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Calcium in PDB 7cme: Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor)

Protein crystallography data

The structure of Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor), PDB code: 7cme 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) 45.04 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.828, 99.113, 107.928, 90, 90, 90
R / Rfree (%) 20.9 / 24.9

Other elements in 7cme:

The structure of Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) (pdb code 7cme). 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-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor), PDB code: 7cme:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 7cme

Go back to Calcium Binding Sites List in 7cme
Calcium binding site 1 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor)


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-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:55.8
occ:1.00
ND2 A:ASN102 2.2 59.9 1.0
O A:HIS104 2.3 68.5 1.0
OD2 A:ASP136 2.4 56.0 1.0
OD2 A:ASP195 2.4 64.4 1.0
O A:ASN143 2.5 68.7 1.0
OD2 A:ASP134 2.5 52.4 1.0
OD1 A:ASP134 2.6 73.5 1.0
CG A:ASP134 2.9 72.1 1.0
CG A:ASP195 3.3 64.0 1.0
CG A:ASP136 3.4 63.0 1.0
CG A:ASN102 3.4 64.3 1.0
C A:HIS104 3.5 68.4 1.0
C A:ASN143 3.6 71.9 1.0
CB A:ASP195 3.7 60.1 1.0
CB A:ASP136 3.9 59.5 1.0
OD1 A:ASN102 4.1 60.2 1.0
N A:HIS104 4.2 62.2 1.0
OD1 A:ASP195 4.3 66.3 1.0
CA A:HIS104 4.3 62.1 1.0
CA A:ASN143 4.4 65.6 1.0
CB A:ASP134 4.4 69.7 1.0
N A:LYS105 4.4 67.9 1.0
OD1 A:ASP136 4.5 62.1 1.0
N A:GLY144 4.5 73.7 1.0
CA A:ASN102 4.5 54.3 1.0
CB A:ASN102 4.5 56.4 1.0
CB A:ASN143 4.5 64.0 1.0
CA A:GLY144 4.6 67.7 1.0
CA A:LYS105 4.6 61.9 1.0
CD A:PRO106 4.6 72.1 1.0
CB A:HIS104 4.7 53.8 1.0
C A:ASN102 4.7 61.3 1.0
C A:LYS105 4.8 61.2 1.0
N A:ASP136 4.9 58.3 1.0
N A:PRO106 4.9 62.9 1.0
N A:ASP103 5.0 55.2 1.0

Calcium binding site 2 out of 6 in 7cme

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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-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor)


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-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:61.7
occ:1.00
OD1 A:ASP103 2.1 63.8 1.0
OE2 A:GLU69 2.2 65.7 1.0
OD1 A:ASP100 2.3 66.0 1.0
O A:GLN101 2.5 58.5 1.0
OE2 A:GLU11 2.5 61.3 1.0
OD1 A:ASP136 2.5 62.1 1.0
CD A:GLU69 2.8 72.4 1.0
OE1 A:GLU69 2.8 72.5 1.0
CG A:ASP103 3.2 61.6 1.0
CG A:ASP136 3.2 63.0 1.0
CD A:GLU11 3.4 60.9 1.0
CG A:ASP100 3.4 65.7 1.0
C A:GLN101 3.6 57.7 1.0
OD2 A:ASP103 3.6 64.5 1.0
OE1 A:GLU11 3.6 63.8 1.0
CB A:ASP136 3.7 59.5 1.0
N A:GLN101 3.8 59.2 1.0
OD2 A:ASP100 4.0 61.6 1.0
CA A:ASP136 4.0 64.0 1.0
ND1 A:HIS104 4.0 78.2 1.0
OD2 A:ASP136 4.1 56.0 1.0
N A:ASP103 4.1 55.2 1.0
CG A:GLU69 4.2 72.5 1.0
CA A:GLN101 4.3 47.7 1.0
CB A:ASP100 4.5 59.0 1.0
CE1 A:HIS104 4.5 77.5 1.0
NE A:ARG68 4.5 67.1 1.0
CB A:ASP103 4.5 45.8 1.0
CA A:ASP100 4.5 56.8 1.0
C A:ASP100 4.6 62.0 1.0
N A:ASN102 4.6 46.6 1.0
CG A:GLU11 4.7 55.3 1.0
NH2 A:ARG68 4.8 62.3 1.0
CA A:ASP103 4.8 55.4 1.0
CA A:ASN102 4.8 54.3 1.0
N A:ASP136 4.9 58.3 1.0
CB A:ARG68 4.9 71.8 1.0
CB A:GLN101 5.0 51.4 1.0

Calcium binding site 3 out of 6 in 7cme

Go back to Calcium Binding Sites List in 7cme
Calcium binding site 3 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor)


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-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:83.9
occ:1.00
O A:HOH508 3.3 61.4 1.0
OE2 A:GLU70 3.7 102.8 1.0
OH A:TYR74 3.8 71.5 1.0
N A:ASP67 3.8 68.3 1.0
CD A:GLU70 4.0 103.0 1.0
CA A:LEU66 4.3 64.6 1.0
O A:PRO65 4.4 77.9 1.0
OE1 A:GLU70 4.4 99.8 1.0
C A:LEU66 4.6 69.1 1.0
CG A:GLU70 4.6 96.5 1.0
CB A:GLU70 4.6 88.6 1.0
O A:ASP67 4.6 61.0 1.0
CB A:ASP67 4.6 60.8 1.0
CD2 A:LEU66 4.7 68.0 1.0
CA A:ASP67 4.7 63.2 1.0

Calcium binding site 4 out of 6 in 7cme

Go back to Calcium Binding Sites List in 7cme
Calcium binding site 4 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor)


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-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:57.6
occ:1.00
O B:HIS104 2.1 72.0 1.0
ND2 B:ASN102 2.3 51.4 1.0
OD2 B:ASP134 2.4 65.2 1.0
OD2 B:ASP136 2.4 66.8 1.0
O B:ASN143 2.5 67.3 1.0
OD2 B:ASP195 2.5 66.9 1.0
OD1 B:ASP134 2.6 64.3 1.0
CG B:ASP134 2.8 68.8 1.0
C B:HIS104 3.3 75.0 1.0
CG B:ASP136 3.4 58.5 1.0
CG B:ASP195 3.4 67.2 1.0
CG B:ASN102 3.5 62.5 1.0
C B:ASN143 3.6 66.5 1.0
CB B:ASP195 3.7 65.7 1.0
CB B:ASP136 3.9 52.8 1.0
CA B:HIS104 4.1 68.5 1.0
N B:HIS104 4.1 62.1 1.0
OD1 B:ASN102 4.1 67.7 1.0
CB B:HIS104 4.2 56.8 1.0
CB B:ASP134 4.3 60.1 1.0
N B:LYS105 4.4 79.1 1.0
OD1 B:ASP136 4.4 57.9 1.0
N B:GLY144 4.5 59.2 1.0
CA B:ASN143 4.5 59.8 1.0
CA B:GLY144 4.5 65.9 1.0
OD1 B:ASP195 4.5 62.2 1.0
CA B:LYS105 4.6 75.2 1.0
CA B:ASN102 4.7 54.8 1.0
CB B:ASN102 4.7 47.7 1.0
CB B:ASN143 4.7 57.2 1.0
C B:LYS105 4.7 70.9 1.0
C B:ASN102 4.8 58.8 1.0
CD B:PRO106 4.8 51.5 1.0
N B:ASP136 4.8 60.4 1.0
N B:PRO106 4.9 60.9 1.0
O B:ASN102 5.0 54.4 1.0

Calcium binding site 5 out of 6 in 7cme

Go back to Calcium Binding Sites List in 7cme
Calcium binding site 5 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor)


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-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca503

b:58.0
occ:1.00
OD1 B:ASP103 2.1 74.6 1.0
OE2 B:GLU69 2.2 56.6 1.0
OE2 B:GLU11 2.3 57.0 1.0
O B:GLN101 2.3 55.3 1.0
OD1 B:ASP100 2.4 63.0 1.0
OD1 B:ASP136 2.6 57.9 1.0
CD B:GLU69 2.8 56.6 1.0
OE1 B:GLU69 2.9 54.7 1.0
CG B:ASP103 3.2 67.4 1.0
CG B:ASP136 3.3 58.5 1.0
CD B:GLU11 3.3 54.9 1.0
CG B:ASP100 3.3 65.5 1.0
C B:GLN101 3.5 59.5 1.0
OE1 B:GLU11 3.6 49.9 1.0
OD2 B:ASP103 3.7 62.9 1.0
OD2 B:ASP100 3.8 65.9 1.0
CB B:ASP136 3.8 52.8 1.0
N B:GLN101 3.8 53.4 1.0
N B:ASP103 3.9 58.4 1.0
ND1 B:HIS104 4.1 72.2 1.0
OD2 B:ASP136 4.1 66.8 1.0
CA B:ASP136 4.1 56.4 1.0
CA B:GLN101 4.3 56.8 1.0
CG B:GLU69 4.3 56.2 1.0
CB B:ASP103 4.5 54.7 1.0
CB B:ASP100 4.5 60.9 1.0
NE B:ARG68 4.5 57.4 1.0
N B:ASN102 4.5 56.1 1.0
CA B:ASP100 4.5 55.7 1.0
C B:ASP100 4.6 56.9 1.0
CE1 B:HIS104 4.6 70.3 1.0
CG B:GLU11 4.6 52.0 1.0
CA B:ASP103 4.7 56.8 1.0
CA B:ASN102 4.7 54.8 1.0
NH2 B:ARG68 4.8 57.2 1.0
C B:ASN102 4.8 58.8 1.0
CB B:GLN101 4.9 52.4 1.0
CB B:ARG68 5.0 56.6 1.0

Calcium binding site 6 out of 6 in 7cme

Go back to Calcium Binding Sites List in 7cme
Calcium binding site 6 out of 6 in the Crystal Structure of Human P-Cadherin MEC12 (X Dimer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor)


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-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:70.6
occ:1.00
O B:HOH607 3.6 56.5 1.0
OH B:TYR74 3.7 62.0 1.0
OE2 B:GLU70 3.8 94.8 1.0
N B:ASP67 3.9 60.4 1.0
CD B:GLU70 4.1 89.2 1.0
O B:PRO65 4.3 61.1 1.0
CA B:LEU66 4.3 54.8 1.0
OE1 B:GLU70 4.5 84.5 1.0
C B:LEU66 4.6 55.1 1.0
CG B:GLU70 4.6 77.1 1.0
CB B:ASP67 4.7 62.3 1.0
CB B:GLU70 4.7 66.2 1.0
O B:ASP67 4.7 58.2 1.0
CD2 B:LEU66 4.8 47.7 1.0
CA B:ASP67 4.8 54.9 1.0

Reference:

A.Senoo, S.Ito, S.Nagatoishi, Y.Saito, G.Ueno, D.Kuroda, K.Yoshida, T.Tashima, S.Kudo, S.Sando, K.Tsumoto. Regulation of Cadherin Dimerization By Chemical Fragments As A Trigger to Inhibit Cell Adhesion Commun Biol V. 4 1041 2021.
ISSN: ESSN 2399-3642
DOI: 10.1038/S42003-021-02575-3
Page generated: Fri Sep 24 12:12:56 2021

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