Calcium in PDB 7n4p: Crystal Structure of Lizard Cadherin-23 EC1-2

The structure of Crystal Structure of Lizard Cadherin-23 EC1-2, PDB code: 7n4p was solved by C.R.Nisler, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.67 / 2.10
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	43.386, 43.386, 296.227, 90, 90, 90
R / Rfree (%)	21.1 / 26.7

The structure of Crystal Structure of Lizard Cadherin-23 EC1-2 also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Calcium atom in the Crystal Structure of Lizard Cadherin-23 EC1-2 (pdb code 7n4p). 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 Lizard Cadherin-23 EC1-2, PDB code: 7n4p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Lizard Cadherin-23 EC1-2


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 Lizard Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca301 b:32.4 occ:1.00 O A:ASN103 2.3 34.3 1.0 OD2 A:ASP184 2.3 33.0 1.0 OD1 A:ASN101 2.3 35.4 1.0 OD2 A:ASP135 2.4 33.1 1.0 O A:GLY139 2.4 33.8 1.0 OD2 A:ASP133 2.5 36.3 1.0 OD1 A:ASP133 2.5 37.1 1.0 CG A:ASP133 2.9 36.8 1.0 CG A:ASP184 3.3 34.0 1.0 CG A:ASP135 3.4 34.7 1.0 CG A:ASN101 3.4 35.1 1.0 C A:ASN103 3.5 33.8 1.0 C A:GLY139 3.5 35.4 1.0 CB A:ASP135 3.6 34.9 1.0 CB A:ASP184 3.8 35.5 1.0 ND2 A:ASN101 3.9 36.1 1.0 N A:ASN103 4.1 33.7 1.0 CA A:GLY139 4.2 35.9 1.0 CA A:ASN103 4.2 33.9 1.0 OD1 A:ASP184 4.4 33.6 1.0 CB A:ASP133 4.4 35.3 1.0 CB A:ASN103 4.4 33.5 1.0 N A:ALA104 4.5 34.8 1.0 OD1 A:ASP135 4.6 33.9 1.0 N A:GLY140 4.6 33.6 1.0 CB A:ASN101 4.7 34.4 1.0 CA A:GLY140 4.8 34.3 1.0 CA A:ALA104 4.8 33.7 1.0 CA A:ASP135 4.8 35.4 1.0 N A:ASP135 4.8 35.2 1.0 CA A:ASN101 4.9 33.3 1.0 CD1 A:LEU191 4.9 37.7 1.0 N A:ASP102 5.0 34.9 1.0 C A:ALA104 5.0 33.8 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Lizard Cadherin-23 EC1-2


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 Lizard Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca302 b:30.9 occ:1.00 OD1 A:ASP99 2.3 33.9 1.0 OD1 A:ASP102 2.3 33.3 1.0 OE2 A:GLU71 2.3 35.8 1.0 OD1 A:ASP135 2.4 33.9 1.0 O A:VAL100 2.4 32.9 1.0 OE2 A:GLU19 2.4 30.3 1.0 OE1 A:GLU71 2.7 32.0 1.0 CD A:GLU71 2.9 34.6 1.0 CG A:ASP99 3.3 34.8 1.0 CG A:ASP102 3.4 34.9 1.0 CD A:GLU19 3.4 32.1 1.0 CG A:ASP135 3.5 34.7 1.0 C A:VAL100 3.6 35.0 1.0 OD2 A:ASP99 3.8 35.9 1.0 OE1 A:GLU19 3.8 33.3 1.0 CA A:CA303 3.9 32.4 1.0 OD2 A:ASP102 3.9 37.5 1.0 N A:VAL100 3.9 35.8 1.0 ND2 A:ASN103 4.0 35.4 1.0 N A:ASP102 4.1 34.9 1.0 CB A:ASP135 4.2 34.9 1.0 CA A:ASP135 4.3 35.4 1.0 NE A:ARG70 4.3 41.8 1.0 CG A:GLU71 4.4 37.1 1.0 CA A:VAL100 4.4 35.5 1.0 CB A:ASP99 4.5 35.5 1.0 CB A:ASP102 4.5 35.3 1.0 OD2 A:ASP135 4.5 33.1 1.0 CA A:ASP99 4.5 35.0 1.0 N A:ASN101 4.6 33.4 1.0 C A:ASP99 4.7 35.7 1.0 CG A:GLU19 4.7 30.1 1.0 NH2 A:ARG70 4.8 39.3 1.0 CA A:ASN101 4.8 33.3 1.0 CA A:ASP102 4.8 34.4 1.0 CG1 A:VAL100 4.8 42.6 1.0 CB A:ARG70 4.9 35.7 1.0 C A:ASN101 4.9 33.1 1.0 O A:HOH515 5.0 32.5 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Lizard Cadherin-23 EC1-2


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 Lizard Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca303 b:32.4 occ:1.00 O A:HOH463 2.2 31.3 1.0 OE1 A:GLU19 2.3 33.3 1.0 OD2 A:ASP102 2.3 37.5 1.0 OE1 A:GLU71 2.3 32.0 1.0 O A:HOH515 2.3 32.5 1.0 OD1 A:ASP69 2.3 37.3 1.0 CG A:ASP102 3.0 34.9 1.0 OD1 A:ASP102 3.1 33.3 1.0 CD A:GLU19 3.2 32.1 1.0 CG A:ASP69 3.3 40.2 1.0 CD A:GLU71 3.5 34.6 1.0 OE2 A:GLU19 3.6 30.3 1.0 O A:HOH432 3.7 35.8 1.0 CA A:CA302 3.9 30.9 1.0 CA A:ASP69 4.1 37.1 1.0 OD2 A:ASP69 4.1 43.6 1.0 N A:ARG70 4.1 34.0 1.0 CB A:ASP69 4.2 39.2 1.0 ND2 A:ASN103 4.3 35.4 1.0 O A:HOH450 4.3 41.0 1.0 N A:GLU71 4.3 35.3 1.0 O A:HOH464 4.3 35.2 1.0 OE2 A:GLU71 4.3 35.8 1.0 C A:ASP69 4.4 36.6 1.0 O A:HOH503 4.4 33.1 1.0 CB A:GLU71 4.4 38.4 1.0 CG A:GLU19 4.4 30.1 1.0 CG A:GLU71 4.4 37.1 1.0 CB A:ASP102 4.5 35.3 1.0 CB A:GLU19 5.0 31.2 1.0 CA A:GLU71 5.0 38.8 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Lizard Cadherin-23 EC1-2


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 Lizard Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca304 b:43.0 occ:1.00 OD2 A:ASP34 2.2 37.7 1.0 OD2 A:ASP38 2.2 46.1 1.0 O A:ARG2 2.4 44.3 1.0 OD1 A:ASP36 2.4 44.4 1.0 OD1 A:ASN1 2.5 49.3 1.0 OD2 A:ASP84 2.5 43.4 1.0 OD1 A:ASP34 2.7 36.9 1.0 CG A:ASP34 2.7 39.1 1.0 CG A:ASP38 3.3 47.2 1.0 CG A:ASN1 3.3 53.6 1.0 CG A:ASP36 3.4 49.2 1.0 CG A:ASP84 3.5 45.5 1.0 ND2 A:ASN1 3.6 52.2 1.0 C A:ARG2 3.6 49.6 1.0 CB A:ASP84 3.6 45.3 1.0 O A:HOH442 3.8 52.3 1.0 CB A:ASP36 3.9 49.8 1.0 N A:ARG2 4.1 56.4 1.0 CB A:ASP38 4.1 46.0 1.0 CB A:ASP34 4.2 39.6 1.0 OD1 A:ASP38 4.2 47.7 1.0 OD2 A:ASP36 4.4 54.0 1.0 CA A:ARG2 4.4 52.9 1.0 N A:LEU3 4.5 48.2 1.0 N A:ASP36 4.6 48.7 1.0 OD1 A:ASP84 4.7 45.6 1.0 CA A:LEU3 4.7 45.0 1.0 CB A:ASN1 4.7 59.5 1.0 N A:PRO4 4.8 41.6 1.0 C A:LEU3 4.8 41.5 1.0 CA A:ASP36 4.9 51.0 1.0 CD A:PRO4 4.9 42.5 1.0 C A:ASN1 5.0 60.8 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Lizard Cadherin-23 EC1-2


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 Lizard Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca305 b:56.1 occ:1.00 O A:VAL204 2.3 50.4 1.0 O A:HOH435 2.3 66.2 1.0 O A:HOH438 2.3 51.2 1.0 OD1 A:ASP203 2.4 48.2 1.0 OE2 A:GLU118 2.5 43.9 1.0 OE2 A:GLU171 2.6 58.8 1.0 OE1 A:GLU171 2.9 56.5 1.0 CD A:GLU171 3.1 57.6 1.0 CD A:GLU118 3.4 42.9 1.0 C A:VAL204 3.4 51.9 1.0 OE1 A:GLU118 3.6 44.4 1.0 CG A:ASP203 3.6 49.5 1.0 CA A:CA306 3.8 58.7 1.0 N A:VAL204 3.8 46.2 1.0 OD2 A:ASP206 4.0 87.0 1.0 CA A:VAL204 4.3 48.5 1.0 OD2 A:ASP203 4.3 53.0 1.0 N A:GLN205 4.4 58.9 1.0 N A:ASP206 4.5 70.3 1.0 CA A:GLN205 4.6 63.5 1.0 CG A:GLU171 4.7 58.4 1.0 O A:HOH488 4.7 57.8 1.0 C A:ASP203 4.7 46.3 1.0 CA A:ASP203 4.7 47.6 1.0 CB A:ASP203 4.7 50.2 1.0 C A:GLN205 4.8 62.8 1.0 CB A:TYR170 4.8 46.5 1.0 CG A:ASP206 4.8 85.3 1.0 CG A:GLU118 4.8 41.7 1.0 CB A:VAL204 4.9 46.8 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Lizard Cadherin-23 EC1-2


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 Lizard Cadherin-23 EC1-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca306 b:58.7 occ:1.00 O A:HOH488 2.1 57.8 1.0 O A:HOH531 2.2 45.3 1.0 OE1 A:GLU118 2.4 44.4 1.0 OE1 A:GLU171 2.4 56.5 1.0 OD1 A:ASP169 2.6 44.5 1.0 O A:HOH438 3.1 51.2 1.0 CD A:GLU118 3.4 42.9 1.0 CG A:ASP169 3.5 44.0 1.0 CD A:GLU171 3.6 57.6 1.0 CA A:CA305 3.8 56.1 1.0 OE2 A:GLU118 3.9 43.9 1.0 OD2 A:ASP206 4.0 87.0 1.0 OD2 A:ASP169 4.2 44.2 1.0 CA A:ASP169 4.2 40.2 1.0 N A:TYR170 4.3 43.8 1.0 OE2 A:GLU171 4.4 58.8 1.0 CB A:ASP169 4.4 41.7 1.0 CG A:GLU171 4.6 58.4 1.0 N A:GLU171 4.6 52.4 1.0 CG A:GLU118 4.6 41.7 1.0 C A:ASP169 4.6 42.7 1.0 CB A:GLU171 4.6 56.9 1.0

C.R.Nisler, M.Sotomayor. Crystal Structure of Lizard Cadherin-23 EC1-2 To Be Published.