Calcium in PDB 8e51: Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2

Protein crystallography data

The structure of Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2, PDB code: 8e51 was solved by E.Scheib, C.R.Nisler, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.60 / 2.59
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 75.816, 75.816, 242.68, 90, 90, 120
R / Rfree (%) 20.2 / 24.2

Other elements in 8e51:

The structure of Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 also contains other interesting chemical elements:

Potassium (K) 2 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 (pdb code 8e51). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 13 binding sites of Calcium where determined in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2, PDB code: 8e51:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in 8e51

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Calcium binding site 1 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca301

b:54.5
occ:1.00
 OD1 C:ASP122 2.4 54.6 1.0
OE1 C:GLU31 2.4 50.5 1.0
O C:ARG123 2.4 54.6 1.0
OD1 C:ASP125 2.4 55.1 1.0
OD2 C:ASP89 2.4 54.7 1.0
OD1 C:ASP89 2.4 50.4 1.0
OD1 C:ASP163 2.5 49.7 1.0
CG C:ASP89 2.8 56.8 1.0
CG C:ASP122 3.3 58.5 1.0
CD C:GLU31 3.5 58.9 1.0
CG C:ASP163 3.5 53.1 1.0
C C:ARG123 3.5 65.2 1.0
N C:ARG123 3.6 64.8 1.0
CG C:ASP125 3.6 61.2 1.0
OD2 C:ASP122 3.7 57.0 1.0
OE2 C:GLU31 3.9 56.8 1.0
CA C:CA302 4.1 66.0 1.0
CB C:ASP163 4.1 52.0 1.0
CA C:ARG123 4.1 61.5 1.0
ND2 C:ASN126 4.2 56.1 1.0
OD2 C:ASP125 4.3 56.4 1.0
CB C:ASP89 4.3 55.8 1.0
N C:ASP125 4.3 56.7 1.0
O C:HOH401 4.4 49.5 1.0
C C:ASP122 4.4 62.3 1.0
OD2 C:ASP163 4.4 50.2 1.0
CA C:ASP163 4.4 55.2 1.0
CB C:ASP122 4.4 54.5 1.0
CA C:ASP122 4.4 59.2 1.0
N C:ASN124 4.6 56.9 1.0
CB C:ASP125 4.7 57.1 1.0
CG C:GLU31 4.7 60.5 1.0
CB C:ARG123 4.7 71.8 1.0
CA C:ASN124 4.9 53.5 1.0

Calcium binding site 2 out of 13 in 8e51

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Calcium binding site 2 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca302

b:66.0
occ:1.00
 O C:HOH413 2.4 60.3 1.0
OD2 C:ASP89 2.4 54.7 1.0
OD2 C:ASP125 2.4 56.4 1.0
OD1 C:ASP87 2.4 74.3 1.0
OE2 C:GLU31 2.4 56.8 1.0
OE1 C:GLU32 2.4 83.9 1.0
CD C:GLU31 3.2 58.9 1.0
CG C:ASP125 3.2 61.2 1.0
OD1 C:ASP125 3.3 55.1 1.0
CD C:GLU32 3.4 91.3 1.0
CG C:ASP89 3.5 56.8 1.0
CG C:ASP87 3.5 67.2 1.0
OE1 C:GLU31 3.6 50.5 1.0
CG C:GLU32 4.0 91.7 1.0
CB C:ASP89 4.1 55.8 1.0
CA C:CA301 4.1 54.5 1.0
OE2 C:GLU32 4.2 82.7 1.0
ND2 C:ASN126 4.2 56.1 1.0
CB C:ASP87 4.3 64.4 1.0
CG C:GLU31 4.3 60.5 1.0
N C:ASP89 4.3 57.4 1.0
CA C:ASP87 4.4 59.8 1.0
OD2 C:ASP87 4.4 71.7 1.0
N C:ARG88 4.4 57.1 1.0
OD1 C:ASP89 4.5 50.4 1.0
CB C:ASP125 4.6 57.1 1.0
C C:ASP87 4.9 59.7 1.0
CA C:ASP89 4.9 58.3 1.0

Calcium binding site 3 out of 13 in 8e51

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Calcium binding site 3 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca303

b:48.7
occ:1.00
 OD1 C:ASN124 2.4 49.7 1.0
O C:ASN126 2.4 46.8 1.0
OD2 C:ASP161 2.4 46.2 1.0
O C:ASN167 2.4 48.3 1.0
OD2 C:ASP219 2.4 44.6 1.0
OD2 C:ASP163 2.4 50.2 1.0
OD1 C:ASP161 2.4 45.1 1.0
CG C:ASP161 2.7 49.3 1.0
CG C:ASP219 3.4 53.6 1.0
CG C:ASN124 3.5 59.0 1.0
CG C:ASP163 3.5 53.1 1.0
C C:ASN167 3.6 51.7 1.0
C C:ASN126 3.6 54.0 1.0
CB C:ASP219 3.7 55.1 1.0
CB C:ASP163 3.9 52.0 1.0
ND2 C:ASN124 4.0 52.9 1.0
CB C:ASP161 4.2 48.0 1.0
N C:ASN126 4.4 54.8 1.0
CA C:ASN126 4.4 59.9 1.0
CA C:ASN167 4.4 53.1 1.0
N C:GLY168 4.5 46.4 1.0
N C:PRO127 4.5 51.5 1.0
CA C:PRO127 4.5 51.9 1.0
CB C:ASN167 4.5 53.5 1.0
CB C:ASN126 4.5 59.5 1.0
OD1 C:ASP219 4.5 54.4 1.0
CA C:GLY168 4.6 48.9 1.0
OD1 C:ASP163 4.7 49.7 1.0
CB C:ASN124 4.7 53.2 1.0
CA C:ASN124 4.8 53.5 1.0
C C:PRO127 4.8 49.1 1.0
CD C:PRO128 4.9 49.6 1.0
CD1 C:LEU228 4.9 63.4 1.0
N C:ASP163 5.0 53.0 1.0
N C:PRO128 5.0 44.0 1.0

Calcium binding site 4 out of 13 in 8e51

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Calcium binding site 4 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca304

b:52.3
occ:1.00
 O C:HOH412 2.3 51.3 1.0
OE1 C:GLU206 2.4 46.5 1.0
OE1 C:GLU248 2.4 57.1 1.0
OD1 C:ASP240 2.4 54.3 1.0
OE1 C:GLU141 2.4 50.8 1.0
O C:GLY241 2.4 42.6 1.0
CD C:GLU206 3.4 53.0 1.0
CD C:GLU248 3.4 64.3 1.0
CG C:ASP240 3.5 54.3 1.0
C C:GLY241 3.6 54.1 1.0
CD C:GLU141 3.7 43.0 1.0
OE2 C:GLU206 3.7 52.4 1.0
CB C:GLU248 3.7 59.2 1.0
N C:GLY241 3.7 54.3 1.0
O C:HOH409 3.9 51.5 1.0
CG C:GLU248 3.9 59.1 1.0
OD2 C:ASP240 4.0 62.8 1.0
CA C:GLY241 4.2 53.6 1.0
OE2 C:GLU141 4.3 39.4 1.0
CA C:CA305 4.5 47.7 1.0
CA C:GLU248 4.5 62.7 1.0
OE2 C:GLU248 4.5 55.4 1.0
C C:ASP240 4.6 53.3 1.0
C C:GLU248 4.7 46.5 1.0
CB C:ASP240 4.7 50.7 1.0
N C:ASP242 4.7 54.9 1.0
CG C:GLU206 4.7 43.4 1.0
CA C:ASP240 4.8 50.4 1.0
CG C:GLU141 4.8 41.8 1.0
CB C:TYR205 5.0 45.8 1.0

Calcium binding site 5 out of 13 in 8e51

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Calcium binding site 5 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca305

b:47.7
occ:1.00
 O C:HOH414 2.3 49.4 1.0
OE2 C:GLU248 2.4 55.4 1.0
OE2 C:GLU206 2.4 52.4 1.0
OE2 C:GLU141 2.4 39.4 1.0
OD1 C:ASN204 2.4 51.8 1.0
OE1 C:GLU248 2.6 57.1 1.0
CD C:GLU248 2.9 64.3 1.0
CD C:GLU141 3.3 43.0 1.0
CG C:ASN204 3.5 56.7 1.0
CD C:GLU206 3.6 53.0 1.0
OE1 C:GLU141 3.6 50.8 1.0
CA C:ASN204 4.1 50.2 1.0
OE1 C:GLU206 4.1 46.5 1.0
N C:TYR205 4.2 49.9 1.0
ND2 C:ASN204 4.3 48.8 1.0
CB C:ASN204 4.3 50.6 1.0
CG C:GLU248 4.4 59.1 1.0
CA C:CA304 4.5 52.3 1.0
C C:ASN204 4.5 48.5 1.0
O C:HOH408 4.6 43.8 1.0
N C:GLU206 4.6 52.1 1.0
CG C:GLU141 4.7 41.8 1.0
O C:HOH412 4.7 51.3 1.0
CG C:GLU206 4.8 43.4 1.0
CB C:GLU206 4.9 43.6 1.0
O C:LEU203 4.9 51.6 1.0

Calcium binding site 6 out of 13 in 8e51

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Calcium binding site 6 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca306

b:52.2
occ:1.00
 O C:HOH411 2.1 50.7 1.0
O C:HOH404 2.4 50.2 1.0
O C:GLY245 2.4 51.7 1.0
O C:ASP243 2.4 42.2 1.0
OD1 C:ASP243 2.4 54.5 1.0
O C:GLU248 2.5 60.9 1.0
CG C:ASP243 3.4 57.7 1.0
C C:ASP243 3.5 54.0 1.0
C C:GLY245 3.6 54.1 1.0
C C:GLU248 3.7 46.5 1.0
N C:GLU248 3.9 52.3 1.0
CA C:CA307 4.0 64.3 1.0
OD2 C:ASP243 4.1 50.6 1.0
N C:ASP243 4.1 49.8 1.0
CA C:ASP243 4.2 54.1 1.0
C C:LEU244 4.2 57.5 1.0
O C:LEU244 4.2 64.8 1.0
N C:LEU247 4.3 54.3 1.0
CA C:GLU248 4.3 62.7 1.0
N C:GLY245 4.4 57.6 1.0
OD1 C:ASP242 4.4 54.6 1.0
CB C:ASP243 4.4 52.3 1.0
CA C:PRO246 4.4 55.2 1.0
N C:PRO246 4.5 57.1 1.0
OD2 C:ASP242 4.5 57.6 1.0
C C:PRO246 4.5 56.5 1.0
N C:LEU244 4.5 55.0 1.0
CA C:GLY245 4.6 48.9 1.0
CG C:ASP242 4.7 58.5 1.0
CA C:LEU244 4.7 61.5 1.0
C C:LEU247 4.9 51.6 1.0

Calcium binding site 7 out of 13 in 8e51

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Calcium binding site 7 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2


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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca307

b:64.3
occ:1.00
 OD2 C:ASP242 2.4 57.6 1.0
O C:GLU248 2.4 60.9 1.0
O C:HOH404 2.7 50.2 1.0
C C:GLU248 2.8 46.5 1.0
CG C:ASP242 3.5 58.5 1.0
CA C:CA306 4.0 52.2 1.0
OD1 C:ASP242 4.1 54.6 1.0
CA C:GLU248 4.3 62.7 1.0
CB C:ASP242 4.7 52.8 1.0
O C:HOH412 4.9 51.3 1.0
CB C:GLU248 5.0 59.2 1.0

Calcium binding site 8 out of 13 in 8e51

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Calcium binding site 8 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2


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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:62.9
occ:1.00
 O B:HOH408 2.3 56.7 1.0
OD2 B:ASP103 2.4 61.4 1.0
OD1 B:ASP70 2.4 67.2 1.0
OE2 B:GLU72 2.4 56.4 1.0
OE2 B:GLU20 2.4 63.7 1.0
CD B:GLU20 3.2 74.0 1.0
CG B:ASP103 3.3 66.1 1.0
CG B:ASP70 3.5 78.1 1.0
OE1 B:GLU20 3.6 66.8 1.0
OD1 B:ASP103 3.6 60.5 1.0
CD B:GLU72 3.6 59.1 1.0
CA B:CA302 4.0 60.0 1.0
CA B:ASP70 4.1 65.3 1.0
CB B:ASP70 4.2 72.7 1.0
ND2 B:ASN104 4.2 70.2 1.0
N B:ARG71 4.2 60.9 1.0
CG B:GLU20 4.4 74.9 1.0
OE1 B:GLU72 4.4 48.8 1.0
OD2 B:ASP70 4.5 74.3 1.0
N B:GLU72 4.5 63.5 1.0
CG B:GLU72 4.5 59.6 1.0
C B:ASP70 4.6 62.7 1.0
CB B:ASP103 4.6 60.6 1.0
CB B:GLU72 4.6 64.2 1.0
CB B:GLU20 5.0 70.7 1.0

Calcium binding site 9 out of 13 in 8e51

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Calcium binding site 9 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2


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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca302

b:60.0
occ:1.00
 OD1 B:ASP103 2.4 60.5 1.0
OE1 B:GLU72 2.4 48.8 1.0
OD1 B:ASP100 2.4 58.5 1.0
OD1 B:ASP136 2.4 61.6 1.0
OE1 B:GLU20 2.4 66.8 1.0
O B:VAL101 2.4 60.4 1.0
OE2 B:GLU72 2.8 56.4 1.0
CD B:GLU72 2.9 59.1 1.0
CG B:ASP103 3.4 66.1 1.0
CG B:ASP100 3.4 62.6 1.0
CD B:GLU20 3.5 74.0 1.0
CG B:ASP136 3.5 55.1 1.0
C B:VAL101 3.6 62.4 1.0
OD2 B:ASP103 3.8 61.4 1.0
OE2 B:GLU20 3.8 63.7 1.0
ND2 B:ASN104 3.8 70.2 1.0
OD2 B:ASP100 3.9 66.8 1.0
CA B:CA301 4.0 62.9 1.0
N B:VAL101 4.1 55.0 1.0
N B:ASP103 4.1 62.9 1.0
CB B:ASP136 4.2 53.0 1.0
CA B:ASP136 4.4 53.6 1.0
CG B:GLU72 4.4 59.6 1.0
OD2 B:ASP136 4.5 58.5 1.0
CA B:VAL101 4.5 56.4 1.0
N B:ASN102 4.6 64.3 1.0
CB B:ARG71 4.7 56.7 1.0
CB B:ASP100 4.7 64.2 1.0
NE B:ARG71 4.7 65.1 1.0
NH2 B:ARG71 4.7 61.8 1.0
CB B:ASP103 4.7 60.6 1.0
CA B:ASN102 4.7 61.5 1.0
CG B:GLU20 4.8 74.9 1.0
CA B:ASP100 4.8 59.1 1.0
O B:HOH408 4.9 56.7 1.0
CA B:ASP103 4.9 64.4 1.0
C B:ASN102 4.9 58.1 1.0
C B:ASP100 5.0 55.3 1.0

Calcium binding site 10 out of 13 in 8e51

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Calcium binding site 10 out of 13 in the Crystal Structure of Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2


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 Iridescent Shark Catfish Cadherin-23 EC1-2 and Protocadherin-15 EC1-2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca303

b:62.6
occ:1.00
 OD2 B:ASP134 2.4 57.7 1.0
O B:ASN104 2.4 66.1 1.0
O B:GLY140 2.4 58.6 1.0
OD2 B:ASP136 2.4 58.5 1.0
OD1 B:ASP134 2.4 57.7 1.0
OD2 B:ASP185 2.4 61.9 1.0
OD1 B:ASN102 2.4 66.7 1.0
CG B:ASP134 2.7 60.9 1.0
CG B:ASN102 3.4 63.7 1.0
CG B:ASP136 3.4 55.1 1.0
CG B:ASP185 3.5 67.0 1.0
C B:ASN104 3.5 68.9 1.0
C B:GLY140 3.5 54.8 1.0
ND2 B:ASN102 3.8 68.7 1.0
CB B:ASP136 3.8 53.0 1.0
CB B:ASP185 3.9 66.8 1.0
CB B:ASP134 4.2 56.1 1.0
CA B:GLY140 4.2 59.5 1.0
CA B:ASN104 4.3 67.2 1.0
N B:ASN104 4.4 64.7 1.0
N B:ALA105 4.4 68.0 1.0
CA B:ALA105 4.4 63.4 1.0
CB B:ASN104 4.5 69.8 1.0
N B:GLY141 4.5 52.9 1.0
OD1 B:ASP136 4.5 61.6 1.0
OD1 B:ASP185 4.6 75.5 1.0
CA B:GLY141 4.7 58.7 1.0
CB B:ASN102 4.7 63.3 1.0
C B:ALA105 4.7 60.7 1.0
N B:ASP136 4.8 55.0 1.0
CA B:ASP136 4.9 53.6 1.0
CB B:LEU192 5.0 70.9 1.0
CD B:PRO106 5.0 57.4 1.0
CA B:ASN102 5.0 61.5 1.0

Reference:

C.R.Nisler, Y.Narui, E.Scheib, D.Choudhary, J.D.Bowman, H.Mandayam Bharathi, V.J.Lynch, M.Sotomayor. Interpreting the Evolutionary Echoes of A Protein Complex Essential For Inner-Ear Mechanosensation. Mol.Biol.Evol. 2023.
ISSN: ESSN 1537-1719
PubMed: 36911992
DOI: 10.1093/MOLBEV/MSAD057
Page generated: Tue Apr 4 19:36:59 2023

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