Calcium in PDB 7cmf: Crystal Structure of Human P-Cadherin REC12 (Monomer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor)

The structure of Crystal Structure of Human P-Cadherin REC12 (Monomer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor), PDB code: 7cmf 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)	36.85 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	74.311, 40.764, 72.567, 90, 97.39, 90
R / Rfree (%)	24.5 / 28.3

The structure of Crystal Structure of Human P-Cadherin REC12 (Monomer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Human P-Cadherin REC12 (Monomer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor) (pdb code 7cmf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human P-Cadherin REC12 (Monomer) in Complex with 2-(5-Chloro-2-Methyl-1H-Indol-3-Yl)Ethan-1-Amine (Inhibitor), PDB code: 7cmf:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of Human P-Cadherin REC12 (Monomer) 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 REC12 (Monomer) 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:Ca301 b:45.7 occ:1.00 OE2 A:GLU69 2.2 72.3 1.0 O A:GLN101 2.3 65.0 1.0 OD1 A:ASP100 2.4 46.2 1.0 OD1 A:ASP103 2.5 51.9 1.0 OD1 A:ASP136 2.5 61.8 1.0 OE2 A:GLU11 2.5 45.2 1.0 CD A:GLU69 3.0 70.8 1.0 OE1 A:GLU69 3.2 68.1 1.0 CG A:ASP136 3.3 59.1 1.0 CG A:ASP103 3.5 52.5 1.0 C A:GLN101 3.5 62.4 1.0 CG A:ASP100 3.5 47.5 1.0 CD A:GLU11 3.6 45.1 1.0 N A:ASP103 3.6 48.2 1.0 OE1 A:GLU11 4.0 46.1 1.0 CB A:ASP136 4.0 54.8 1.0 N A:GLN101 4.1 64.4 1.0 OD2 A:ASP100 4.1 44.7 1.0 OD2 A:ASP136 4.1 62.1 1.0 CB A:ASP103 4.2 53.5 1.0 CA A:ASP136 4.2 49.6 1.0 CG A:GLU69 4.2 74.4 1.0 ND1 A:HIS104 4.2 53.0 1.0 OD2 A:ASP103 4.3 53.1 1.0 NH1 A:ARG68 4.3 70.7 1.0 CA A:ASP103 4.3 49.1 1.0 N A:ASN102 4.4 60.3 1.0 CA A:GLN101 4.4 63.0 1.0 CA A:ASN102 4.4 59.1 1.0 C A:ASN102 4.5 51.0 1.0 CB A:ASP100 4.7 53.5 1.0 CA A:CA303 4.7 53.1 1.0 C A:ASP103 4.7 47.8 1.0 N A:HIS104 4.8 50.3 1.0 CA A:ASP100 4.8 58.0 1.0 CG A:GLU11 4.8 43.9 1.0 C A:ASP100 4.9 64.6 1.0 N A:ASP136 5.0 48.0 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of Human P-Cadherin REC12 (Monomer) 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 REC12 (Monomer) 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:Ca302 b:34.9 occ:1.00 OD2 A:ASP136 2.2 62.1 1.0 O A:HIS104 2.3 49.1 1.0 OD2 A:ASP134 2.3 55.7 1.0 OD2 A:ASP195 2.3 43.2 1.0 O A:ASN143 2.4 39.2 1.0 OD1 A:ASN102 2.4 71.2 1.0 OD1 A:ASP134 2.8 57.2 1.0 CG A:ASP134 2.9 56.7 1.0 CG A:ASP136 3.2 59.1 1.0 CG A:ASP195 3.3 42.1 1.0 C A:HIS104 3.4 49.8 1.0 CG A:ASN102 3.5 69.5 1.0 C A:ASN143 3.6 43.9 1.0 CB A:ASP195 3.7 39.6 1.0 CB A:ASP136 3.7 54.8 1.0 N A:HIS104 3.9 50.3 1.0 CA A:HIS104 4.0 51.1 1.0 ND2 A:ASN102 4.1 70.7 1.0 CB A:HIS104 4.1 51.1 1.0 OD1 A:ASP136 4.2 61.8 1.0 CB A:ASP134 4.4 56.2 1.0 OD1 A:ASP195 4.4 44.1 1.0 N A:LYS105 4.4 50.4 1.0 N A:GLY144 4.4 44.0 1.0 CD A:PRO106 4.4 51.0 1.0 CA A:ASN143 4.5 49.3 1.0 CA A:GLY144 4.5 44.0 1.0 CB A:ASN102 4.6 65.9 1.0 CB A:ASN143 4.6 53.6 1.0 CA A:ASN102 4.7 59.1 1.0 C A:ASN102 4.7 51.0 1.0 CA A:LYS105 4.8 51.9 1.0 N A:ASP103 4.8 48.2 1.0 N A:PRO106 4.9 51.1 1.0 N A:ASP136 4.9 48.0 1.0 CA A:ASP136 4.9 49.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of Human P-Cadherin REC12 (Monomer) 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 REC12 (Monomer) 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:Ca303 b:53.1 occ:1.00 OE1 A:GLU69 2.2 68.1 1.0 OD1 A:ASP67 2.4 53.2 1.0 OD2 A:ASP103 2.5 53.1 1.0 O A:HOH406 2.6 67.2 1.0 OE1 A:GLU11 2.6 46.1 1.0 CG A:ASP67 3.1 55.5 1.0 CG A:ASP103 3.4 52.5 1.0 CD A:GLU69 3.4 70.8 1.0 OD1 A:ASP103 3.6 51.9 1.0 OD2 A:ASP67 3.7 54.2 1.0 CD A:GLU11 3.8 45.1 1.0 OD1 A:ASN12 3.8 63.8 1.0 ND2 A:ASN12 3.9 65.2 1.0 CB A:GLU69 3.9 73.1 1.0 CB A:ASP67 4.0 57.4 1.0 N A:GLU69 4.1 66.7 1.0 CA A:ASP67 4.1 58.4 1.0 CG A:GLU69 4.1 74.4 1.0 OE2 A:GLU11 4.2 45.2 1.0 CE1 A:HIS104 4.2 53.5 1.0 CG A:ASN12 4.3 64.8 1.0 N A:ARG68 4.3 63.3 1.0 C A:ASP67 4.3 60.1 1.0 OE2 A:GLU69 4.3 72.3 1.0 CA A:GLU69 4.6 69.6 1.0 ND1 A:HIS104 4.7 53.0 1.0 CA A:CA301 4.7 45.7 1.0 CB A:ASP103 4.7 53.5 1.0 O A:ASP67 5.0 59.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of Human P-Cadherin REC12 (Monomer) 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 REC12 (Monomer) 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:Ca304 b:90.8 occ:1.00 O A:ASP199 2.6 54.8 1.0 C A:ASP199 3.8 51.3 1.0 CA A:GLY200 4.6 45.8 1.0 N A:GLY200 4.6 47.1 1.0 O A:GLY200 4.6 43.4 1.0 CA A:ASP199 4.8 54.0 1.0 C A:GLY200 4.9 44.6 1.0

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