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Calcium in PDB 1nx1: Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic)

Protein crystallography data

The structure of Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic), PDB code: 1nx1 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 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.746, 61.055, 143.704, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic) (pdb code 1nx1). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic), PDB code: 1nx1:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1nx1

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Calcium binding site 1 out of 8 in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:44.1
occ:1.00
 OE2 A:GLU117 2.6 30.0 1.0
O A:GLU112 2.9 25.6 1.0
NZ A:LYS156 2.9 29.7 1.0
O A:HOH972 3.0 34.7 1.0
OD2 A:ASP110 3.0 29.5 1.0
OE1 A:GLU117 3.1 33.7 1.0
CD A:GLU117 3.2 32.9 1.0
CA A:GLY108 3.5 34.7 1.0
CD A:LYS156 3.7 29.0 1.0
CE A:LYS156 3.8 29.3 1.0
CG A:ASP110 3.8 31.5 1.0
N A:GLY108 3.8 31.6 1.0
C A:GLU112 3.9 25.9 1.0
N A:SER114 4.1 21.9 1.0
OD1 A:ASP110 4.1 32.8 1.0
C A:GLY108 4.1 36.0 1.0
O A:HOH995 4.1 39.3 1.0
N A:ASP109 4.3 35.6 1.0
CB A:SER114 4.4 25.3 1.0
OG A:SER114 4.6 20.8 1.0
CA A:VAL113 4.6 21.1 1.0
N A:GLU112 4.7 26.3 1.0
N A:ASP110 4.7 30.6 1.0
N A:VAL113 4.7 22.9 1.0
C A:VAL113 4.7 21.5 1.0
CG A:GLU117 4.7 28.8 1.0
CA A:GLU112 4.8 25.2 1.0
CA A:SER114 4.8 23.8 1.0
O A:GLY108 4.8 33.9 1.0
CB A:GLU112 4.9 27.8 1.0

Calcium binding site 2 out of 8 in 1nx1

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Calcium binding site 2 out of 8 in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:39.3
occ:1.00
 O A:LYS156 2.3 16.9 1.0
O A:HOH959 2.4 28.2 1.0
OE1 A:GLU161 2.4 24.6 1.0
OD1 A:ASP150 2.4 22.7 1.0
OG1 A:THR154 2.5 25.8 1.0
OD1 A:ASP152 2.5 31.0 1.0
CD A:GLU161 3.2 29.1 1.0
OE2 A:GLU161 3.2 28.4 1.0
CG A:ASP152 3.4 32.6 1.0
C A:LYS156 3.5 23.2 1.0
CG A:ASP150 3.6 25.8 1.0
OD2 A:ASP152 3.7 27.6 1.0
CB A:THR154 3.7 30.9 1.0
N A:GLY158 3.9 24.2 1.0
N A:THR154 3.9 28.4 1.0
CG2 A:THR154 4.0 31.4 1.0
CA A:LEU157 4.2 20.9 1.0
OE1 A:GLU112 4.3 29.9 1.0
N A:LYS156 4.3 24.3 1.0
N A:LEU157 4.3 21.7 1.0
CA A:THR154 4.3 27.7 1.0
CA A:ASP150 4.3 25.1 1.0
CB A:ASP150 4.4 24.2 1.0
OE2 A:GLU112 4.4 31.6 1.0
OD2 A:ASP150 4.5 29.0 1.0
C A:LEU157 4.5 27.8 1.0
CA A:LYS156 4.6 21.7 1.0
CG A:GLU161 4.6 24.3 1.0
CD A:GLU112 4.7 28.4 1.0
N A:GLY155 4.7 28.4 1.0
O A:HOH915 4.8 26.2 1.0
C A:THR154 4.8 30.4 1.0
C A:ASP150 4.8 26.9 1.0
CA A:GLY158 4.8 26.3 1.0
CB A:ASP152 4.8 30.6 1.0
N A:ASP152 4.8 33.1 1.0
CD2 A:LEU157 4.8 27.9 1.0
N A:THR153 4.9 33.3 1.0
C A:ASP152 4.9 32.7 1.0

Calcium binding site 3 out of 8 in 1nx1

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Calcium binding site 3 out of 8 in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:47.3
occ:1.00
 OD1 A:ASP180 2.3 24.5 1.0
OD1 A:ASP182 2.3 37.4 1.0
O A:THR186 2.4 27.6 1.0
OG A:SER184 2.5 31.3 1.0
O A:HOH923 2.7 26.2 1.0
O A:HOH980 2.8 44.8 1.0
CG A:ASP182 3.4 39.9 1.0
CG A:ASP180 3.4 28.7 1.0
CB A:SER184 3.4 30.5 1.0
C A:THR186 3.6 26.5 1.0
OD2 A:ASP182 3.7 38.8 1.0
CA A:ASP180 3.7 28.0 1.0
N A:SER184 3.8 32.7 1.0
N A:GLY188 3.9 27.6 1.0
CB A:ASP180 4.1 24.5 1.0
C A:ASP180 4.1 27.8 1.0
CA A:SER184 4.2 30.9 1.0
N A:THR186 4.2 22.6 1.0
OG1 A:THR186 4.3 38.2 1.0
N A:VAL181 4.3 30.3 1.0
OD2 A:ASP180 4.3 28.0 1.0
CA A:ILE187 4.4 27.0 1.0
N A:ASP182 4.4 31.7 1.0
N A:ILE187 4.5 24.4 1.0
C A:ILE187 4.5 22.3 1.0
CA A:THR186 4.5 25.7 1.0
N A:GLY185 4.6 27.8 1.0
C A:SER184 4.6 30.6 1.0
N A:ARG183 4.6 37.4 1.0
CA A:GLY188 4.6 26.2 1.0
CB A:ASP182 4.7 34.8 1.0
O A:ASP180 4.8 21.9 1.0
OE1 A:GLU191 4.8 47.2 1.0
C A:ASP182 4.9 37.3 1.0
O A:PHE179 4.9 22.8 1.0
CA A:ASP182 4.9 35.1 1.0
C A:ARG183 4.9 36.5 1.0

Calcium binding site 4 out of 8 in 1nx1

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Calcium binding site 4 out of 8 in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:53.0
occ:1.00
 OD1 A:ASP135 2.2 43.8 1.0
OD1 A:ASP225 2.3 23.8 1.0
OD2 A:ASP225 2.3 22.8 1.0
CG A:ASP225 2.6 19.6 1.0
OD1 A:ASP223 2.8 29.0 1.0
OD2 A:ASP223 2.8 36.3 1.0
ND2 A:ASN226 2.9 28.4 1.0
CG A:ASP223 3.2 31.1 1.0
CG A:ASP135 3.2 44.9 1.0
OD2 A:ASP135 3.5 44.8 1.0
CG A:ASN226 3.9 31.4 1.0
N A:ASN226 4.0 16.7 1.0
CB A:ASP225 4.1 18.5 1.0
OG1 A:THR134 4.3 26.6 1.0
N A:ASP135 4.4 26.0 1.0
CB A:ASN226 4.4 23.6 1.0
O A:GLY136 4.6 26.1 1.0
C A:ASP225 4.6 20.6 1.0
CB A:ASP135 4.6 36.1 1.0
CB A:ASP223 4.6 28.0 1.0
N A:ASP225 4.7 18.4 1.0
CA A:ASP225 4.7 17.4 1.0
CA A:ASN226 4.7 20.1 1.0
OD1 A:ASN226 4.9 37.1 1.0
O A:HOH934 5.0 25.4 1.0
CA A:THR134 5.0 23.7 1.0

Calcium binding site 5 out of 8 in 1nx1

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Calcium binding site 5 out of 8 in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5

b:62.3
occ:1.00
 OE2 B:GLU417 2.5 30.3 1.0
OE1 B:GLU417 2.7 36.1 1.0
O B:GLU412 2.9 26.4 1.0
CD B:GLU417 3.0 36.0 1.0
CA B:GLY408 3.0 32.7 1.0
OD1 B:ASP410 3.1 30.9 1.0
N B:GLY408 3.4 31.4 1.0
NZ B:LYS456 3.5 23.7 1.0
C B:GLY408 3.8 38.2 1.0
CG B:ASP410 3.9 33.6 1.0
N B:ASP409 4.0 36.6 1.0
C B:GLU412 4.0 30.4 1.0
N B:SER414 4.1 25.2 1.0
CD B:LYS456 4.2 23.6 1.0
OD2 B:ASP410 4.2 32.0 1.0
CE B:LYS456 4.3 30.2 1.0
CB B:SER414 4.5 27.1 1.0
CG B:GLU417 4.5 33.6 1.0
N B:ASP410 4.5 31.1 1.0
N B:GLU412 4.6 31.5 1.0
CA B:VAL413 4.6 27.6 1.0
OG B:SER414 4.6 23.9 1.0
O B:GLY408 4.6 36.9 1.0
C B:ALA407 4.7 33.3 1.0
N B:VAL413 4.8 26.0 1.0
C B:VAL413 4.8 27.6 1.0
CA B:SER414 4.9 24.8 1.0
CA B:GLU412 4.9 30.8 1.0

Calcium binding site 6 out of 8 in 1nx1

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Calcium binding site 6 out of 8 in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca6

b:37.6
occ:1.00
 OD1 B:ASP450 2.2 24.3 1.0
O B:LYS456 2.3 21.3 1.0
OD1 B:ASP452 2.4 34.8 1.0
OE1 B:GLU461 2.4 23.4 1.0
O B:HOH931 2.5 27.4 1.0
OG1 B:THR454 2.6 29.9 1.0
CD B:GLU461 3.1 29.4 1.0
OE2 B:GLU461 3.1 26.1 1.0
CG B:ASP450 3.3 26.9 1.0
CG B:ASP452 3.3 38.7 1.0
C B:LYS456 3.6 22.9 1.0
CG2 B:THR454 3.6 33.7 1.0
OD2 B:ASP452 3.6 40.2 1.0
CB B:THR454 3.6 36.2 1.0
N B:THR454 3.8 33.3 1.0
CA B:ASP450 4.1 24.6 1.0
N B:GLY458 4.1 23.8 1.0
CB B:ASP450 4.1 24.5 1.0
N B:LYS456 4.2 25.4 1.0
OD2 B:ASP450 4.2 28.9 1.0
CA B:THR454 4.2 32.3 1.0
OE1 B:GLU412 4.2 30.2 1.0
CA B:LEU457 4.3 21.6 1.0
OE2 B:GLU412 4.4 30.6 1.0
N B:LEU457 4.4 19.3 1.0
N B:GLY455 4.5 25.6 1.0
CA B:LYS456 4.5 23.8 1.0
C B:ASP450 4.6 31.0 1.0
CG B:GLU461 4.6 25.0 1.0
C B:LEU457 4.6 22.7 1.0
CD B:GLU412 4.6 30.5 1.0
N B:THR453 4.7 38.4 1.0
N B:ASP452 4.7 35.7 1.0
CB B:ASP452 4.7 38.1 1.0
C B:THR454 4.7 30.1 1.0
C B:ASP452 4.8 37.5 1.0
O B:HOH963 4.8 33.5 1.0
C B:THR453 4.9 38.4 1.0
CA B:ASP452 5.0 37.3 1.0

Calcium binding site 7 out of 8 in 1nx1

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Calcium binding site 7 out of 8 in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca7

b:74.7
occ:1.00
 O B:THR486 2.5 54.2 1.0
OD1 B:ASP480 2.5 61.2 1.0
OE2 B:GLU491 2.6 62.2 1.0
OG B:SER484 2.6 64.5 1.0
OD2 B:ASP482 3.2 75.0 1.0
N B:GLY488 3.6 57.0 1.0
CG B:ASP480 3.6 56.6 1.0
C B:THR486 3.6 53.3 1.0
CB B:ASP482 3.6 68.5 1.0
CG B:ASP482 3.6 72.2 1.0
CB B:SER484 3.7 63.8 1.0
CD B:GLU491 3.8 65.5 1.0
CA B:ASP480 3.8 55.5 1.0
N B:ASP482 3.9 65.6 1.0
N B:SER484 3.9 63.4 1.0
C B:ASP480 4.1 58.7 1.0
CA B:ILE487 4.1 54.4 1.0
CB B:ASP480 4.2 53.9 1.0
N B:ARG483 4.2 66.2 1.0
CA B:ASP482 4.2 67.5 1.0
C B:ILE487 4.3 56.9 1.0
N B:VAL481 4.3 60.3 1.0
N B:ILE487 4.3 53.6 1.0
OE1 B:GLU491 4.4 64.3 1.0
CA B:GLY488 4.4 55.8 1.0
CA B:SER484 4.4 63.6 1.0
N B:THR486 4.4 52.4 1.0
OG1 B:THR486 4.5 51.8 1.0
C B:ASP482 4.5 67.0 1.0
OD2 B:ASP480 4.6 53.2 1.0
O B:PHE479 4.6 54.8 1.0
OD1 B:ASP482 4.6 72.5 1.0
CA B:THR486 4.6 51.7 1.0
O B:ASP480 4.7 57.0 1.0
N B:GLY485 4.8 61.1 1.0
CG B:GLU491 4.8 65.5 1.0
C B:VAL481 4.9 64.0 1.0
CG2 B:VAL481 4.9 59.6 1.0

Calcium binding site 8 out of 8 in 1nx1

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Calcium binding site 8 out of 8 in the Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Calpain Domain VI Complexed with Calpastatin Inhibitory Domain C (Dic) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca8

b:64.0
occ:1.00
 ND2 B:ASN526 2.2 40.2 1.0
OD1 B:ASP525 2.3 31.9 1.0
OD1 B:ASP435 2.4 55.4 1.0
OD2 B:ASP523 2.6 37.8 1.0
OD2 B:ASP525 2.8 30.8 1.0
OD1 B:ASP523 2.8 38.5 1.0
CG B:ASP525 2.9 35.4 1.0
CG B:ASP523 3.1 42.0 1.0
CG B:ASN526 3.5 36.5 1.0
CG B:ASP435 3.6 57.3 1.0
OD2 B:ASP435 4.1 60.2 1.0
N B:ASP435 4.2 41.1 1.0
N B:ASN526 4.3 30.6 1.0
CB B:ASN526 4.3 33.7 1.0
OD1 B:ASN526 4.4 39.1 1.0
CB B:ASP525 4.4 27.2 1.0
OG1 B:THR434 4.4 42.8 1.0
CB B:ASP523 4.5 44.0 1.0
CA B:THR434 4.7 43.2 1.0
O B:GLY436 4.8 29.6 1.0
CB B:ASP435 4.8 51.5 1.0
CA B:ASN526 4.8 33.7 1.0
CB B:THR434 4.9 42.3 1.0
O B:HOH1005 5.0 34.5 1.0
N B:ASP525 5.0 35.1 1.0
C B:ASP525 5.0 32.0 1.0
C B:THR434 5.0 39.6 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 13:04:29 2024

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