Calcium in PDB 5t4n: Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant

Protein crystallography data

The structure of Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant, PDB code: 5t4n was solved by R.E.Powers, R.Gaudet, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.38 / 2.70
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 105.655, 105.655, 193.767, 90.00, 90.00, 120.00
R / Rfree (%) 20.2 / 23.9

Other elements in 5t4n:

The structure of Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant (pdb code 5t4n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant, PDB code: 5t4n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5t4n

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Calcium binding site 1 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:80.4
occ:1.00
 O A:GLU367 2.4 77.9 1.0
OD1 A:ASP411 2.4 74.7 1.0
O A:HOH827 2.4 69.7 1.0
OD1 A:ASN369 2.4 87.4 1.0
O A:HOH833 2.4 70.1 1.0
O A:HOH898 2.4 61.2 1.0
O A:HOH895 2.4 52.0 1.0
CG A:ASN369 3.4 88.9 1.0
CG A:ASP411 3.4 75.5 1.0
C A:GLU367 3.6 78.0 1.0
ND2 A:ASN369 3.9 94.7 1.0
N A:ASN369 4.0 75.2 1.0
N A:GLU367 4.1 83.2 1.0
OD2 A:ASP411 4.2 88.8 1.0
OD1 A:ASP366 4.2 98.1 1.0
CB A:ASP411 4.2 76.3 1.0
CG A:GLN370 4.3 91.6 1.0
CA A:ASP411 4.4 81.1 1.0
CA A:GLU367 4.4 81.9 1.0
N A:ASN368 4.5 77.0 1.0
CB A:ASN369 4.6 83.6 1.0
CA A:ASN368 4.7 77.6 1.0
CA A:ASN369 4.7 77.4 1.0
N A:GLN370 4.8 78.7 1.0
C A:ASN368 4.8 81.1 1.0
OE1 A:GLU267 4.9 93.9 1.0
C A:ASN369 5.0 78.4 1.0

Calcium binding site 2 out of 10 in 5t4n

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Calcium binding site 2 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:75.4
occ:1.00
 O A:GLN370 2.4 76.7 1.0
OD2 A:ASP409 2.4 93.3 1.0
OD2 A:ASP411 2.4 88.8 1.0
O A:HOH854 2.4 61.0 1.0
OD2 A:ASP464 2.4 75.5 1.0
OD1 A:ASN368 2.4 78.1 1.0
OD1 A:ASP409 2.4 78.2 1.0
CG A:ASP409 2.7 86.5 1.0
CG A:ASP411 3.3 75.5 1.0
CG A:ASP464 3.3 69.6 1.0
CG A:ASN368 3.4 77.2 1.0
C A:GLN370 3.5 80.4 1.0
CB A:ASP411 3.6 76.3 1.0
CB A:ASP464 3.7 65.3 1.0
ND2 A:ASN368 3.9 76.8 1.0
N A:GLN370 4.1 78.7 1.0
CA A:GLN370 4.2 84.8 1.0
OE1 A:GLN467 4.2 86.0 1.0
CB A:ASP409 4.3 81.8 1.0
OD1 A:ASP464 4.4 67.4 1.0
OD1 A:ASP411 4.4 74.7 1.0
CB A:GLN370 4.5 87.8 1.0
CB A:ASN368 4.6 76.3 1.0
C A:ASN368 4.6 81.1 1.0
N A:SER371 4.6 82.7 1.0
CA A:ASN368 4.6 77.6 1.0
CD A:PRO372 4.6 60.1 1.0
N A:PRO372 4.7 63.8 1.0
N A:ASP411 4.7 84.3 1.0
C A:SER371 4.8 70.5 1.0
CA A:ASP411 4.8 81.1 1.0
N A:ASN369 4.8 75.2 1.0
CA A:SER371 4.8 75.3 1.0
O A:HOH836 4.9 79.4 1.0
O A:ASN368 4.9 91.2 1.0

Calcium binding site 3 out of 10 in 5t4n

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Calcium binding site 3 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:72.2
occ:1.00
 OE1 A:GLU451 2.2 75.3 1.0
OD2 A:ASP483 2.3 82.2 1.0
OE2 A:GLU385 2.3 68.7 1.0
O A:HOH823 2.4 44.7 1.0
O A:HOH856 2.4 66.9 1.0
OD1 A:ASP449 2.5 77.6 1.0
OD1 A:ASP483 2.6 74.5 1.0
CG A:ASP483 2.8 78.8 1.0
CD A:GLU385 3.2 75.3 1.0
CA A:CA704 3.4 75.5 1.0
CG A:ASP449 3.4 83.0 1.0
CD A:GLU451 3.5 68.8 1.0
OE1 A:GLU385 3.6 85.0 1.0
ND2 A:ASN484 3.7 65.5 1.0
OD2 A:ASP449 4.0 91.1 1.0
CB A:ASP483 4.3 81.2 1.0
OE2 A:GLU451 4.3 72.1 1.0
CG A:GLU385 4.4 75.0 1.0
CG A:GLU451 4.4 68.3 1.0
CB A:ASP449 4.5 77.5 1.0
CB A:GLU451 4.5 69.4 1.0
N A:ARG450 4.5 61.1 1.0
N A:GLU451 4.5 62.5 1.0
CA A:ASP449 4.6 72.5 1.0
C A:ASP449 4.8 63.9 1.0
CG A:ASN484 4.9 67.5 1.0
OD1 A:ASP516 5.0 86.4 1.0

Calcium binding site 4 out of 10 in 5t4n

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Calcium binding site 4 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:75.5
occ:1.00
 OD1 A:ASP516 2.4 86.4 1.0
OD1 A:ASP480 2.4 70.8 1.0
OE1 A:GLU451 2.4 75.3 1.0
OE1 A:GLU385 2.4 85.0 1.0
OE2 A:GLU451 2.5 72.1 1.0
OD1 A:ASP483 2.5 74.5 1.0
O A:ALA481 2.6 64.5 1.0
CD A:GLU451 2.7 68.8 1.0
CD A:GLU385 3.3 75.3 1.0
CA A:CA703 3.4 72.2 1.0
CG A:ASP516 3.5 86.5 1.0
CG A:ASP480 3.5 79.9 1.0
OE2 A:GLU385 3.6 68.7 1.0
ND2 A:ASN484 3.6 65.5 1.0
CG A:ASP483 3.6 78.8 1.0
C A:ALA481 3.8 67.1 1.0
N A:ALA481 4.0 73.4 1.0
OD2 A:ASP480 4.1 92.8 1.0
N A:ASP483 4.1 69.5 1.0
CG A:GLU451 4.2 68.3 1.0
OD2 A:ASP483 4.2 82.2 1.0
CB A:ASP516 4.2 82.3 1.0
CA A:ASP516 4.3 79.1 1.0
NE A:ARG450 4.4 74.7 1.0
OD2 A:ASP516 4.5 87.4 1.0
CA A:ALA481 4.5 68.0 1.0
CG A:GLU385 4.7 75.0 1.0
CB A:ASP480 4.7 71.8 1.0
CB A:ASP483 4.7 81.2 1.0
CA A:ASP480 4.7 69.3 1.0
NH2 A:ARG450 4.7 83.9 1.0
N A:ASN482 4.8 68.6 1.0
CG A:ASN484 4.8 67.5 1.0
C A:ASP480 4.8 71.6 1.0
N A:ASN484 4.8 60.1 1.0
CA A:ASP483 4.8 73.3 1.0
CA A:ASN482 4.9 68.2 1.0
O A:HOH856 4.9 66.9 1.0
CB A:ARG450 5.0 59.8 1.0

Calcium binding site 5 out of 10 in 5t4n

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Calcium binding site 5 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca705

b:66.6
occ:1.00
 OD2 A:ASP514 2.3 74.4 1.0
OD2 A:ASP516 2.4 87.4 1.0
OD1 A:ASN482 2.4 70.8 1.0
O A:ASN520 2.4 71.9 1.0
O A:ASN484 2.4 63.1 1.0
OD2 A:ASP566 2.5 67.3 1.0
OD1 A:ASP514 2.5 72.0 1.0
CG A:ASP514 2.7 72.4 1.0
CG A:ASP566 3.4 72.5 1.0
CG A:ASP516 3.4 86.5 1.0
CG A:ASN482 3.5 69.9 1.0
C A:ASN484 3.6 62.6 1.0
C A:ASN520 3.6 78.4 1.0
CB A:ASP566 3.6 75.6 1.0
CB A:ASP516 3.7 82.3 1.0
ND2 A:ASN482 4.1 71.6 1.0
CB A:ASP514 4.3 74.7 1.0
CA A:ASN484 4.4 59.9 1.0
N A:ASN484 4.4 60.1 1.0
CA A:ASN520 4.5 83.7 1.0
OD1 A:ASP566 4.5 76.7 1.0
N A:GLY521 4.5 77.7 1.0
CD A:PRO486 4.5 73.4 1.0
OD1 A:ASP516 4.5 86.4 1.0
CB A:ASN484 4.5 58.8 1.0
CA A:GLY521 4.6 80.1 1.0
N A:THR485 4.6 64.4 1.0
CB A:ASN520 4.7 78.7 1.0
CB A:ASN482 4.7 65.5 1.0
CA A:THR485 4.8 64.8 1.0
CA A:ASN482 4.9 68.2 1.0
N A:ASP516 4.9 73.8 1.0
CA A:ASP516 4.9 79.1 1.0
CD A:ARG574 5.0 70.8 1.0

Calcium binding site 6 out of 10 in 5t4n

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Calcium binding site 6 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:66.9
occ:1.00
 OD1 B:ASP480 2.3 64.2 1.0
OD1 B:ASP516 2.4 70.7 1.0
O B:ALA481 2.4 81.4 1.0
OE2 B:GLU451 2.5 75.8 1.0
OE2 B:GLU385 2.5 66.3 1.0
OE1 B:GLU451 2.5 63.4 1.0
OD1 B:ASP483 2.5 72.7 1.0
CD B:GLU451 2.8 66.3 1.0
CG B:ASP480 3.3 65.9 1.0
CG B:ASP516 3.4 79.3 1.0
C B:ALA481 3.6 79.6 1.0
CG B:ASP483 3.7 73.1 1.0
CD B:GLU385 3.8 72.5 1.0
OD2 B:ASP480 3.8 75.4 1.0
ND2 B:ASN484 3.9 65.2 1.0
CA B:CA703 3.9 76.1 1.0
N B:ASP483 4.0 77.0 1.0
N B:ALA481 4.0 74.2 1.0
CB B:ASP516 4.0 74.7 1.0
CA B:ASP516 4.1 67.9 1.0
CG B:GLU451 4.2 63.9 1.0
OD2 B:ASP483 4.3 84.6 1.0
OD2 B:ASP516 4.4 87.6 1.0
NE B:ARG450 4.4 70.0 1.0
CA B:ALA481 4.4 76.4 1.0
OE1 B:GLU385 4.4 83.6 1.0
CB B:ASP480 4.5 66.8 1.0
N B:ASN482 4.6 79.0 1.0
CA B:ASP480 4.6 68.8 1.0
CA B:ASN482 4.6 73.3 1.0
NH2 B:ARG450 4.7 72.3 1.0
C B:ASP480 4.7 71.8 1.0
CB B:ASP483 4.8 71.6 1.0
CA B:ASP483 4.8 74.5 1.0
C B:ASN482 4.8 69.6 1.0
CG B:GLU385 4.9 65.8 1.0
N B:GLU517 4.9 78.4 1.0
N B:ASP516 4.9 72.1 1.0
N B:ASN484 5.0 67.8 1.0
O B:ALA515 5.0 78.6 1.0

Calcium binding site 7 out of 10 in 5t4n

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Calcium binding site 7 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:65.9
occ:1.00
 OD2 B:ASP514 2.4 75.6 1.0
OD2 B:ASP516 2.4 87.6 1.0
OD1 B:ASN482 2.4 89.5 1.0
O B:ASN520 2.4 63.8 1.0
O B:ASN484 2.4 65.5 1.0
OD1 B:ASP514 2.5 71.6 1.0
OD2 B:ASP566 2.5 78.0 1.0
CG B:ASP514 2.8 72.4 1.0
CG B:ASP566 3.4 73.0 1.0
CG B:ASP516 3.4 79.3 1.0
CG B:ASN482 3.5 82.0 1.0
C B:ASN520 3.6 66.6 1.0
C B:ASN484 3.6 66.1 1.0
CB B:ASP566 3.6 72.5 1.0
CB B:ASP516 3.7 74.7 1.0
ND2 B:ASN482 4.0 86.1 1.0
CB B:ASP514 4.3 74.8 1.0
CA B:ASN484 4.4 62.3 1.0
OD1 B:ASP566 4.4 69.6 1.0
N B:ASN484 4.4 67.8 1.0
CD B:PRO486 4.5 59.1 1.0
N B:GLY521 4.5 65.8 1.0
CA B:ASN520 4.5 71.9 1.0
OD1 B:ASP516 4.5 70.7 1.0
CA B:GLY521 4.5 66.7 1.0
CB B:ASN484 4.6 62.2 1.0
N B:THR485 4.6 69.1 1.0
CB B:ASN520 4.7 72.0 1.0
CB B:ASN482 4.8 69.8 1.0
CA B:THR485 4.9 70.4 1.0
N B:PRO486 5.0 64.5 1.0
CG B:PRO486 5.0 55.6 1.0
CA B:ASN482 5.0 73.3 1.0
N B:ASP516 5.0 72.1 1.0
CA B:ASP516 5.0 67.9 1.0

Calcium binding site 8 out of 10 in 5t4n

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Calcium binding site 8 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:76.1
occ:1.00
 OD2 B:ASP483 2.2 84.6 1.0
OE1 B:GLU385 2.2 83.6 1.0
OE1 B:GLU451 2.3 63.4 1.0
O B:HOH881 2.4 61.1 1.0
O B:HOH849 2.4 45.9 1.0
OD1 B:ASP449 2.5 74.5 1.0
CD B:GLU385 2.7 72.5 1.0
OE2 B:GLU385 2.7 66.3 1.0
OD1 B:ASP483 2.7 72.7 1.0
CG B:ASP483 2.8 73.1 1.0
CG B:ASP449 3.3 74.0 1.0
CD B:GLU451 3.6 66.3 1.0
OD2 B:ASP449 3.8 79.0 1.0
CA B:CA701 3.9 66.9 1.0
CG B:GLU385 4.0 65.8 1.0
ND2 B:ASN484 4.2 65.2 1.0
CB B:ASP449 4.2 71.2 1.0
CB B:ASP483 4.2 71.6 1.0
N B:ARG450 4.4 57.9 1.0
CG B:GLU451 4.4 63.9 1.0
CB B:GLU451 4.4 64.1 1.0
CA B:ASP449 4.4 66.2 1.0
N B:GLU451 4.4 74.2 1.0
OE2 B:GLU451 4.4 75.8 1.0
C B:ASP449 4.7 60.1 1.0
CB B:GLU385 4.9 65.7 1.0

Calcium binding site 9 out of 10 in 5t4n

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Calcium binding site 9 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca704

b:67.4
occ:1.00
 OD2 B:ASP464 2.3 76.4 1.0
OD1 B:ASP409 2.3 63.9 1.0
OD2 B:ASP411 2.4 81.3 1.0
O B:GLN370 2.4 77.1 1.0
OD1 B:ASN368 2.4 86.8 1.0
OD2 B:ASP409 2.4 70.9 1.0
O B:HOH866 2.4 74.3 1.0
CG B:ASP409 2.7 68.7 1.0
CG B:ASP464 3.4 71.4 1.0
CG B:ASP411 3.4 72.6 1.0
CG B:ASN368 3.4 79.3 1.0
C B:GLN370 3.6 75.3 1.0
CB B:ASP411 3.7 75.0 1.0
CB B:ASP464 3.7 63.8 1.0
ND2 B:ASN368 3.9 81.1 1.0
N B:GLN370 4.1 71.3 1.0
CB B:ASP409 4.2 69.7 1.0
OE1 B:GLN467 4.2 0.7 1.0
CA B:GLN370 4.2 72.2 1.0
OD1 B:ASP464 4.5 73.6 1.0
OD1 B:ASP411 4.5 73.2 1.0
CB B:GLN370 4.5 74.4 1.0
N B:SER371 4.6 79.1 1.0
CB B:ASN368 4.6 73.9 1.0
CD B:PRO372 4.7 66.1 1.0
N B:ASP411 4.7 80.9 1.0
N B:PRO372 4.7 68.3 1.0
C B:SER371 4.8 69.9 1.0
CA B:ASN368 4.8 74.5 1.0
C B:ASN368 4.8 74.2 1.0
N B:ASN369 4.8 74.5 1.0
CA B:SER371 4.9 75.5 1.0
CA B:ASP411 4.9 75.2 1.0
O B:HOH844 4.9 76.1 1.0

Calcium binding site 10 out of 10 in 5t4n

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Calcium binding site 10 out of 10 in the Crystal Structure of Human Protocadherin-15 EC3-5 D414A Variant


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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-15 EC3-5 D414A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca705

b:79.0
occ:1.00
 O B:GLU367 2.3 81.0 1.0
OD1 B:ASP366 2.4 84.6 1.0
OD1 B:ASP411 2.4 73.2 1.0
O B:HOH845 2.4 90.8 1.0
OD2 B:ASP366 2.5 97.4 1.0
OD1 B:ASN369 2.5 79.8 1.0
CG B:ASP366 2.7 86.7 1.0
CL B:CL706 2.9 74.6 1.0
CG B:ASP411 3.4 72.6 1.0
CG B:ASN369 3.4 79.6 1.0
C B:GLU367 3.5 82.1 1.0
ND2 B:ASN369 3.8 90.5 1.0
N B:ASN369 4.0 74.5 1.0
N B:GLU367 4.0 79.7 1.0
CB B:ASP411 4.1 75.0 1.0
CB B:ASP366 4.2 74.0 1.0
CA B:ASP411 4.3 75.2 1.0
OD2 B:ASP411 4.3 81.3 1.0
CA B:GLU367 4.3 82.6 1.0
OE1 B:GLU267 4.3 0.3 1.0
N B:ASN368 4.4 79.5 1.0
CA B:ASN368 4.5 74.5 1.0
CG B:GLN370 4.5 78.1 1.0
CB B:ASN369 4.7 73.7 1.0
C B:ASP366 4.7 75.1 1.0
C B:ASN368 4.8 74.2 1.0
CA B:ASN369 4.8 73.3 1.0
OE1 B:GLN370 4.8 94.5 1.0
O B:HOH863 4.9 68.5 1.0
O B:HOH802 4.9 88.8 1.0
N B:GLN370 4.9 71.3 1.0
CA B:ASP366 4.9 74.6 1.0
CB B:GLU367 4.9 86.8 1.0

Reference:

R.E.Powers, R.Gaudet, M.Sotomayor. A Partial Calcium-Free Linker Confers Flexibility to Inner-Ear Protocadherin-15. Structure V. 25 482 2017.
ISSN: ISSN 1878-4186
PubMed: 28238533
DOI: 10.1016/J.STR.2017.01.014
Page generated: Sat Dec 12 05:43:24 2020

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