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Calcium in PDB 1alw: Inhibitor and Calcium Bound Domain VI of Porcine Calpain

Protein crystallography data

The structure of Inhibitor and Calcium Bound Domain VI of Porcine Calpain, PDB code: 1alw was solved by S.V.L.Narayana, G.Lin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.03
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.870, 80.460, 57.080, 90.00, 91.20, 90.00
R / Rfree (%) 21 / 27

Other elements in 1alw:

The structure of Inhibitor and Calcium Bound Domain VI of Porcine Calpain also contains other interesting chemical elements:

Iodine (I) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain (pdb code 1alw). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain, PDB code: 1alw:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 1alw

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Calcium binding site 1 out of 8 in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Inhibitor and Calcium Bound Domain VI of Porcine Calpain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1

b:21.9
occ:1.00
O A:GLU112 2.1 21.6 1.0
OE2 A:GLU117 2.2 22.8 1.0
OD1 A:ASP110 2.2 24.0 1.0
O A:ALA107 2.3 25.0 1.0
O A:HOH549 2.3 26.0 1.0
OE1 A:GLU117 2.4 22.5 1.0
O A:HOH538 2.5 22.6 1.0
CD A:GLU117 2.6 22.0 1.0
CG A:ASP110 3.3 24.5 1.0
C A:GLU112 3.3 21.8 1.0
C A:ALA107 3.4 25.2 1.0
OD2 A:ASP110 3.6 25.5 1.0
CA A:ALA107 4.0 24.8 1.0
N A:GLU112 4.0 24.6 1.0
CG A:GLU117 4.1 22.1 1.0
CA A:GLU112 4.2 22.9 1.0
N A:VAL113 4.2 20.9 1.0
CA A:VAL113 4.3 20.3 1.0
N A:SER114 4.4 19.8 1.0
N A:GLY108 4.5 25.6 1.0
CB A:ASP110 4.6 24.4 1.0
N A:ASP110 4.7 25.1 1.0
CB A:ALA107 4.7 24.5 1.0
O A:LEU106 4.7 24.7 1.0
CA A:GLY108 4.8 25.9 1.0
CB A:GLU112 4.8 24.2 1.0
N A:MET111 4.8 24.4 1.0
C A:VAL113 4.8 19.9 1.0
CA A:ASP110 4.9 24.2 1.0
C A:ASP110 5.0 24.1 1.0
C A:GLY108 5.0 26.2 1.0

Calcium binding site 2 out of 8 in 1alw

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Calcium binding site 2 out of 8 in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Inhibitor and Calcium Bound Domain VI of Porcine Calpain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2

b:19.0
occ:1.00
OD1 A:ASP152 2.0 29.2 1.0
OE1 A:GLU161 2.1 18.0 1.0
OD1 A:ASP150 2.2 20.7 1.0
O A:LYS156 2.2 20.1 1.0
OE2 A:GLU161 2.3 17.8 1.0
OG1 A:THR154 2.4 22.8 1.0
CD A:GLU161 2.6 18.5 1.0
O A:HOH544 2.7 33.0 1.0
CG A:ASP152 3.0 28.4 1.0
CG A:ASP150 3.4 22.1 1.0
OD2 A:ASP152 3.4 29.2 1.0
C A:LYS156 3.5 19.4 1.0
CB A:THR154 3.8 24.2 1.0
N A:THR154 4.0 25.1 1.0
OE2 A:GLU112 4.1 25.9 1.0
CG A:GLU161 4.1 19.3 1.0
CB A:ASP150 4.1 22.0 1.0
CA A:ASP150 4.2 22.9 1.0
N A:GLY158 4.2 20.3 1.0
N A:ASP152 4.2 25.7 1.0
CB A:ASP152 4.3 27.5 1.0
N A:LYS156 4.3 21.2 1.0
CA A:LEU157 4.3 18.3 1.0
N A:LEU157 4.3 18.5 1.0
OD2 A:ASP150 4.3 22.1 1.0
CG2 A:THR154 4.4 23.8 1.0
CA A:THR154 4.4 24.7 1.0
CA A:LYS156 4.4 20.1 1.0
CA A:ASP152 4.6 26.6 1.0
N A:THR153 4.6 27.0 1.0
C A:ASP150 4.6 24.0 1.0
C A:LEU157 4.7 19.2 1.0
N A:GLY155 4.7 23.7 1.0
C A:ASP152 4.7 27.2 1.0
N A:SER151 4.7 24.8 1.0
C A:THR154 4.9 24.1 1.0
CB A:GLU161 4.9 21.2 1.0

Calcium binding site 3 out of 8 in 1alw

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Calcium binding site 3 out of 8 in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Inhibitor and Calcium Bound Domain VI of Porcine Calpain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca3

b:19.5
occ:1.00
O A:HOH547 2.1 23.9 1.0
OD1 A:ASP180 2.1 16.9 1.0
OE1 A:GLU191 2.1 25.3 1.0
OD1 A:ASP182 2.2 26.9 1.0
OE2 A:GLU191 2.3 24.3 1.0
O A:THR186 2.5 20.9 1.0
CD A:GLU191 2.5 23.8 1.0
OG A:SER184 2.7 23.4 1.0
CG A:ASP182 3.2 26.8 1.0
CG A:ASP180 3.3 18.9 1.0
OD2 A:ASP182 3.5 29.2 1.0
C A:THR186 3.7 19.8 1.0
CB A:SER184 3.8 24.5 1.0
CG A:GLU191 4.0 22.7 1.0
CA A:ASP180 4.0 21.5 1.0
N A:SER184 4.0 26.1 1.0
CB A:ASP180 4.2 19.1 1.0
N A:ASP182 4.2 26.1 1.0
OD2 A:ASP180 4.2 19.3 1.0
N A:GLY188 4.2 20.7 1.0
C A:ASP180 4.2 22.3 1.0
N A:THR186 4.4 20.1 1.0
CA A:ILE187 4.4 19.9 1.0
CB A:ASP182 4.4 26.6 1.0
CA A:SER184 4.5 25.3 1.0
OG1 A:THR186 4.5 20.2 1.0
N A:ILE187 4.5 19.8 1.0
N A:ARG183 4.5 27.3 1.0
O A:ASP180 4.6 22.2 1.0
N A:VAL181 4.6 23.0 1.0
CA A:ASP182 4.6 26.7 1.0
CA A:THR186 4.6 19.4 1.0
C A:ASP182 4.7 27.2 1.0
C A:ILE187 4.7 20.2 1.0
N A:GLY185 4.7 23.8 1.0
OD1 A:ASN221 4.9 24.8 1.0
CB A:GLU191 5.0 21.9 1.0

Calcium binding site 4 out of 8 in 1alw

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Calcium binding site 4 out of 8 in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Inhibitor and Calcium Bound Domain VI of Porcine Calpain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca4

b:18.3
occ:1.00
OD1 A:ASP135 2.2 21.8 1.0
OD2 A:ASP223 2.2 11.9 1.0
O A:HOH506 2.3 23.5 1.0
O A:HOH501 2.3 20.9 1.0
OD1 A:ASN226 2.4 12.4 1.0
OD1 A:ASP225 2.5 13.8 1.0
OD1 A:ASP223 2.6 15.5 1.0
OD2 A:ASP225 2.7 13.7 1.0
CG A:ASP223 2.8 13.1 1.0
CG A:ASP225 2.9 13.8 1.0
CG A:ASP135 3.3 21.1 1.0
CG A:ASN226 3.4 13.0 1.0
OD2 A:ASP135 3.9 22.6 1.0
ND2 A:ASN226 4.1 12.9 1.0
N A:ASN226 4.3 12.6 1.0
CB A:ASP223 4.3 13.8 1.0
CB A:ASN226 4.3 12.3 1.0
N A:ASP135 4.3 18.6 1.0
CB A:ASP225 4.4 12.7 1.0
CB A:ASP135 4.5 19.1 1.0
NH1 B:ARG143 4.6 22.0 1.0
O A:HOH518 4.7 32.6 1.0
OG1 A:THR134 4.8 16.5 1.0
CA A:ASN226 4.8 12.1 1.0
O A:GLY136 4.9 17.7 1.0
C A:ASP225 5.0 11.9 1.0
CA A:ASP135 5.0 19.2 1.0
N A:ASP225 5.0 13.4 1.0
OD1 B:ASP140 5.0 20.4 1.0
CA A:ASP225 5.0 12.5 1.0

Calcium binding site 5 out of 8 in 1alw

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Calcium binding site 5 out of 8 in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Inhibitor and Calcium Bound Domain VI of Porcine Calpain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca5

b:17.2
occ:1.00
O B:GLU112 2.1 11.9 1.0
O B:HOH503 2.2 16.8 1.0
O B:HOH514 2.2 26.8 1.0
O B:ALA107 2.3 22.4 1.0
OD1 B:ASP110 2.4 21.2 1.0
OE1 B:GLU117 2.5 16.6 1.0
OE2 B:GLU117 2.6 15.8 1.0
CD B:GLU117 2.9 14.6 1.0
C B:GLU112 3.3 13.8 1.0
C B:ALA107 3.4 22.0 1.0
CG B:ASP110 3.5 21.2 1.0
OD2 B:ASP110 3.8 20.6 1.0
CA B:ALA107 4.0 21.8 1.0
CA B:VAL113 4.1 14.0 1.0
N B:GLU112 4.2 17.4 1.0
N B:VAL113 4.2 13.5 1.0
CA B:GLU112 4.3 15.9 1.0
N B:SER114 4.4 12.4 1.0
CG B:GLU117 4.4 12.8 1.0
N B:GLY108 4.5 22.6 1.0
O B:LEU106 4.6 21.6 1.0
N B:ASP110 4.6 22.2 1.0
C B:VAL113 4.7 12.9 1.0
CA B:GLY108 4.7 23.1 1.0
O B:HOH557 4.8 34.2 1.0
CB B:ASP110 4.8 20.9 1.0
CB B:ALA107 4.8 22.0 1.0
OG B:SER114 4.8 13.5 1.0
C B:GLY108 4.9 23.5 1.0
CB B:GLU112 5.0 17.9 1.0

Calcium binding site 6 out of 8 in 1alw

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Calcium binding site 6 out of 8 in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Inhibitor and Calcium Bound Domain VI of Porcine Calpain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca6

b:17.6
occ:1.00
OD1 B:ASP150 2.1 17.9 1.0
OG1 B:THR154 2.2 19.5 1.0
OD1 B:ASP152 2.3 23.4 1.0
O B:LYS156 2.3 14.7 1.0
O B:HOH592 2.3 21.6 1.0
OE1 B:GLU161 2.3 15.6 1.0
OE2 B:GLU161 2.6 15.1 1.0
CD B:GLU161 2.8 14.1 1.0
CG B:ASP150 3.3 16.8 1.0
CG B:ASP152 3.3 22.4 1.0
C B:LYS156 3.5 14.0 1.0
CB B:THR154 3.6 19.7 1.0
OD2 B:ASP152 3.7 22.2 1.0
N B:GLY158 4.0 14.4 1.0
CA B:LEU157 4.0 13.0 1.0
N B:THR154 4.0 21.8 1.0
OE2 B:GLU112 4.1 27.1 1.0
CB B:ASP150 4.1 15.9 1.0
CA B:ASP150 4.1 16.4 1.0
OD2 B:ASP150 4.1 15.4 1.0
CG2 B:THR154 4.2 17.6 1.0
N B:LEU157 4.2 13.1 1.0
CG B:GLU161 4.3 14.3 1.0
CA B:THR154 4.4 20.1 1.0
N B:LYS156 4.5 16.4 1.0
C B:LEU157 4.5 13.5 1.0
N B:ASP152 4.5 21.7 1.0
C B:ASP150 4.5 17.3 1.0
CA B:LYS156 4.6 14.8 1.0
CB B:ASP152 4.6 22.6 1.0
N B:THR153 4.8 23.3 1.0
CA B:ASP152 4.8 22.8 1.0
N B:GLY155 4.8 18.4 1.0
N B:SER151 4.9 18.6 1.0
O B:ASP150 4.9 17.1 1.0
C B:THR154 4.9 19.6 1.0
C B:ASP152 4.9 23.8 1.0
CD B:GLU112 5.0 25.0 1.0

Calcium binding site 7 out of 8 in 1alw

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Calcium binding site 7 out of 8 in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Inhibitor and Calcium Bound Domain VI of Porcine Calpain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca7

b:16.0
occ:1.00
OD1 B:ASP180 2.1 14.8 1.0
OG B:SER184 2.2 15.6 1.0
OE1 B:GLU191 2.3 19.8 1.0
OD1 B:ASP182 2.3 18.4 1.0
O B:HOH502 2.4 31.9 1.0
OE2 B:GLU191 2.4 19.3 1.0
O B:THR186 2.5 14.2 1.0
CD B:GLU191 2.7 19.9 1.0
CG B:ASP180 3.3 14.8 1.0
CG B:ASP182 3.4 18.8 1.0
CB B:SER184 3.6 14.3 1.0
C B:THR186 3.7 14.1 1.0
OD2 B:ASP182 3.8 19.1 1.0
CA B:ASP180 4.0 16.0 1.0
CB B:ASP180 4.0 15.6 1.0
N B:SER184 4.1 16.0 1.0
N B:GLY188 4.1 17.3 1.0
OD2 B:ASP180 4.2 15.4 1.0
CG B:GLU191 4.2 19.1 1.0
OG1 B:THR186 4.4 16.9 1.0
C B:ASP180 4.4 16.6 1.0
N B:THR186 4.4 13.7 1.0
CA B:SER184 4.4 14.5 1.0
N B:ASP182 4.5 18.6 1.0
CA B:ILE187 4.5 14.9 1.0
N B:ILE187 4.5 14.5 1.0
CA B:THR186 4.6 14.4 1.0
CB B:ASP182 4.7 18.5 1.0
C B:ILE187 4.7 16.5 1.0
N B:VAL181 4.8 17.1 1.0
N B:ARG183 4.9 16.8 1.0
O B:ASP180 4.9 16.4 1.0
N B:GLY185 4.9 14.0 1.0
O B:HOH561 4.9 33.1 1.0
CA B:ASP182 4.9 18.4 1.0
CA B:GLY188 4.9 17.6 1.0
C B:ASP182 5.0 17.8 1.0
C B:SER184 5.0 14.1 1.0

Calcium binding site 8 out of 8 in 1alw

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Calcium binding site 8 out of 8 in the Inhibitor and Calcium Bound Domain VI of Porcine Calpain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Inhibitor and Calcium Bound Domain VI of Porcine Calpain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca8

b:9.8
occ:1.00
O B:HOH508 2.1 16.3 1.0
OD1 B:ASN226 2.2 10.4 1.0
OD1 B:ASP135 2.2 15.3 1.0
OD2 B:ASP225 2.3 10.6 1.0
O A:HOH532 2.4 16.3 1.0
OD2 B:ASP223 2.5 12.9 1.0
OD1 B:ASP223 2.5 15.0 1.0
OD1 B:ASP225 2.6 11.6 1.0
CG B:ASP225 2.7 12.1 1.0
CG B:ASP223 2.8 14.0 1.0
CG B:ASP135 3.3 15.5 1.0
CG B:ASN226 3.3 11.2 1.0
OD2 B:ASP135 3.7 17.5 1.0
N B:ASN226 4.1 12.3 1.0
ND2 B:ASN226 4.2 12.7 1.0
CB B:ASP225 4.2 12.0 1.0
CB B:ASN226 4.2 11.9 1.0
O B:HOH531 4.3 19.3 1.0
CB B:ASP223 4.3 13.3 1.0
NH2 A:ARG143 4.4 31.7 1.0
N B:ASP135 4.4 13.2 1.0
CB B:ASP135 4.6 14.3 1.0
CA B:ASN226 4.7 12.2 1.0
N B:ASP225 4.8 11.6 1.0
O B:GLY136 4.8 12.8 1.0
CA B:ASP225 4.9 12.0 1.0
C B:ASP225 4.9 12.1 1.0
O B:HOH505 4.9 14.0 1.0
OG1 B:THR134 4.9 11.2 1.0
OD1 A:ASP140 4.9 17.5 1.0
CA B:ASP135 5.0 13.8 1.0

Reference:

G.D.Lin, D.Chattopadhyay, M.Maki, K.K.Wang, M.Carson, L.Jin, P.W.Yuen, E.Takano, M.Hatanaka, L.J.Delucas, S.V.Narayana. Crystal Structure of Calcium Bound Domain VI of Calpain at 1.9 A Resolution and Its Role in Enzyme Assembly, Regulation, and Inhibitor Binding. Nat.Struct.Biol. V. 4 539 1997.
ISSN: ISSN 1072-8368
PubMed: 9228946
DOI: 10.1038/NSB0797-539
Page generated: Sat Dec 12 02:48:22 2020

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