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Calcium in PDB 4phj: The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein

Protein crystallography data

The structure of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein, PDB code: 4phj was solved by S.E.Adams, P.J.Rizkallah, R.K.Allemann, D.J.Miller, M.B.Hallett, E.Robinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.61 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 49.630, 79.310, 57.100, 90.00, 91.52, 90.00
R / Rfree (%) 16.6 / 20

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein (pdb code 4phj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein, PDB code: 4phj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 4phj

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Calcium binding site 1 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca301

b:20.5
occ:1.00
 OD1 A:ASN228 2.4 20.6 1.0
OD1 A:ASP137 2.4 23.0 1.0
O A:HOH443 2.4 21.2 1.0
O A:HOH445 2.5 22.2 1.0
OD1 A:ASP227 2.5 21.7 1.0
OD2 A:ASP227 2.5 21.0 1.0
OD2 A:ASP225 2.6 21.4 1.0
OD1 A:ASP225 2.6 19.3 1.0
CG A:ASP227 2.8 19.5 1.0
CG A:ASP225 3.0 19.0 1.0
CG A:ASN228 3.3 20.5 1.0
CG A:ASP137 3.4 29.2 1.0
OD2 A:ASP137 3.7 29.9 1.0
ND2 A:ASN228 4.0 20.8 1.0
N A:ASN228 4.1 17.1 1.0
CB A:ASN228 4.3 17.6 1.0
CB A:ASP227 4.3 19.5 1.0
N A:ASP137 4.5 25.8 1.0
CB A:ASP225 4.5 19.4 1.0
O A:HOH508 4.5 36.3 1.0
CA A:ASN228 4.7 17.8 1.0
CB A:ASP137 4.7 28.5 1.0
O A:HOH449 4.7 24.7 1.0
OG1 A:THR136 4.7 24.1 1.0
O A:GLY138 4.8 23.6 1.0
C A:ASP227 4.8 17.9 1.0
O A:HOH468 4.8 26.8 1.0
CA A:ASP227 4.9 18.4 1.0
N A:ASP227 4.9 18.7 1.0

Calcium binding site 2 out of 8 in 4phj

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Calcium binding site 2 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca302

b:23.7
occ:1.00
 OD1 A:ASP152 2.3 22.1 1.0
OD1 A:ASP154 2.3 24.4 1.0
O A:HOH457 2.3 24.7 1.0
O A:LYS158 2.3 23.5 1.0
OE1 A:GLU163 2.3 23.2 1.0
OG1 A:THR156 2.5 23.7 1.0
OE2 A:GLU163 2.8 26.0 1.0
CD A:GLU163 2.9 22.6 1.0
CG A:ASP154 3.3 29.8 1.0
CG A:ASP152 3.5 26.0 1.0
C A:LYS158 3.6 22.2 1.0
OD2 A:ASP154 3.7 29.9 1.0
CB A:THR156 3.7 25.0 1.0
N A:THR156 3.9 26.4 1.0
CG2 A:THR156 4.0 25.8 1.0
N A:GLY160 4.0 22.9 1.0
OE1 A:GLU114 4.2 25.4 1.0
CA A:LEU159 4.2 21.9 1.0
CA A:ASP152 4.3 23.5 1.0
CB A:ASP152 4.3 23.3 1.0
N A:LYS158 4.3 22.3 1.0
CA A:THR156 4.3 26.1 1.0
N A:LEU159 4.3 22.3 1.0
OD2 A:ASP152 4.3 23.0 1.0
CG A:GLU163 4.4 22.6 1.0
N A:ASP154 4.5 28.2 1.0
OE2 A:GLU114 4.5 26.4 1.0
C A:LEU159 4.6 21.8 1.0
CA A:LYS158 4.6 23.4 1.0
CD A:GLU114 4.6 26.0 1.0
C A:ASP152 4.6 25.8 1.0
CB A:ASP154 4.6 29.4 1.0
N A:THR155 4.7 30.5 1.0
C A:ASP154 4.7 29.5 1.0
N A:GLY157 4.7 22.8 1.0
C A:THR156 4.8 24.9 1.0
CA A:ASP154 4.8 30.3 1.0
N A:SER153 4.9 27.4 1.0
O A:ASP152 5.0 28.2 1.0

Calcium binding site 3 out of 8 in 4phj

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Calcium binding site 3 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca303

b:24.4
occ:1.00
 O A:HOH438 2.3 22.9 1.0
O A:GLU114 2.3 24.8 1.0
O A:ALA109 2.3 25.6 1.0
O A:HOH452 2.4 32.0 1.0
OD1 A:ASP112 2.4 26.2 1.0
OE1 A:GLU119 2.4 26.4 1.0
OE2 A:GLU119 2.5 25.3 1.0
CD A:GLU119 2.8 24.7 1.0
CG A:ASP112 3.4 26.4 1.0
C A:ALA109 3.4 26.1 1.0
C A:GLU114 3.5 22.6 1.0
OD2 A:ASP112 3.6 28.2 1.0
CA A:ALA109 4.0 25.2 1.0
N A:GLU114 4.2 25.6 1.0
CG A:GLU119 4.3 24.9 1.0
N A:SER116 4.4 24.4 1.0
N A:VAL115 4.4 23.1 1.0
N A:GLY110 4.5 28.8 1.0
CA A:GLU114 4.5 24.6 1.0
CA A:VAL115 4.5 22.2 1.0
N A:ASP112 4.7 25.2 1.0
O A:HOH461 4.7 36.6 1.0
CB A:ALA109 4.7 26.1 1.0
O A:HOH536 4.7 52.2 1.0
CB A:ASP112 4.7 25.9 1.0
O A:LEU108 4.8 30.0 1.0
CA A:GLY110 4.8 30.0 1.0
C A:GLY110 4.8 30.9 1.0
C A:VAL115 4.9 23.1 1.0
N A:ASP111 4.9 29.1 1.0
N A:MET113 4.9 27.3 1.0
OG A:SER116 4.9 25.8 1.0
CB A:SER116 5.0 25.1 1.0

Calcium binding site 4 out of 8 in 4phj

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Calcium binding site 4 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca304

b:30.1
occ:1.00
 OD1 A:ASP182 2.3 29.4 1.0
O A:THR188 2.3 24.0 1.0
OD1 A:ASP184 2.3 35.0 1.0
O A:HOH476 2.4 41.5 1.0
OE1 A:GLU193 2.5 26.5 1.0
OG A:SER186 2.6 32.1 1.0
OE2 A:GLU193 2.6 31.0 1.0
CD A:GLU193 2.9 27.3 1.0
CG A:ASP184 3.4 42.2 1.0
CG A:ASP182 3.4 29.8 1.0
C A:THR188 3.6 24.0 1.0
CB A:SER186 3.7 32.3 1.0
OD2 A:ASP184 3.9 41.5 1.0
CA A:ASP182 4.0 30.0 1.0
N A:SER186 4.1 36.0 1.0
CB A:ASP182 4.1 29.6 1.0
OG1 A:THR188 4.2 27.6 1.0
N A:CYS190 4.2 24.9 0.5
N A:CYS190 4.2 24.7 0.5
OD2 A:ASP182 4.3 30.5 1.0
CA A:ILE189 4.3 23.8 1.0
N A:ILE189 4.4 25.5 1.0
C A:ASP182 4.4 32.4 1.0
CG A:GLU193 4.4 28.7 1.0
N A:ASP184 4.4 40.7 1.0
CA A:SER186 4.5 33.1 1.0
N A:THR188 4.5 25.2 1.0
CA A:THR188 4.6 25.0 1.0
N A:THR183 4.7 34.9 1.0
CB A:ASP184 4.7 41.9 1.0
N A:ARG185 4.7 37.3 1.0
C A:ILE189 4.7 24.3 1.0
CB A:CYS190 4.8 26.0 0.5
CA A:ASP184 4.8 40.8 1.0
OD1 A:ASN223 4.9 23.5 0.5
C A:ASP184 4.9 40.9 1.0
O A:ASP182 4.9 30.7 1.0
N A:GLY187 5.0 30.2 1.0
SG A:CYS190 5.0 27.0 0.5
O A:HOH517 5.0 45.3 1.0
CB A:CYS190 5.0 25.5 0.5

Calcium binding site 5 out of 8 in 4phj

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Calcium binding site 5 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:16.8
occ:1.00
 OD1 B:ASN228 2.3 15.3 1.0
OD1 B:ASP137 2.4 19.8 1.0
O A:HOH435 2.4 18.5 1.0
O B:HOH481 2.5 18.0 1.0
OD1 B:ASP225 2.5 16.3 1.0
OD2 B:ASP225 2.6 16.5 1.0
OD1 B:ASP227 2.6 16.4 1.0
OD2 B:ASP227 2.6 15.4 1.0
CG B:ASP227 2.9 13.8 1.0
CG B:ASP225 2.9 16.6 1.0
CG B:ASP137 3.4 25.8 1.0
CG B:ASN228 3.4 17.0 1.0
O B:HOH620 3.5 35.0 1.0
OD2 B:ASP137 3.8 26.7 1.0
N B:ASN228 4.1 14.3 1.0
ND2 B:ASN228 4.1 19.1 1.0
CB B:ASP227 4.3 14.8 1.0
CB B:ASN228 4.3 13.7 1.0
CB B:ASP225 4.4 16.3 1.0
O B:HOH487 4.4 25.4 1.0
O B:HOH559 4.5 40.1 1.0
N B:ASP137 4.5 17.2 1.0
O B:HOH507 4.5 22.5 1.0
NH2 A:ARG145 4.5 22.6 0.5
CB B:ASP137 4.7 18.7 1.0
OG1 B:THR136 4.7 18.1 1.0
CA B:ASN228 4.7 13.6 1.0
O B:GLY138 4.7 17.8 1.0
OD1 A:ASP142 4.8 28.9 1.0
C B:ASP227 4.9 12.3 1.0
N B:ASP227 4.9 12.9 1.0
CA B:ASP227 4.9 13.0 1.0
O B:HOH518 4.9 23.4 1.0

Calcium binding site 6 out of 8 in 4phj

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Calcium binding site 6 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:18.2
occ:1.00
 O B:ALA109 2.3 17.2 1.0
O B:GLU114 2.4 17.7 1.0
O B:HOH482 2.4 18.4 1.0
O B:HOH501 2.4 21.8 1.0
OD1 B:ASP112 2.4 18.1 1.0
OE1 B:GLU119 2.5 17.8 1.0
OE2 B:GLU119 2.5 18.4 1.0
CD B:GLU119 2.8 17.2 1.0
CG B:ASP112 3.3 21.4 1.0
C B:ALA109 3.4 19.3 1.0
C B:GLU114 3.6 17.3 1.0
OD2 B:ASP112 3.7 20.7 1.0
CA B:ALA109 3.9 17.6 1.0
N B:GLU114 4.2 18.9 1.0
CG B:GLU119 4.3 16.7 1.0
N B:SER116 4.4 14.8 1.0
N B:GLY110 4.4 21.2 1.0
N B:VAL115 4.5 16.4 1.0
CA B:VAL115 4.5 16.8 1.0
N B:ASP112 4.6 19.8 1.0
CA B:GLU114 4.6 17.5 1.0
CB B:ASP112 4.6 20.6 1.0
O B:HOH463 4.6 32.2 1.0
CB B:ALA109 4.7 19.0 1.0
O B:LEU108 4.7 19.9 1.0
N B:MET113 4.8 19.6 1.0
CA B:GLY110 4.8 23.8 1.0
O B:HOH516 4.8 32.5 1.0
C B:GLY110 4.8 22.1 1.0
CA B:ASP112 4.9 18.9 1.0
O B:HOH446 4.9 29.1 1.0
C B:VAL115 4.9 15.6 1.0
OG B:SER116 5.0 14.8 1.0
N B:ASP111 5.0 21.4 1.0
C B:ASP112 5.0 19.1 1.0

Calcium binding site 7 out of 8 in 4phj

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Calcium binding site 7 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:18.9
occ:1.00
 OD1 B:ASP152 2.3 19.1 1.0
OD1 B:ASP154 2.3 22.9 1.0
OE1 B:GLU163 2.4 19.4 1.0
O B:HOH488 2.4 22.9 1.0
O B:LYS158 2.4 16.9 1.0
OG1 B:THR156 2.5 20.6 1.0
OE2 B:GLU163 2.8 22.0 1.0
CD B:GLU163 2.9 19.8 1.0
CG B:ASP154 3.3 26.8 1.0
CG B:ASP152 3.5 18.8 1.0
C B:LYS158 3.6 17.1 1.0
OD2 B:ASP154 3.6 27.1 1.0
CB B:THR156 3.7 25.2 1.0
N B:THR156 4.0 23.1 1.0
CG2 B:THR156 4.0 27.5 1.0
N B:GLY160 4.1 17.3 1.0
OE1 B:GLU114 4.1 22.3 1.0
CA B:LEU159 4.2 14.3 1.0
OD2 B:ASP152 4.2 18.7 1.0
CA B:ASP152 4.3 18.8 1.0
CB B:ASP152 4.3 18.3 1.0
N B:LYS158 4.3 16.6 1.0
CA B:THR156 4.3 24.9 1.0
N B:LEU159 4.4 16.3 1.0
OE2 B:GLU114 4.4 24.7 1.0
CG B:GLU163 4.5 19.2 1.0
N B:ASP154 4.5 24.7 1.0
CD B:GLU114 4.6 24.8 1.0
C B:LEU159 4.6 17.2 1.0
CB B:ASP154 4.6 23.8 1.0
CA B:LYS158 4.7 14.7 1.0
C B:ASP152 4.7 21.4 1.0
N B:GLY157 4.7 19.8 1.0
N B:THR155 4.7 26.8 1.0
O B:HOH595 4.7 57.2 1.0
C B:ASP154 4.8 25.4 1.0
C B:THR156 4.8 23.7 1.0
CA B:ASP154 4.8 25.5 1.0
N B:SER153 4.9 24.6 1.0
O B:ASP152 5.0 21.4 1.0

Calcium binding site 8 out of 8 in 4phj

Go back to Calcium Binding Sites List in 4phj
Calcium binding site 8 out of 8 in the The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids: Human Unliganded Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca304

b:23.2
occ:1.00
 OD1 B:ASP182 2.3 21.4 1.0
O B:HOH497 2.3 33.2 1.0
O B:THR188 2.4 18.8 1.0
OD1 B:ASP184 2.4 23.7 1.0
OE1 B:GLU193 2.4 20.1 1.0
OE2 B:GLU193 2.5 21.3 1.0
OG B:SER186 2.5 26.6 1.0
CD B:GLU193 2.8 19.5 1.0
CG B:ASP182 3.4 20.1 1.0
CG B:ASP184 3.4 25.4 1.0
C B:THR188 3.6 18.7 1.0
CB B:SER186 3.6 25.3 1.0
OD2 B:ASP184 3.8 27.1 1.0
CA B:ASP182 4.0 20.9 1.0
N B:SER186 4.1 26.2 1.0
CB B:ASP182 4.1 21.1 1.0
OG1 B:THR188 4.2 25.9 1.0
OD2 B:ASP182 4.3 21.7 1.0
CG B:GLU193 4.3 20.0 1.0
N B:CYS190 4.3 23.2 1.0
C B:ASP182 4.3 22.4 1.0
N B:THR188 4.4 20.4 1.0
CA B:ILE189 4.4 17.8 1.0
N B:ILE189 4.4 19.0 1.0
CA B:SER186 4.4 26.7 1.0
N B:ASP184 4.4 25.1 1.0
CA B:THR188 4.5 19.9 1.0
N B:THR183 4.6 23.0 1.0
N B:ARG185 4.7 26.7 1.0
CB B:ASP184 4.7 26.6 1.0
C B:ILE189 4.9 21.2 1.0
CA B:ASP184 4.9 25.9 1.0
O B:ASP182 4.9 22.5 1.0
SG B:CYS190 4.9 31.9 1.0
C B:ASP184 4.9 27.2 1.0
O B:HOH420 4.9 26.7 1.0
N B:GLY187 4.9 22.1 1.0

Reference:

S.E.Adams, P.J.Rizkallah, D.J.Miller, E.J.Robinson, M.B.Hallett, R.K.Allemann. The Structural Basis of Differential Inhibition of Human Calpain By Indole and Phenyl Alpha-Mercaptoacrylic Acids. J.Struct.Biol. V. 187 236 2014.
ISSN: ESSN 1095-8657
PubMed: 25086406
DOI: 10.1016/J.JSB.2014.07.004
Page generated: Wed Jul 9 01:20:56 2025

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