Atomistry » Calcium » PDB 7cji-7d4p » 7cme
Atomistry »
  Calcium »
    PDB 7cji-7d4p »
      7cme »

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

Go back to Calcium Binding Sites List in 7cme
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: Thu Jul 18 23:45:45 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy