Atomistry » Calcium » PDB 1nmb-1nxc » 1nx0
Atomistry »
  Calcium »
    PDB 1nmb-1nxc »
      1nx0 »

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

Go back to Calcium Binding Sites List in 1nx0
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

Go back to Calcium Binding Sites List in 1nx0
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

Go back to Calcium Binding Sites List in 1nx0
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

Go back to Calcium Binding Sites List in 1nx0
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

Go back to Calcium Binding Sites List in 1nx0
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

Go back to Calcium Binding Sites List in 1nx0
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: Sat Dec 12 03:09:42 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy