Calcium in PDB 7n86: Crystal Structure of Human Protocadherin-24 EC1-2 Form II

The structure of Crystal Structure of Human Protocadherin-24 EC1-2 Form II, PDB code: 7n86 was solved by D.Modak, M.E.Gray, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.15 / 3.18
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.899, 86.641, 104.892, 90, 103.46, 90
R / Rfree (%)	21.4 / 29

The structure of Crystal Structure of Human Protocadherin-24 EC1-2 Form II also contains other interesting chemical elements:

Sodium	(Na)	2 atoms
Chlorine	(Cl)	6 atoms
Iodine	(I)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II (pdb code 7n86). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 14 binding sites of Calcium where determined in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II, PDB code: 7n86:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


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 Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:36.2 occ:1.00 OD2 A:ASP36 1.8 64.3 1.0 OD1 A:ASN1 2.0 85.6 1.0 OD2 A:ASP32 2.1 72.9 1.0 O A:VAL2 2.6 31.3 1.0 OD2 A:ASP81 2.6 33.2 1.0 CG A:ASP32 2.8 71.0 1.0 OD1 A:ASP32 3.0 112.5 1.0 CG A:ASP36 3.0 62.3 1.0 CG A:ASN1 3.2 76.7 1.0 CB A:ASP34 3.5 58.5 1.0 CG A:ASP81 3.6 29.1 1.0 C A:VAL2 3.7 35.6 1.0 OD2 A:ASP34 3.8 75.5 1.0 CB A:ASP36 3.8 50.2 1.0 ND2 A:ASN1 3.8 69.5 1.0 OD1 A:ASP36 4.0 89.2 1.0 CG A:ASP34 4.0 77.1 1.0 CB A:ASP81 4.1 24.4 1.0 N A:VAL2 4.1 49.4 1.0 CB A:ASP32 4.2 55.8 1.0 CB A:ASN1 4.3 72.1 1.0 CA A:VAL2 4.5 46.5 1.0 CA A:ASP34 4.6 56.4 1.0 C A:ASN1 4.6 69.7 1.0 OD1 A:ASP81 4.7 35.3 1.0 N A:ASP34 4.7 63.5 1.0 N A:ALA3 4.7 32.4 1.0 CA A:ASN1 4.7 70.2 1.0 N A:ASP36 4.8 67.7 1.0 CA A:ASP36 4.9 52.8 1.0 CA A:ALA3 5.0 27.4 1.0 CD A:PRO4 5.0 24.6 1.0

Calcium binding site 2 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


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 Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:33.7 occ:1.00 OD1 A:ASP96 1.9 54.3 1.0 OD1 A:ASP132 2.0 47.3 1.0 OD1 A:ASP99 2.4 38.8 1.0 OE1 A:GLU17 2.4 30.1 1.0 OE2 A:GLU68 2.5 33.3 1.0 O A:ARG97 2.6 26.4 1.0 CG A:ASP96 3.0 43.2 1.0 CG A:ASP132 3.1 38.2 1.0 CD A:GLU68 3.3 35.1 1.0 OE1 A:GLU68 3.3 30.8 1.0 CD A:GLU17 3.4 29.3 1.0 OD2 A:ASP96 3.5 43.1 1.0 CG A:ASP99 3.5 35.0 1.0 NA A:NA306 3.6 20.0 1.0 OD2 A:ASP132 3.6 44.8 1.0 OE2 A:GLU17 3.7 36.1 1.0 C A:ARG97 3.8 24.2 1.0 N A:ARG97 3.9 24.4 1.0 OD2 A:ASP99 4.1 41.4 1.0 ND2 A:ASN100 4.2 34.7 1.0 CB A:ASP96 4.3 34.5 1.0 N A:ASP99 4.3 24.6 1.0 CB A:ASP132 4.3 35.2 1.0 CA A:ASP96 4.5 29.6 1.0 CA A:ARG97 4.5 26.4 1.0 CA A:ASP132 4.5 34.2 1.0 C A:ASP96 4.6 24.2 1.0 CB A:ASP99 4.6 31.5 1.0 CG A:GLU68 4.7 39.5 1.0 CG A:GLU17 4.7 29.0 1.0 CB A:TYR67 4.7 38.2 1.0 N A:ASN98 4.9 21.7 1.0 CA A:ASP99 5.0 27.0 1.0

Calcium binding site 3 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


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 Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:24.3 occ:1.00 OD1 A:ASN98 2.0 25.4 1.0 OD2 A:ASP130 2.1 32.2 1.0 OD2 A:ASP188 2.2 38.4 1.0 O A:ALA136 2.4 30.4 1.0 O A:ASN100 2.4 24.5 1.0 CG A:ASP130 2.9 33.5 1.0 OD1 A:ASP130 3.1 51.4 1.0 OD2 A:ASP132 3.1 44.8 1.0 CG A:ASN98 3.1 24.0 1.0 CG A:ASP188 3.3 37.7 1.0 C A:ASN100 3.5 25.7 1.0 CB A:ASP132 3.5 35.2 1.0 C A:ALA136 3.5 32.3 1.0 ND2 A:ASN98 3.6 25.8 1.0 CB A:ASP188 3.8 34.8 1.0 CG A:ASP132 3.8 38.2 1.0 CA A:ALA136 4.2 34.1 1.0 CB A:ALA136 4.2 35.9 1.0 CB A:ASP130 4.3 29.4 1.0 N A:ASN100 4.4 24.9 1.0 OD1 A:ASP188 4.4 45.0 1.0 CA A:ASN100 4.4 25.9 1.0 N A:ALA101 4.4 25.3 1.0 CB A:ASN98 4.4 20.6 1.0 CA A:ALA101 4.5 27.2 1.0 N A:GLY137 4.6 31.3 1.0 CA A:ASN98 4.6 21.9 1.0 CB A:GLN200 4.6 35.5 1.0 CB A:ASN100 4.7 25.8 1.0 C A:ASN98 4.9 24.1 1.0 CA A:ASP132 4.9 34.2 1.0 CA A:GLY137 5.0 34.6 1.0 OD1 A:ASP132 5.0 47.3 1.0 CG A:GLN200 5.0 36.9 1.0

Calcium binding site 4 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


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 Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca301 b:63.4 occ:1.00 O B:VAL2 2.1 57.9 1.0 OD1 B:ASP32 2.2 66.1 1.0 OD1 B:ASN1 2.3 93.0 1.0 OD2 B:ASP36 2.4 81.6 1.0 OD2 B:ASP32 2.8 94.7 1.0 CG B:ASP32 2.8 71.4 1.0 N B:VAL2 3.1 79.1 1.0 OD2 B:ASP81 3.2 42.5 1.0 C B:VAL2 3.2 64.3 1.0 CG B:ASN1 3.3 85.5 1.0 OD2 B:ASP34 3.4 119.3 1.0 CG B:ASP34 3.5 126.4 1.0 CB B:ASP34 3.6 119.3 1.0 CG B:ASP36 3.6 87.7 1.0 CA B:VAL2 3.7 74.5 1.0 ND2 B:ASN1 4.0 82.0 1.0 C B:ASN1 4.1 67.9 1.0 OD1 B:ASP34 4.1 114.2 1.0 CG B:ASP81 4.1 44.8 1.0 CB B:VAL2 4.1 90.9 1.0 CA B:ASN1 4.2 74.5 1.0 CB B:ASN1 4.3 86.8 1.0 N B:ASP34 4.3 95.8 1.0 CB B:ASP32 4.3 69.8 1.0 OD1 B:ASP36 4.4 101.7 1.0 N B:ALA3 4.4 51.0 1.0 CA B:ASP34 4.5 97.6 1.0 CB B:ASP81 4.6 43.3 1.0 CB B:ASP36 4.6 89.0 1.0 CG1 B:VAL2 4.8 85.5 1.0 C B:ALA3 4.9 56.9 1.0 CA B:ALA3 4.9 53.7 1.0

Calcium binding site 5 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


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 Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca302 b:27.6 occ:1.00 OE2 B:GLU68 1.8 45.7 1.0 OD1 B:ASP99 1.9 38.0 1.0 OD1 B:ASP96 2.1 28.5 1.0 OD1 B:ASP132 2.4 29.9 1.0 OE1 B:GLU17 2.4 38.5 1.0 O B:ARG97 2.7 20.9 1.0 CD B:GLU68 2.8 40.2 1.0 OE1 B:GLU68 3.1 32.3 1.0 CG B:ASP99 3.1 35.2 1.0 CG B:ASP96 3.2 31.8 1.0 CD B:GLU17 3.3 34.5 1.0 CG B:ASP132 3.6 26.4 1.0 OE2 B:GLU17 3.6 31.0 1.0 OD2 B:ASP99 3.8 41.5 1.0 C B:ARG97 3.9 23.6 1.0 OD2 B:ASP96 3.9 30.7 1.0 N B:ARG97 3.9 28.8 1.0 ND2 B:ASN100 3.9 34.5 1.0 CG B:GLU68 4.2 40.1 1.0 N B:ASP99 4.2 31.9 1.0 CB B:ASP99 4.3 32.0 1.0 OD2 B:ASP132 4.4 18.8 1.0 CB B:ASP96 4.4 30.2 1.0 CA B:ASP96 4.4 27.1 1.0 CA B:ARG97 4.5 30.0 1.0 C B:ASP96 4.6 27.7 1.0 CB B:ASP132 4.6 30.4 1.0 NA B:NA306 4.6 37.2 1.0 CG B:GLU17 4.7 33.8 1.0 CB B:TYR67 4.7 32.6 1.0 CA B:ASP99 4.8 32.0 1.0 N B:ASN98 4.8 22.0 1.0 CA B:ASP132 4.9 33.8 1.0 OD1 B:ASP66 4.9 70.2 1.0 CA B:ASN98 5.0 23.9 1.0

Calcium binding site 6 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


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 Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca303 b:25.7 occ:1.00 OD1 B:ASN98 1.9 22.4 1.0 OD2 B:ASP188 2.1 28.8 1.0 O B:ASN100 2.2 24.1 1.0 OD2 B:ASP130 2.4 16.7 1.0 O B:ALA136 2.5 35.3 1.0 OD2 B:ASP132 2.7 18.8 1.0 CG B:ASN98 2.9 22.3 1.0 OD1 B:ASP130 2.9 20.5 1.0 CG B:ASP130 2.9 17.7 1.0 CG B:ASP188 3.2 35.2 1.0 ND2 B:ASN98 3.4 22.0 1.0 C B:ASN100 3.4 23.5 1.0 CG B:ASP132 3.6 26.4 1.0 C B:ALA136 3.7 35.2 1.0 OE1 B:GLN200 3.8 111.3 1.0 CB B:ASP188 3.8 36.6 1.0 CB B:ASP132 3.9 30.4 1.0 CB B:ASN98 4.2 22.9 1.0 N B:ASN100 4.2 27.9 1.0 CB B:ALA136 4.2 40.3 1.0 OD1 B:ASP188 4.3 43.2 1.0 N B:ALA101 4.3 22.6 1.0 CA B:ASN100 4.3 25.8 1.0 CB B:ASP130 4.4 16.1 1.0 CA B:ALA136 4.4 36.5 1.0 CA B:ALA101 4.4 23.5 1.0 CA B:ASN98 4.5 23.9 1.0 CB B:GLN200 4.6 35.2 1.0 C B:ASN98 4.7 27.0 1.0 CB B:ASN100 4.7 30.5 1.0 OD1 B:ASP132 4.7 29.9 1.0 N B:GLY137 4.8 36.8 1.0 CD B:GLN200 4.8 67.5 1.0 N B:ASP99 4.9 31.9 1.0

Calcium binding site 7 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca301 b:56.2 occ:1.00 O C:VAL2 2.0 65.9 1.0 OD1 C:ASN1 2.1 125.0 1.0 OD2 C:ASP32 2.5 66.9 1.0 OD1 C:ASP32 2.6 56.6 1.0 OD2 C:ASP36 2.6 62.1 1.0 OD2 C:ASP81 2.9 46.6 1.0 CG C:ASP32 2.9 61.2 1.0 CG C:ASN1 3.0 116.9 1.0 OD2 C:ASP34 3.1 111.3 1.0 C C:VAL2 3.1 63.5 1.0 N C:VAL2 3.2 76.5 1.0 CB C:ASP34 3.4 86.6 1.0 CG C:ASP34 3.5 90.0 1.0 ND2 C:ASN1 3.5 124.4 1.0 CG C:ASP36 3.6 71.9 1.0 CA C:VAL2 3.7 65.7 1.0 CG C:ASP81 3.7 46.6 1.0 C C:ASN1 4.0 84.6 1.0 CB C:ASN1 4.2 109.3 1.0 CA C:ASN1 4.2 97.9 1.0 N C:ALA3 4.2 51.6 1.0 CB C:ASP36 4.3 66.8 1.0 CB C:VAL2 4.3 61.2 1.0 CB C:ASP81 4.4 40.8 1.0 CB C:ASP32 4.4 63.0 1.0 OD1 C:ASP34 4.5 86.3 1.0 N C:ASP34 4.5 75.4 1.0 OD1 C:ASP36 4.5 88.6 1.0 OD1 C:ASP81 4.5 57.3 1.0 CA C:ASP34 4.5 71.5 1.0 CA C:ALA3 4.6 47.9 1.0 C C:ALA3 4.7 42.3 1.0 O C:ASN1 5.0 92.3 1.0 N C:PRO4 5.0 43.4 1.0

Calcium binding site 8 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca302 b:56.0 occ:1.00 OD1 C:ASP66 2.0 74.7 1.0 OD2 C:ASP99 2.1 46.6 1.0 OE2 C:GLU17 2.9 25.0 1.0 CG C:ASP99 3.1 34.6 1.0 CG C:ASP66 3.2 59.4 1.0 OE1 C:GLU68 3.2 30.4 1.0 OD1 C:ASP99 3.8 36.1 1.0 CD C:GLU17 3.8 31.4 1.0 CB C:ASP66 4.0 41.4 1.0 CB C:ASP99 4.0 30.3 1.0 OD2 C:ASP66 4.1 85.4 1.0 OD1 C:ASN100 4.2 20.9 1.0 CD C:GLU68 4.2 34.9 1.0 CA C:ASP66 4.4 38.4 1.0 CG C:GLU17 4.4 33.2 1.0 ND2 C:ASN100 4.5 28.3 1.0 OE2 C:GLU68 4.6 34.3 1.0 OE1 C:GLU17 4.6 37.7 1.0 CG C:ASN100 4.7 23.1 1.0 CA C:CA303 4.8 35.4 1.0 O C:LEU65 4.9 40.2 1.0

Calcium binding site 9 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Human Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca303 b:35.4 occ:1.00 OD1 C:ASP132 2.1 48.7 1.0 OD1 C:ASP96 2.2 36.9 1.0 OE2 C:GLU68 2.2 34.3 1.0 O C:ARG97 2.2 21.4 1.0 OD1 C:ASP99 2.5 36.1 1.0 OE1 C:GLU17 2.6 37.7 1.0 CG C:ASP99 3.0 34.6 1.0 OD2 C:ASP99 3.2 46.6 1.0 CG C:ASP132 3.2 34.0 1.0 CD C:GLU17 3.2 31.4 1.0 OE2 C:GLU17 3.3 25.0 1.0 CD C:GLU68 3.3 34.9 1.0 CG C:ASP96 3.4 41.1 1.0 C C:ARG97 3.4 26.3 1.0 N C:ARG97 3.5 29.2 1.0 OE1 C:GLU68 3.6 30.4 1.0 OD2 C:ASP132 3.7 29.5 1.0 N C:ASP99 3.9 27.5 1.0 ND2 C:ASN100 4.0 28.3 1.0 OD2 C:ASP96 4.0 31.5 1.0 CA C:ARG97 4.1 26.3 1.0 CB C:ASP99 4.2 30.3 1.0 C C:ASP96 4.4 32.4 1.0 CA C:ASP96 4.5 35.8 1.0 CB C:ASP132 4.5 31.5 1.0 N C:ASN98 4.5 29.9 1.0 CB C:ASP96 4.5 41.6 1.0 CG C:GLU68 4.6 39.4 1.0 CA C:ASP99 4.6 29.2 1.0 CG C:GLU17 4.7 33.2 1.0 CA C:ASN98 4.7 30.8 1.0 CB C:ARG97 4.8 25.7 1.0 CA C:ASP132 4.8 33.3 1.0 CA C:CA302 4.8 56.0 1.0 C C:ASN98 4.9 27.8 1.0

Calcium binding site 10 out of 14 in the Crystal Structure of Human Protocadherin-24 EC1-2 Form II


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Human Protocadherin-24 EC1-2 Form II within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca304 b:25.7 occ:1.00 OD1 C:ASN98 2.1 37.5 1.0 O C:ASN100 2.2 29.5 1.0 OD2 C:ASP130 2.2 25.7 1.0 O C:ALA136 2.6 26.2 1.0 OD2 C:ASP132 2.8 29.5 1.0 CG C:ASP130 2.8 25.5 1.0 OD1 C:ASP130 2.9 29.0 1.0 OD2 C:ASP188 3.1 36.3 1.0 CG C:ASN98 3.2 37.6 1.0 C C:ASN100 3.3 22.0 1.0 CB C:ASP132 3.4 31.5 1.0 CG C:ASP132 3.5 34.0 1.0 C C:ALA136 3.8 25.0 1.0 ND2 C:ASN98 3.9 40.1 1.0 N C:ASN100 4.0 21.6 1.0 CG C:ASP188 4.0 47.8 1.0 CA C:ASN100 4.1 20.8 1.0 CB C:ASP130 4.2 26.0 1.0 CB C:ASP188 4.3 47.2 1.0 N C:ALA101 4.3 23.3 1.0 CB C:ALA136 4.3 20.6 1.0 CB C:ASN98 4.4 35.7 1.0 CB C:ASN100 4.4 21.4 1.0 CA C:ALA136 4.5 23.9 1.0 CA C:ASN98 4.5 30.8 1.0 CA C:ALA101 4.6 26.0 1.0 C C:ASN98 4.6 27.8 1.0 N C:ASP99 4.7 27.5 1.0 OD1 C:ASP132 4.8 48.7 1.0 N C:GLY137 4.8 26.0 1.0 CA C:ASP132 4.8 33.3 1.0 CG C:GLN200 4.8 30.7 1.0 CB C:GLN200 4.9 25.7 1.0 N C:ASP132 4.9 35.6 1.0 CA C:GLY137 5.0 26.6 1.0

M.E.Gray, Z.R.Johnson, D.Modak, T.J.Tyska, M.Sotomayor. Species-Dependent Heterophilic and Homophilic Cadherin Interactions in Intestinal Intermicrovillar Links To Be Published.