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Calcium in PDB 8hyi: Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine

Protein crystallography data

The structure of Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine, PDB code: 8hyi was solved by A.Senoo, S.Ito, G.Ueno, S.Nagatoishi, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.31 / 2.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 80, 99.498, 107.568, 90, 90, 90
R / Rfree (%) 22 / 27.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine (pdb code 8hyi). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine, PDB code: 8hyi:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8hyi

Go back to Calcium Binding Sites List in 8hyi
Calcium binding site 1 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:54.2
occ:1.00
 OD2 A:ASP136 2.2 58.9 1.0
O A:HIS104 2.3 45.4 1.0
OD2 A:ASP134 2.3 62.5 1.0
OD1 A:ASN102 2.4 70.3 1.0
O A:ASN143 2.5 64.8 1.0
OD2 A:ASP195 2.6 62.8 1.0
OD1 A:ASP134 2.7 57.8 1.0
CG A:ASP134 2.9 53.7 1.0
CG A:ASP136 3.4 65.2 1.0
C A:HIS104 3.5 50.2 1.0
CG A:ASP195 3.5 57.2 1.0
CG A:ASN102 3.6 59.5 1.0
C A:ASN143 3.7 61.6 1.0
CB A:ASP195 3.8 36.1 1.0
CB A:ASP136 4.0 70.6 1.0
N A:HIS104 4.1 63.3 1.0
CA A:HIS104 4.2 43.8 1.0
CB A:HIS104 4.4 37.9 1.0
CB A:ASP134 4.4 51.4 1.0
OD1 A:ASP136 4.4 55.4 1.0
CA A:GLY144 4.4 64.2 1.0
ND2 A:ASN102 4.4 66.6 1.0
OD1 A:ASP195 4.5 63.5 1.0
N A:LYS105 4.5 57.9 1.0
N A:GLY144 4.5 65.1 1.0
CA A:ASN102 4.5 50.8 1.0
CD A:PRO106 4.6 61.1 1.0
C A:ASN102 4.6 49.3 1.0
CB A:ASN102 4.6 57.0 1.0
CA A:ASN143 4.6 55.2 1.0
CA A:LYS105 4.7 64.8 1.0
O A:ASN102 4.7 60.4 1.0
CB A:ASN143 4.8 59.4 1.0
C A:LYS105 4.8 56.5 1.0
N A:PRO106 4.9 54.7 1.0
N A:ASP136 5.0 55.9 1.0
N A:ASP103 5.0 40.6 1.0

Calcium binding site 2 out of 6 in 8hyi

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Calcium binding site 2 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:56.1
occ:1.00
 OD1 A:ASP103 2.1 57.9 1.0
OE2 A:GLU69 2.2 55.1 1.0
OD1 A:ASP136 2.2 55.4 1.0
OD1 A:ASP100 2.2 61.6 1.0
OE2 A:GLU11 2.4 58.9 1.0
O A:GLN101 2.5 43.6 1.0
CD A:GLU69 2.7 55.5 1.0
OE1 A:GLU69 2.8 48.1 1.0
CG A:ASP103 3.2 50.1 1.0
CG A:ASP136 3.2 65.2 1.0
CG A:ASP100 3.3 57.7 1.0
CD A:GLU11 3.4 53.3 1.0
C A:GLN101 3.6 40.3 1.0
CD2 A:HIS104 3.7 53.6 1.0
OE1 A:GLU11 3.7 46.0 1.0
OD2 A:ASP103 3.8 61.8 1.0
CB A:ASP136 3.8 70.6 1.0
OD2 A:ASP100 3.9 53.8 1.0
N A:GLN101 3.9 36.7 1.0
N A:ASP103 4.0 40.6 1.0
CA A:ASP136 4.0 62.8 1.0
CG A:GLU69 4.1 51.0 1.0
OD2 A:ASP136 4.3 58.9 1.0
NE2 A:HIS104 4.3 58.2 1.0
CA A:GLN101 4.4 34.4 1.0
NE A:ARG68 4.4 62.1 1.0
CB A:ASP100 4.4 44.0 1.0
CB A:ASP103 4.4 30.7 1.0
NH2 A:ARG68 4.5 61.3 1.0
CA A:ASP100 4.6 39.9 1.0
N A:ASN102 4.7 43.8 1.0
C A:ASP100 4.7 43.4 1.0
CG A:GLU11 4.7 42.9 1.0
CA A:ASP103 4.7 41.7 1.0
CA A:ASN102 4.8 50.8 1.0
N A:ASP136 4.9 55.9 1.0
CG A:HIS104 4.9 52.4 1.0
C A:ASN102 5.0 49.3 1.0
CZ A:ARG68 5.0 61.4 1.0

Calcium binding site 3 out of 6 in 8hyi

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Calcium binding site 3 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:71.3
occ:1.00
 OE2 A:GLU70 3.5 83.4 1.0
N A:ASP67 3.7 59.1 1.0
OH A:TYR74 3.8 56.6 1.0
CD A:GLU70 4.0 88.8 1.0
O A:ASP67 4.1 64.8 1.0
CA A:LEU66 4.3 39.3 1.0
CB A:ASP67 4.5 62.0 1.0
C A:LEU66 4.5 52.5 1.0
CA A:ASP67 4.5 57.2 1.0
CB A:GLU70 4.5 71.4 1.0
OE1 A:GLU70 4.5 93.0 1.0
CD2 A:LEU66 4.5 42.9 1.0
CG A:GLU70 4.6 75.7 1.0
O A:PRO65 4.7 62.5 1.0
C A:ASP67 4.8 57.2 1.0
CB A:LEU66 4.8 24.9 1.0

Calcium binding site 4 out of 6 in 8hyi

Go back to Calcium Binding Sites List in 8hyi
Calcium binding site 4 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:49.2
occ:1.00
 OD2 B:ASP136 1.6 75.3 1.0
ND2 B:ASN102 2.3 56.0 1.0
OD2 B:ASP134 2.3 56.1 1.0
O B:HIS104 2.4 54.8 1.0
O B:ASN143 2.5 64.3 1.0
OD2 B:ASP195 2.5 53.0 1.0
OD1 B:ASP134 2.6 45.2 1.0
CG B:ASP134 2.7 52.0 1.0
CG B:ASP136 2.9 65.5 1.0
CG B:ASP195 3.4 47.4 1.0
CG B:ASN102 3.5 54.9 1.0
CB B:ASP195 3.6 27.8 1.0
C B:HIS104 3.6 64.0 1.0
C B:ASN143 3.7 43.8 1.0
OD1 B:ASP136 3.8 42.2 1.0
CB B:ASP136 3.8 58.7 1.0
OD1 B:ASN102 4.1 70.7 1.0
CB B:ASP134 4.2 48.4 1.0
N B:HIS104 4.3 73.0 1.0
CA B:HIS104 4.4 64.7 1.0
CA B:GLY144 4.5 51.6 1.0
N B:GLY144 4.5 44.2 1.0
OD1 B:ASP195 4.5 48.1 1.0
CA B:ASN143 4.6 44.5 1.0
N B:LYS105 4.6 69.8 1.0
CB B:HIS104 4.7 52.2 1.0
CB B:ASN102 4.7 42.3 1.0
CD B:PRO106 4.7 57.4 1.0
CA B:LYS105 4.7 65.3 1.0
CA B:ASN102 4.7 44.5 1.0
CB B:ASN143 4.8 42.5 1.0
C B:LYS105 4.8 65.0 1.0
N B:PRO106 4.8 59.9 1.0
C B:ASN102 4.8 47.9 1.0
N B:ASP136 5.0 49.5 1.0

Calcium binding site 5 out of 6 in 8hyi

Go back to Calcium Binding Sites List in 8hyi
Calcium binding site 5 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:92.0
occ:1.00
 OE2 B:GLU69 1.2 82.4 1.0
CD B:GLU69 1.7 74.9 1.0
OE1 B:GLU69 1.8 82.9 1.0
OD1 B:ASP103 2.2 72.2 1.0
OE2 B:GLU11 2.2 53.6 1.0
O B:GLN101 2.2 45.6 1.0
OD1 B:ASP100 2.3 77.3 1.0
OD1 B:ASP136 3.1 42.2 1.0
CG B:GLU69 3.3 49.7 1.0
CD B:GLU11 3.3 47.5 1.0
CG B:ASP103 3.3 64.7 1.0
CG B:ASP100 3.3 62.6 1.0
C B:GLN101 3.4 54.2 1.0
OE1 B:GLU11 3.8 51.8 1.0
OD2 B:ASP100 3.8 58.7 1.0
N B:GLN101 3.9 54.3 1.0
N B:ASP103 3.9 48.5 1.0
OD2 B:ASP103 3.9 57.8 1.0
CG B:ASP136 4.0 65.5 1.0
CB B:ASP136 4.1 58.7 1.0
CA B:GLN101 4.2 52.6 1.0
ND1 B:HIS104 4.3 58.9 1.0
N B:ASN102 4.4 47.2 1.0
CA B:ASP136 4.4 51.7 1.0
CB B:ASP103 4.4 57.6 1.0
CB B:ASP100 4.5 44.4 1.0
CA B:ASP100 4.5 39.2 1.0
CB B:GLU69 4.6 37.3 1.0
CG B:GLU11 4.6 50.6 1.0
CA B:ASN102 4.6 44.5 1.0
C B:ASP100 4.6 53.9 1.0
NE B:ARG68 4.6 62.6 1.0
CA B:ASP103 4.7 49.5 1.0
C B:ASN102 4.8 47.9 1.0
CE1 B:HIS104 4.8 67.6 1.0
CB B:GLN101 5.0 46.9 1.0

Calcium binding site 6 out of 6 in 8hyi

Go back to Calcium Binding Sites List in 8hyi
Calcium binding site 6 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(2-Methyl-5-Phenyl-1H-Indole-3-Yl)Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:53.9
occ:1.00
 OH B:TYR74 3.5 59.1 1.0
N B:ASP67 3.8 43.5 1.0
CA B:LEU66 4.1 35.1 1.0
O B:PRO65 4.3 55.8 1.0
OE2 B:GLU70 4.3 96.7 1.0
CD B:GLU70 4.4 96.1 1.0
C B:LEU66 4.5 43.0 1.0
OE1 B:GLU70 4.6 90.1 1.0
CB B:LEU66 4.7 33.1 1.0
O B:ASP67 4.8 46.2 1.0
CB B:GLU70 4.8 73.5 1.0
CA B:ASP67 4.8 42.7 1.0
CB B:ASP67 4.9 52.6 1.0
CZ B:TYR74 4.9 53.9 1.0
CD2 B:LEU66 4.9 38.7 1.0

Reference:

A.Senoo, S.Nagatoishi, D.Kuroda, S.Ito, G.Ueno, J.M.M.Caaveiro, K.Tsumoto. Modulation of A Conformational Ensemble By A Small Molecule That Inhibits Key Protein-Protein Interactions Involved in Cell Adhesion. Protein Sci. E4744 2023.
ISSN: ESSN 1469-896X
PubMed: 37531208
DOI: 10.1002/PRO.4744
Page generated: Thu Jul 10 05:09:33 2025

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