8 24.8 1.0
CG A:ASP299 3.2 25.5 1.0
OD1 A:ASP299 3.4 26.2 1.0
C A:GLU323 3.5 23.6 1.0
C A:GLN319 3.6 26.4 1.0
CG A:ASP321 3.7 25.5 1.0
N A:ASP321 4.0 25.8 1.0
N A:GLU323 4.0 24.1 1.0
CA A:GLU323 4.2 23.6 1.0
OD2 A:ASP321 4.2 25.4 1.0
CG A:GLU292 4.3 24.2 1.0
N A:GLN319 4.3 26.6 1.0
O A:HOH352 4.4 19.2 1.0
O A:GLU317 4.4 29.4 1.0
CA A:GLN319 4.4 28.1 1.0
CA A:GLU320 4.5 26.2 1.0
N A:PHE324 4.5 23.1 1.0
N A:GLU320 4.5 25.8 1.0
N A:GLY322 4.6 25.0 1.0
CB A:ASP299 4.6 24.8 1.0
O A:HOH365 4.6 28.3 1.0
O A:HOH509 4.6 38.1 1.0
CA A:PHE324 4.7 22.9 1.0
CB A:GLU323 4.7 23.4 1.0
CB A:GLN319 4.8 31.2 1.0
C A:GLU320 4.8 26.4 1.0
CB A:ASP321 4.8 24.6 1.0
C A:GLY322 4.8 24.4 1.0
CA A:ASP321 4.8 25.3 1.0
CB A:PHE324 4.9 23.9 1.0
C A:ASP321 5.0 25.3 1.0

Calcium binding site 3 out of 4 in 1mdw

Go back to Calcium Binding Sites List in 1mdw
Calcium binding site 3 out of 4 in the Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca3

b:29.9
occ:1.00
 O B:HOH413 2.3 29.4 1.0
O B:HOH414 2.3 33.3 1.0
O B:ILE89 2.4 34.4 1.0
O B:GLY91 2.4 31.2 1.0
OE2 B:GLU175 2.5 29.0 1.0
OD1 B:ASP96 2.5 25.9 1.0
OE1 B:GLU175 2.5 28.9 1.0
OD2 B:ASP96 2.6 27.6 1.0
CG B:ASP96 2.8 26.3 1.0
CD B:GLU175 2.8 29.2 1.0
C B:ILE89 3.6 33.8 1.0
C B:GLY91 3.7 31.3 1.0
O B:HOH443 4.0 37.5 1.0
O B:GLY90 4.1 32.4 1.0
C B:GLY90 4.1 32.4 1.0
N B:ILE89 4.2 34.0 1.0
CB B:ASP96 4.2 26.2 1.0
CG B:GLU175 4.3 28.8 1.0
CA B:ILE89 4.4 33.7 1.0
O B:HOH502 4.4 45.4 1.0
N B:GLY91 4.4 31.7 1.0
N B:THR93 4.4 29.0 1.0
OG1 B:THR93 4.5 29.8 1.0
NE1 B:TRP177 4.5 26.6 1.0
CA B:ALA92 4.5 30.6 1.0
N B:GLY90 4.5 33.0 1.0
N B:ALA92 4.6 30.8 1.0
OG B:SER170 4.6 27.6 1.0
CA B:GLY90 4.6 32.3 1.0
CA B:GLY91 4.6 31.3 1.0
CB B:ILE89 4.7 34.1 1.0
O B:HOH433 4.9 54.1 1.0
OG1 B:THR95 4.9 32.7 1.0

Calcium binding site 4 out of 4 in 1mdw

Go back to Calcium Binding Sites List in 1mdw
Calcium binding site 4 out of 4 in the Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Calcium-Bound Protease Core of Calpain II Reveals the Basis For Intrinsic Inactivation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca4

b:26.1
occ:1.00
 O B:GLU323 2.3 26.8 1.0
OD2 B:ASP299 2.3 33.4 1.0
O B:HOH367 2.4 27.9 1.0
OE2 B:GLU292 2.5 28.2 1.0
O B:GLN319 2.5 34.3 1.0
OE1 B:GLU292 2.5 26.9 1.0
OD1 B:ASP321 2.5 26.6 1.0
CD B:GLU292 2.8 28.6 1.0
CG B:ASP299 3.2 32.2 1.0
OD1 B:ASP299 3.3 32.0 1.0
C B:GLU323 3.4 26.5 1.0
CG B:ASP321 3.6 28.2 1.0
C B:GLN319 3.7 35.9 1.0
N B:GLU323 3.9 26.3 1.0
N B:ASP321 4.0 29.9 1.0
OD2 B:ASP321 4.2 29.1 1.0
CA B:GLU323 4.2 26.5 1.0
CG B:GLU292 4.3 28.3 1.0
O B:GLU317 4.3 42.1 1.0
N B:PHE324 4.4 26.4 1.0
O B:HOH403 4.5 34.3 1.0
N B:GLN319 4.5 38.8 1.0
O B:HOH365 4.5 26.5 1.0
N B:GLY322 4.5 27.9 1.0
CA B:GLU320 4.5 32.6 1.0
CB B:ASP299 4.6 31.6 1.0
CA B:GLN319 4.6 37.7 1.0
N B:GLU320 4.6 33.6 1.0
CA B:PHE324 4.6 26.0 1.0
CB B:GLU323 4.7 27.2 1.0
CB B:ASP321 4.8 27.8 1.0
CB B:PHE324 4.8 25.6 1.0
CA B:ASP321 4.8 28.9 1.0
C B:GLY322 4.8 27.2 1.0
C B:GLU320 4.8 31.8 1.0
CB B:GLN319 4.9 39.4 1.0
C B:ASP321 5.0 28.2 1.0

Reference:

T.Moldoveanu, C.M.Hosfield, D.Lim, Z.Jia, P.L.Davies. Calpain Silencing By A Reversible Intrinsic Mechanism. Nat.Struct.Biol. V. 10 371 2003.
ISSN: ISSN 1072-8368
PubMed: 12665854
DOI: 10.1038/NSB917
Page generated: Thu Jul 11 12:30:02 2024

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