Calcium in PDB 6e8f: Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1

The structure of Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1, PDB code: 6e8f was solved by D.Choudhary, E.Tamilselvan, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.95 / 2.99
Space group	P 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	95.735, 95.906, 258.604, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.4

The structure of Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1 also contains other interesting chemical elements:

Sodium

(Na)

1 atom

Pages:

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

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1 (pdb code 6e8f). 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 Human Protocadherin-15 EC3-5 CD2-1, PDB code: 6e8f:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:76.6 occ:1.00 OD2 A:ASP409 2.1 79.1 1.0 O A:GLN370 2.4 74.2 1.0 OD2 A:ASP411 2.4 84.7 1.0 OD2 A:ASP471 2.5 78.4 1.0 OD1 A:ASP409 2.5 75.2 1.0 CG A:ASP409 2.7 76.1 1.0 OD1 A:ASN368 3.0 94.8 1.0 CG A:ASN368 3.3 89.9 1.0 CG A:ASP471 3.3 71.8 1.0 ND2 A:ASN368 3.4 85.6 1.0 CG A:ASP411 3.5 82.6 1.0 C A:GLN370 3.6 74.7 1.0 CB A:ASP471 3.6 68.1 1.0 CB A:ASP411 3.9 82.0 1.0 OE1 A:GLN474 4.2 74.5 1.0 N A:GLN370 4.2 73.8 1.0 CB A:ASP409 4.2 76.8 1.0 CA A:ASN368 4.3 85.8 1.0 C A:ASN368 4.3 84.5 1.0 O A:ASN368 4.3 88.1 1.0 CA A:GLN370 4.4 75.5 1.0 CB A:ASN368 4.4 87.5 1.0 OD1 A:ASP471 4.5 69.5 1.0 OD1 A:ASP411 4.6 86.8 1.0 N A:SER371 4.6 72.0 1.0 CB A:GLN370 4.7 75.4 1.0 CA A:SER371 4.7 70.7 1.0 N A:ASN369 4.8 82.8 1.0 N A:ASP411 4.9 83.2 1.0 CA A:ASP411 5.0 82.3 1.0

Calcium binding site 2 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:58.6 occ:1.00 OE2 A:GLU385 2.2 65.3 1.0 OE2 A:GLU458 2.3 63.4 1.0 OD1 A:ASP487 2.4 73.7 1.0 OD1 A:ASP523 2.5 68.3 1.0 O A:ALA488 2.6 64.8 1.0 OD1 A:ASP490 2.7 73.8 1.0 OE1 A:GLU458 2.8 60.8 1.0 CD A:GLU458 2.8 66.0 1.0 CD A:GLU385 3.2 66.2 1.0 CG A:ASP487 3.3 73.6 1.0 CG A:ASP523 3.5 68.9 1.0 OE1 A:GLU385 3.6 69.1 1.0 CG A:ASP490 3.6 72.8 1.0 C A:ALA488 3.8 66.3 1.0 N A:ALA488 3.8 68.1 1.0 OD2 A:ASP487 3.8 77.7 1.0 ND2 A:ASN491 3.9 78.3 1.0 OD2 A:ASP490 4.0 73.5 1.0 NE A:ARG457 4.1 67.9 1.0 CB A:ASP523 4.2 67.6 1.0 CA A:ASP523 4.2 68.0 1.0 CG A:GLU458 4.3 66.9 1.0 N A:ASP490 4.4 66.7 1.0 CA A:CA703 4.4 77.5 1.0 CA A:ALA488 4.4 65.0 1.0 CA A:ASP487 4.4 70.2 1.0 CB A:ASP487 4.4 71.3 1.0 OD2 A:ASP523 4.4 68.0 1.0 CG A:GLU385 4.6 65.3 1.0 C A:ASP487 4.6 69.5 1.0 CB A:ARG457 4.7 64.7 1.0 CD A:ARG457 4.8 66.9 1.0 N A:ASN489 4.8 67.9 1.0 CB A:ASP490 4.9 70.3 1.0 N A:GLU524 5.0 71.8 1.0 NH2 A:ARG457 5.0 65.4 1.0

Calcium binding site 3 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:77.5 occ:1.00 OD1 A:ASP456 2.4 77.2 1.0 OE1 A:GLU385 2.5 69.1 1.0 OD2 A:ASP490 2.6 73.5 1.0 OE1 A:GLU458 2.6 60.8 1.0 CG A:ASP490 3.1 72.8 1.0 OD1 A:ASP490 3.2 73.8 1.0 CG A:ASP456 3.3 74.8 1.0 CD A:GLU385 3.4 66.2 1.0 CD A:GLU458 3.8 66.0 1.0 OD2 A:ASP456 3.8 78.4 1.0 OE2 A:GLU385 4.0 65.3 1.0 ND2 A:ASN491 4.2 78.3 1.0 CB A:ASP456 4.2 70.8 1.0 CA A:ASP456 4.3 66.1 1.0 CB A:ASP490 4.3 70.3 1.0 N A:ARG457 4.3 65.8 1.0 CA A:CA702 4.4 58.6 1.0 CG A:GLU385 4.5 65.3 1.0 N A:GLU458 4.6 69.3 1.0 CG A:GLU458 4.6 66.9 1.0 CB A:GLU458 4.7 68.4 1.0 C A:ASP456 4.7 66.7 1.0 OE2 A:GLU458 4.8 63.4 1.0 CB A:GLU385 4.9 62.8 1.0

Calcium binding site 4 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:64.6 occ:1.00 OD1 A:ASN489 2.1 68.8 1.0 O A:ASN491 2.2 69.7 1.0 OD2 A:ASP573 2.3 70.7 1.0 OD2 A:ASP521 2.3 62.9 1.0 O A:ASN527 2.3 69.1 1.0 OD2 A:ASP523 2.4 68.0 1.0 OD1 A:ASP521 2.7 62.3 1.0 CG A:ASP521 2.8 63.4 1.0 CG A:ASN489 3.2 67.2 1.0 CG A:ASP573 3.3 71.3 1.0 C A:ASN491 3.4 72.5 1.0 CG A:ASP523 3.4 68.9 1.0 C A:ASN527 3.5 71.8 1.0 CB A:ASP573 3.6 71.1 1.0 ND2 A:ASN489 3.7 66.1 1.0 CB A:ASP523 3.8 67.6 1.0 N A:ASN491 4.2 72.0 1.0 CA A:ASN491 4.2 72.1 1.0 CB A:ASP521 4.3 63.0 1.0 OD1 A:ASP573 4.4 71.3 1.0 CA A:ASN527 4.4 71.6 1.0 CB A:ASN489 4.5 65.4 1.0 N A:GLY528 4.5 71.9 1.0 N A:THR492 4.5 72.0 1.0 CB A:ASN491 4.5 73.8 1.0 CB A:ASN527 4.5 72.8 1.0 OD1 A:ASP523 4.6 68.3 1.0 CA A:GLY528 4.6 72.6 1.0 CA A:ASN489 4.6 66.1 1.0 CA A:THR492 4.7 70.2 1.0 CD A:PRO493 4.8 68.1 1.0 CD A:ARG581 4.8 76.0 1.0 C A:ASN489 4.9 66.2 1.0 C A:THR492 5.0 70.2 1.0

Calcium binding site 5 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca701 b:89.5 occ:1.00 O C:HOH802 2.1 60.0 1.0 OD2 C:ASP471 2.4 88.2 1.0 OD2 C:ASP411 2.4 99.3 1.0 O C:GLN370 2.5 85.2 1.0 OD1 C:ASN368 2.5 85.5 1.0 OD2 C:ASP409 2.6 83.0 1.0 OD1 C:ASP409 2.7 86.2 1.0 CG C:ASP409 3.0 84.3 1.0 CG C:ASP411 3.4 96.2 1.0 CG C:ASP471 3.4 90.2 1.0 CG C:ASN368 3.4 84.5 1.0 C C:GLN370 3.6 87.0 1.0 OE1 C:GLN474 3.6 0.3 1.0 CB C:ASP411 3.7 92.7 1.0 N C:GLN370 3.8 91.8 1.0 CB C:ASP471 4.0 91.1 1.0 CA C:ASN368 4.1 82.2 1.0 CB C:ASN368 4.1 82.7 1.0 CA C:GLN370 4.1 87.3 1.0 N C:ASN369 4.3 88.0 1.0 C C:ASN368 4.3 84.5 1.0 ND2 C:ASN368 4.3 87.1 1.0 OD1 C:ASP471 4.4 91.8 1.0 CB C:GLN370 4.4 85.0 1.0 OD1 C:ASP411 4.5 95.6 1.0 CB C:ASP409 4.6 84.0 1.0 N C:SER371 4.7 87.3 1.0 N C:ASP411 4.7 94.6 1.0 CA C:ASP411 4.8 93.7 1.0 CD C:GLN474 4.9 0.5 1.0 C C:ASN369 4.9 92.0 1.0

Calcium binding site 6 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca702 b:0.1 occ:1.00 OD1 C:ASP487 1.9 0.4 1.0 OD1 C:ASP523 2.2 0.5 1.0 OE2 C:GLU385 2.4 0.2 1.0 OE1 C:GLU458 2.6 0.7 1.0 O C:ALA488 2.7 0.8 1.0 OD1 C:ASP490 2.8 0.8 1.0 OE2 C:GLU458 2.9 0.5 1.0 CG C:ASP487 2.9 0.1 1.0 CD C:GLU458 3.0 0.6 1.0 CG C:ASP523 3.1 0.1 1.0 OD2 C:ASP487 3.3 0.2 1.0 CD C:GLU385 3.4 0.1 1.0 CB C:ASP523 3.6 0.1 1.0 CG C:ASP490 3.7 0.8 1.0 OE1 C:GLU385 3.7 0.5 1.0 C C:ALA488 3.8 0.8 1.0 N C:ALA488 4.0 0.8 1.0 CA C:ASP523 4.0 0.8 1.0 OD2 C:ASP490 4.0 0.5 1.0 CA C:CA704 4.1 0.6 1.0 OD2 C:ASP523 4.1 0.8 1.0 CB C:ASP487 4.2 0.8 1.0 OD1 C:ASN491 4.4 0.9 1.0 N C:ASP490 4.4 0.5 1.0 CA C:ASP487 4.4 0.5 1.0 CG C:GLU458 4.5 0.6 1.0 CA C:ALA488 4.5 0.9 1.0 C C:ASP487 4.6 0.9 1.0 CG C:GLU385 4.8 0.6 1.0 N C:ASP523 4.8 0.8 1.0 N C:ASN489 4.8 0.0 1.0 CB C:ARG457 4.8 0.9 1.0 CB C:ASP490 4.9 0.3 1.0 CA C:ASN489 5.0 0.4 1.0

Calcium binding site 7 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca703 b:0.3 occ:1.00 OD2 C:ASP521 2.2 0.8 1.0 OD1 C:ASN489 2.5 0.7 1.0 OD1 C:ASP521 2.5 0.3 1.0 O C:ASN491 2.5 0.8 1.0 O C:ASN527 2.6 0.4 1.0 CG C:ASP521 2.7 0.1 1.0 OD2 C:ASP523 2.7 0.8 1.0 OD2 C:ASP573 3.0 0.6 1.0 CG C:ASN489 3.4 0.4 1.0 CG C:ASP573 3.4 0.7 1.0 C C:ASN491 3.6 0.4 1.0 CB C:ASP573 3.7 0.0 1.0 CG C:ASP523 3.7 0.1 1.0 C C:ASN527 3.7 0.0 1.0 ND2 C:ASN489 3.9 0.4 1.0 CB C:ASP523 4.0 0.1 1.0 N C:ASN491 4.1 0.3 1.0 CB C:ASP521 4.2 0.9 1.0 CA C:ASN491 4.2 0.6 1.0 CB C:ASN491 4.2 0.4 1.0 OD1 C:ASP573 4.3 0.6 1.0 CA C:ASN527 4.5 0.7 1.0 CB C:ASN489 4.6 0.6 1.0 CB C:ASN527 4.6 0.1 1.0 CA C:ASN489 4.6 0.4 1.0 C C:ASN489 4.7 0.7 1.0 N C:GLY528 4.8 0.3 1.0 CD C:PRO493 4.8 0.5 1.0 N C:THR492 4.8 0.7 1.0 N C:ASP490 4.8 0.5 1.0 OD1 C:ASP523 4.8 0.5 1.0 N C:ASP523 4.9 0.8 1.0 CD C:ARG581 5.0 0.2 1.0 CA C:GLY528 5.0 0.1 1.0

Calcium binding site 8 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca704 b:0.6 occ:1.00 OD1 C:ASP456 2.0 0.1 1.0 OD2 C:ASP490 2.5 0.5 1.0 OE1 C:GLU385 2.7 0.5 1.0 OE1 C:GLU458 2.7 0.7 1.0 OD1 C:ASP490 3.0 0.8 1.0 CG C:ASP490 3.0 0.8 1.0 CG C:ASP456 3.3 0.6 1.0 CD C:GLU385 3.5 0.1 1.0 CD C:GLU458 3.9 0.6 1.0 OE2 C:GLU385 3.9 0.2 1.0 OD2 C:ASP456 4.0 0.2 1.0 CA C:CA702 4.1 0.1 1.0 OD1 C:ASN491 4.3 0.9 1.0 CB C:ASP456 4.3 0.7 1.0 CB C:ASP490 4.4 0.3 1.0 CG C:GLU458 4.5 0.6 1.0 CB C:GLU458 4.5 0.9 1.0 CG C:GLU385 4.5 0.6 1.0 N C:ARG457 4.6 0.5 1.0 CA C:ASP456 4.6 0.2 1.0 N C:GLU458 4.7 0.8 1.0 OE2 C:GLU458 4.9 0.5 1.0 C C:ASP456 4.9 1.0 1.0 OD1 C:ASP523 4.9 0.5 1.0

Calcium binding site 9 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:69.9 occ:1.00 OD2 B:ASP409 2.2 70.0 1.0 OD2 B:ASP411 2.3 81.8 1.0 OD2 B:ASP471 2.4 66.4 1.0 OD1 B:ASP409 2.4 65.8 1.0 O B:GLN370 2.5 62.7 1.0 OD1 B:ASN368 2.5 85.1 1.0 CG B:ASP409 2.6 68.8 1.0 CG B:ASP471 3.3 64.4 1.0 CG B:ASP411 3.3 79.2 1.0 CG B:ASN368 3.4 85.0 1.0 C B:GLN370 3.6 68.4 1.0 CB B:ASP411 3.7 77.7 1.0 CB B:ASP471 3.7 63.3 1.0 ND2 B:ASN368 4.1 82.0 1.0 CB B:ASP409 4.1 70.9 1.0 OD1 B:ASP471 4.3 62.0 1.0 OE1 B:GLN474 4.3 81.0 1.0 N B:GLN370 4.3 72.6 1.0 CB B:ASN368 4.4 84.3 1.0 OD1 B:ASP411 4.4 81.3 1.0 CA B:GLN370 4.4 70.9 1.0 CA B:ASN368 4.5 83.3 1.0 N B:SER371 4.7 66.7 1.0 C B:ASN368 4.7 81.5 1.0 CB B:GLN370 4.7 73.2 1.0 CD B:PRO372 4.8 64.5 1.0 CA B:ASP411 4.9 77.3 1.0 N B:ASP411 4.9 76.6 1.0 CD B:GLN474 5.0 80.0 1.0 N B:PRO372 5.0 64.1 1.0

Calcium binding site 10 out of 13 in the Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1


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-15 EC3-5 CD2-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca702 b:68.8 occ:1.00 OE2 B:GLU385 2.2 70.2 1.0 OD1 B:ASP487 2.3 77.4 1.0 OD1 B:ASP490 2.3 69.7 1.0 OD1 B:ASP523 2.3 77.0 1.0 OE2 B:GLU458 2.4 73.5 1.0 O B:ALA488 2.4 73.5 1.0 OE1 B:GLU458 2.7 73.7 1.0 CD B:GLU458 2.9 75.1 1.0 CD B:GLU385 3.2 69.4 1.0 CG B:ASP523 3.3 72.3 1.0 CG B:ASP487 3.4 76.9 1.0 CG B:ASP490 3.4 74.0 1.0 OE1 B:GLU385 3.6 70.9 1.0 C B:ALA488 3.6 74.1 1.0 N B:ALA488 3.7 73.1 1.0 OD2 B:ASP490 3.8 77.1 1.0 CA B:CA703 3.9 95.8 1.0 OD2 B:ASP487 4.0 77.4 1.0 CB B:ASP523 4.0 71.1 1.0 CA B:ASP523 4.1 71.6 1.0 N B:ASP490 4.2 75.2 1.0 OD2 B:ASP523 4.2 71.3 1.0 ND2 B:ASN491 4.3 70.8 1.0 CA B:ALA488 4.3 71.9 1.0 CG B:GLU458 4.4 76.3 1.0 CG B:GLU385 4.4 69.7 1.0 CA B:ASP487 4.4 77.3 1.0 CB B:ASP487 4.4 75.2 1.0 NE B:ARG457 4.5 73.8 1.0 CB B:ARG457 4.5 70.2 1.0 C B:ASP487 4.6 76.9 1.0 N B:ASN489 4.7 75.8 1.0 CB B:ASP490 4.7 73.2 1.0 CA B:ASN489 4.9 75.8 1.0 CB B:ALA488 5.0 71.8 1.0 N B:GLU524 5.0 75.9 1.0 CA B:ASP490 5.0 72.6 1.0 N B:ASP523 5.0 72.2 1.0

D.Choudhary, E.Tamilselvan, M.Sotomayor. Crystal Structure of Human Protocadherin-15 EC3-5 CD2-1 To Be Published.