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Calcium in PDB 1nx0: Structure of Calpain Domain 6 in Complex with Calpastatin Dic

Protein crystallography data

The structure of Structure of Calpain Domain 6 in Complex with Calpastatin Dic, PDB code: 1nx0 was solved by B.Todd, D.Moore, C.C.S.Deivanayagam, G.-D.Lin, D.Chattopadhyay, M.Maki, K.K.W.Wang, S.V.L.Narayana, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 100.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.780, 83.300, 92.150, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 26.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Calpain Domain 6 in Complex with Calpastatin Dic (pdb code 1nx0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Calpain Domain 6 in Complex with Calpastatin Dic, PDB code: 1nx0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1nx0

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Calcium binding site 1 out of 6 in the Structure of Calpain Domain 6 in Complex with Calpastatin Dic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Calpain Domain 6 in Complex with Calpastatin Dic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca900

b:41.5
occ:1.00
 O A:ALA107 2.2 35.0 1.0
OD1 A:ASP110 2.4 51.1 1.0
O A:GLU112 2.4 29.8 1.0
OE1 A:GLU117 2.4 25.8 1.0
OE2 A:GLU117 2.6 29.0 1.0
CD A:GLU117 2.9 27.1 1.0
CG A:ASP110 3.2 47.5 1.0
OD2 A:ASP110 3.2 49.5 1.0
C A:ALA107 3.4 36.4 1.0
C A:GLU112 3.6 32.1 1.0
CA A:ALA107 4.2 36.7 1.0
N A:GLU112 4.3 31.9 1.0
CG A:GLU117 4.4 24.8 1.0
O A:HOH1119 4.4 60.3 1.0
N A:GLY108 4.4 39.6 1.0
CA A:VAL113 4.5 27.5 1.0
N A:SER114 4.5 23.9 1.0
N A:VAL113 4.5 30.1 1.0
CA A:GLY108 4.5 41.8 1.0
CA A:GLU112 4.6 32.1 1.0
CB A:ASP110 4.6 47.8 1.0
N A:ASP110 4.8 49.8 1.0
C A:GLY108 4.9 45.6 1.0
O A:LEU106 4.9 40.0 1.0
C A:VAL113 5.0 26.4 1.0
N A:MET111 5.0 43.3 1.0
CB A:ALA107 5.0 36.7 1.0

Calcium binding site 2 out of 6 in 1nx0

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Calcium binding site 2 out of 6 in the Structure of Calpain Domain 6 in Complex with Calpastatin Dic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Calpain Domain 6 in Complex with Calpastatin Dic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:47.1
occ:0.98
 OD1 A:ASP150 2.2 29.1 1.0
O A:LYS156 2.4 25.3 1.0
OD1 A:ASP152 2.4 26.2 1.0
OG1 A:THR154 2.4 30.1 1.0
O A:HOH1069 2.5 18.3 1.0
OE1 A:GLU161 2.6 30.4 1.0
CG A:ASP152 3.4 28.4 1.0
CD A:GLU161 3.4 28.1 1.0
CG A:ASP150 3.4 28.8 1.0
OE2 A:GLU161 3.5 30.7 1.0
C A:LYS156 3.5 24.7 1.0
CB A:THR154 3.6 30.5 1.0
OD2 A:ASP152 3.6 28.0 1.0
CG2 A:THR154 3.8 29.7 1.0
N A:THR154 3.9 33.7 1.0
N A:GLY158 3.9 28.0 1.0
CA A:LEU157 4.0 26.7 1.0
OE2 A:GLU112 4.1 39.5 1.0
N A:LEU157 4.2 26.2 1.0
CA A:ASP150 4.2 29.6 1.0
OD2 A:ASP150 4.3 23.4 1.0
CA A:THR154 4.3 29.0 1.0
CB A:ASP150 4.3 26.6 1.0
OE1 A:GLU112 4.3 40.1 1.0
N A:LYS156 4.3 26.7 1.0
C A:LEU157 4.4 25.6 1.0
CD A:GLU112 4.5 37.1 1.0
CA A:LYS156 4.6 26.8 1.0
N A:GLY155 4.7 29.0 1.0
C A:THR154 4.7 27.1 1.0
CB A:ASP152 4.7 30.2 1.0
C A:ASP150 4.7 31.9 1.0
N A:ASP152 4.7 31.7 1.0
C A:ASP152 4.8 32.3 1.0
N A:THR153 4.8 32.5 1.0
CG A:GLU161 4.8 29.4 1.0
CD2 A:LEU157 4.9 30.2 1.0
CA A:GLY158 4.9 26.2 1.0
CA A:ASP152 5.0 30.8 1.0

Calcium binding site 3 out of 6 in 1nx0

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Calcium binding site 3 out of 6 in the Structure of Calpain Domain 6 in Complex with Calpastatin Dic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Calpain Domain 6 in Complex with Calpastatin Dic within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:47.0
occ:0.99
 O A:THR186 2.3 25.2 1.0
OD1 A:ASP182 2.3 37.2 1.0
OD1 A:ASP180 2.3 29.3 1.0
OG A:SER184 2.5 32.3 1.0
O A:HOH1168 2.7 44.2 1.0
CG A:ASP182 3.3 40.1 1.0
OE1 A:GLU191 3.3 61.8 1.0
C A:THR186 3.4 27.6 1.0
CG A:ASP180 3.4 30.9 1.0
OD2 A:ASP182 3.6 38.6 1.0
CB A:SER184 3.7 33.7 1.0
CA A:ASP180 3.8 29.2 1.0
N A:GLY188 3.9 31.0 1.0
N A:SER184 3.9 33.9 1.0
CB A:ASP180 4.1 29.2 1.0
C A:ASP180 4.2 29.2 1.0
N A:THR186 4.2 28.3 1.0
OG1 A:THR186 4.2 24.5 1.0
CD A:GLU191 4.3 58.5 1.0
N A:ILE187 4.3 27.8 1.0
CA A:THR186 4.3 28.4 1.0
CA A:SER184 4.3 33.0 1.0
CA A:ILE187 4.4 27.7 1.0
N A:ASP182 4.4 36.3 1.0
OD2 A:ASP180 4.4 30.5 1.0
OE2 A:GLU191 4.4 59.7 1.0
N A:VAL181 4.5 31.3 1.0
C A:ILE187 4.6 27.7 1.0
N A:ARG183 4.6 38.9 1.0
CB A:ASP182 4.7 36.6 1.0
N A:GLY185 4.7 30.9 1.0
O A:PHE179 4.7 27.1 1.0
O A:ASP180 4.7 27.7 1.0
CA A:GLY188 4.8 33.3 1.0
C A:SER184 4.8 32.5 1.0
CA A:ASP182 4.9 36.8 1.0
CB A:THR186 4.9 27.6 1.0
C A:ASP182 4.9 38.7 1.0

Calcium binding site 4 out of 6 in 1nx0

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Calcium binding site 4 out of 6 in the Structure of Calpain Domain 6 in Complex with Calpastatin Dic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Calpain Domain 6 in Complex with Calpastatin Dic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:58.7
occ:0.97
 O B:GLU412 2.3 46.5 1.0
OE2 B:GLU417 2.3 44.6 1.0
O B:ALA407 2.4 51.3 1.0
OD2 B:ASP410 2.6 67.8 1.0
OE1 B:GLU417 2.8 48.3 1.0
CD B:GLU417 2.9 44.6 1.0
C B:ALA407 3.4 51.0 1.0
CG B:ASP410 3.4 65.5 1.0
C B:GLU412 3.5 45.0 1.0
OD1 B:ASP410 3.6 66.8 1.0
CA B:ALA407 4.0 48.9 1.0
N B:SER414 4.3 37.3 1.0
N B:GLU412 4.3 49.1 1.0
CA B:VAL413 4.3 41.0 1.0
CG B:GLU417 4.4 41.5 1.0
N B:VAL413 4.4 42.8 1.0
N B:GLY408 4.4 55.3 1.0
CA B:GLU412 4.5 47.0 1.0
CB B:ALA407 4.6 48.9 1.0
O B:GLY408 4.6 57.5 1.0
CA B:GLY408 4.7 57.5 1.0
CB B:ASP410 4.7 62.9 1.0
C B:GLY408 4.7 58.8 1.0
C B:VAL413 4.8 39.2 1.0
N B:ASP410 4.8 62.6 1.0
O B:LEU406 5.0 47.4 1.0
CB B:SER414 5.0 32.6 1.0
N B:MET411 5.0 55.0 1.0

Calcium binding site 5 out of 6 in 1nx0

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Calcium binding site 5 out of 6 in the Structure of Calpain Domain 6 in Complex with Calpastatin Dic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Calpain Domain 6 in Complex with Calpastatin Dic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca904

b:41.1
occ:0.99
 OD1 B:ASP450 2.4 30.4 1.0
OD1 B:ASP452 2.4 37.2 1.0
OG1 B:THR454 2.4 31.5 1.0
O B:LYS456 2.4 30.6 1.0
OE1 B:GLU461 2.5 27.1 1.0
O B:HOH1115 2.7 27.0 0.9
OE2 B:GLU461 3.1 35.1 1.0
CD B:GLU461 3.2 31.2 1.0
CG B:ASP452 3.4 36.1 1.0
CG B:ASP450 3.5 31.6 1.0
CB B:THR454 3.6 32.0 1.0
C B:LYS456 3.6 33.6 1.0
N B:THR454 3.7 34.8 1.0
OD2 B:ASP452 3.7 31.6 1.0
CG2 B:THR454 3.8 36.0 1.0
N B:GLY458 4.1 36.2 1.0
CA B:ASP450 4.1 32.8 1.0
CA B:THR454 4.1 33.7 1.0
CB B:ASP450 4.2 31.9 1.0
OE2 B:GLU412 4.2 48.1 1.0
OE1 B:GLU412 4.3 43.5 1.0
CA B:LEU457 4.3 34.6 1.0
N B:LYS456 4.3 34.3 1.0
OD2 B:ASP450 4.3 32.0 1.0
N B:LEU457 4.4 33.6 1.0
N B:GLY455 4.5 35.3 1.0
CD B:GLU412 4.5 46.2 1.0
C B:ASP450 4.6 32.2 1.0
CG B:GLU461 4.6 30.2 1.0
CA B:LYS456 4.6 33.9 1.0
C B:THR454 4.6 34.1 1.0
N B:THR453 4.6 37.2 1.0
C B:LEU457 4.7 35.4 1.0
N B:ASP452 4.7 37.6 1.0
CB B:ASP452 4.8 36.9 1.0
C B:ASP452 4.8 38.5 1.0
C B:THR453 4.8 37.8 1.0
O B:ASP450 4.9 29.3 1.0

Calcium binding site 6 out of 6 in 1nx0

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Calcium binding site 6 out of 6 in the Structure of Calpain Domain 6 in Complex with Calpastatin Dic


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Calpain Domain 6 in Complex with Calpastatin Dic within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca905

b:67.5
occ:0.85
 OD1 B:ASP480 2.5 55.6 1.0
OD1 B:ASP482 2.6 65.5 1.0
O B:THR486 2.8 57.6 1.0
OG B:SER484 2.9 57.8 1.0
OE1 B:GLU491 3.1 64.9 1.0
CA B:ASP480 3.4 54.0 1.0
CG B:ASP482 3.4 66.7 1.0
C B:ASP480 3.5 56.1 1.0
CG B:ASP480 3.5 55.3 1.0
N B:VAL481 3.7 58.0 1.0
OD2 B:ASP482 3.7 68.0 1.0
N B:ASP482 3.8 62.2 1.0
CB B:ASP480 3.9 53.4 1.0
C B:THR486 4.0 57.6 1.0
CB B:SER484 4.0 62.2 1.0
N B:GLY488 4.0 55.8 1.0
CD B:GLU491 4.1 63.1 1.0
O B:ASP480 4.1 56.4 1.0
O B:PHE479 4.2 50.1 1.0
N B:SER484 4.2 62.9 1.0
CG2 B:VAL481 4.3 59.0 1.0
OE2 B:GLU491 4.3 62.7 1.0
CA B:ILE487 4.3 54.7 1.0
CA B:ASP482 4.5 63.4 1.0
N B:ARG483 4.5 64.6 1.0
CB B:ASP482 4.5 65.2 1.0
C B:ILE487 4.5 55.5 1.0
CA B:VAL481 4.6 59.6 1.0
C B:VAL481 4.6 60.9 1.0
N B:ASP480 4.6 51.1 1.0
N B:ILE487 4.6 56.4 1.0
OD2 B:ASP480 4.6 56.3 1.0
CA B:SER484 4.7 62.6 1.0
C B:ASP482 4.7 63.6 1.0
CA B:GLY488 4.8 55.9 1.0
C B:PHE479 4.8 49.4 1.0
CG2 B:THR486 4.9 56.4 1.0
N B:THR486 4.9 58.5 1.0

Reference:

B.Todd, D.Moore, C.C.S.Deivanayagam, G.-D.Lin, D.Chattopadhyay, M.Maki, K.K.W.Wang, S.V.L.Narayana. A Structural Model For the Inhibition of Calpain By Calpastatin: Crystal Structures of the Native Domain VI of Calpain and Its Complexes with Calpastatin Peptide and A Small Molecule Inhibitor. J.Mol.Biol. V. 328 131 2003.
ISSN: ISSN 0022-2836
PubMed: 12684003
DOI: 10.1016/S0022-2836(03)00274-2
Page generated: Thu Jul 11 13:04:08 2024

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