Calcium in PDB 5w1d: Crystal Structure of Mouse Protocadherin-15 EC4-7

The structure of Crystal Structure of Mouse Protocadherin-15 EC4-7, PDB code: 5w1d was solved by C.F.Klanseck, B.L.Neel, M.Sotomayor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.09 / 3.35
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	78.863, 78.863, 289.469, 90.00, 90.00, 90.00
R / Rfree (%)	22.7 / 27.9

The structure of Crystal Structure of Mouse Protocadherin-15 EC4-7 also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Calcium atom in the Crystal Structure of Mouse Protocadherin-15 EC4-7 (pdb code 5w1d). 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 Mouse Protocadherin-15 EC4-7, PDB code: 5w1d:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Crystal Structure of Mouse Protocadherin-15 EC4-7


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 Mouse Protocadherin-15 EC4-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1001 b:0.5 occ:1.00 OD2 A:ASP724 2.3 95.6 1.0 O A:ASN692 2.3 0.1 1.0 OD1 A:ASP722 2.4 0.9 1.0 OD1 A:ASN690 2.4 0.8 1.0 OD2 A:ASP722 2.6 0.3 1.0 OD2 A:ASP772 2.6 0.6 1.0 O A:ASN728 2.6 0.2 1.0 CG A:ASP722 2.8 0.7 1.0 CG A:ASP772 3.4 0.4 1.0 CG A:ASP724 3.4 0.6 1.0 CG A:ASN690 3.5 0.9 1.0 C A:ASN692 3.5 0.8 1.0 CB A:ASP772 3.6 0.8 1.0 C A:ASN728 3.8 0.7 1.0 CB A:ASP724 3.9 0.8 1.0 ND2 A:ASN690 4.1 0.1 1.0 CB A:ASP722 4.3 0.1 1.0 CA A:ASN692 4.3 0.6 1.0 N A:ASN692 4.4 0.3 1.0 CA A:ASN728 4.4 0.3 1.0 CB A:ASN728 4.4 0.9 1.0 OD1 A:ASP772 4.4 0.3 1.0 OD1 A:ASP724 4.4 0.7 1.0 N A:ALA693 4.5 0.1 1.0 CB A:ASN690 4.6 0.1 1.0 CB A:ASN692 4.6 0.6 1.0 CA A:ALA693 4.6 0.1 1.0 CD A:PRO694 4.7 0.5 1.0 N A:PRO694 4.7 0.8 1.0 C A:ALA693 4.8 0.8 1.0 CG A:ARG778 4.8 0.6 1.0 CA A:ASN690 4.8 0.5 1.0 CD A:ARG778 4.8 0.0 1.0 N A:GLY729 4.8 0.4 1.0

Calcium binding site 2 out of 6 in the Crystal Structure of Mouse Protocadherin-15 EC4-7


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 Mouse Protocadherin-15 EC4-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1002 b:95.5 occ:1.00 OD1 A:ASP688 2.0 97.0 1.0 OD1 A:ASP724 2.3 0.7 1.0 OE1 A:GLU658 2.4 0.8 1.0 O A:VAL689 2.5 0.7 1.0 OE2 A:GLU606 2.6 0.0 1.0 OD1 A:ASP691 2.7 0.2 1.0 CG A:ASP688 3.1 0.0 1.0 CD A:GLU658 3.2 0.6 1.0 OE2 A:GLU658 3.2 0.2 1.0 CG A:ASP691 3.4 0.2 1.0 CG A:ASP724 3.4 0.6 1.0 OD2 A:ASP691 3.5 0.0 1.0 OD2 A:ASP688 3.5 0.8 1.0 CD A:GLU606 3.6 0.5 1.0 C A:VAL689 3.7 1.0 1.0 CB A:ASP724 3.8 0.8 1.0 CA A:ASP724 3.9 0.4 1.0 OE1 A:GLU606 3.9 0.2 1.0 NH2 A:ARG657 3.9 0.8 1.0 N A:VAL689 4.0 0.9 1.0 N A:ASP691 4.2 0.9 1.0 NE A:ARG657 4.3 0.1 1.0 OD1 A:ASN692 4.4 0.2 1.0 CB A:ASP688 4.4 0.4 1.0 CA A:CA1003 4.5 0.9 1.0 OD2 A:ASP724 4.5 95.6 1.0 CG A:GLU658 4.5 0.5 1.0 CA A:VAL689 4.6 0.9 1.0 N A:ASP724 4.6 0.1 1.0 CB A:ASP691 4.6 0.5 1.0 CZ A:ARG657 4.6 0.8 1.0 N A:ASN690 4.6 0.3 1.0 CA A:ASP688 4.7 0.7 1.0 CA A:ASN690 4.7 0.5 1.0 CG2 A:VAL689 4.8 0.0 1.0 C A:ASP688 4.9 0.1 1.0 CA A:ASP691 4.9 0.5 1.0 C A:ASN690 4.9 0.4 1.0 CG A:GLU606 5.0 0.9 1.0 C A:ASP724 5.0 0.9 1.0

Calcium binding site 3 out of 6 in the Crystal Structure of Mouse Protocadherin-15 EC4-7


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 Mouse Protocadherin-15 EC4-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1003 b:0.9 occ:1.00 OD2 A:ASP691 2.4 0.0 1.0 OE1 A:GLU606 2.5 0.2 1.0 OD1 A:ASP656 2.7 0.3 1.0 OE1 A:GLU658 2.7 0.8 1.0 CG A:ASP691 3.2 0.2 1.0 CG A:ASP656 3.4 0.2 1.0 CD A:GLU606 3.5 0.5 1.0 OD1 A:ASP691 3.5 0.2 1.0 CD A:GLU658 3.5 0.6 1.0 CG A:GLU658 3.6 0.5 1.0 OE2 A:GLU606 3.9 0.0 1.0 CA A:ASP656 4.0 0.8 1.0 OD2 A:ASP656 4.0 0.0 1.0 CB A:ASP656 4.2 0.4 1.0 N A:ARG657 4.2 0.5 1.0 CB A:ASP691 4.4 0.5 1.0 CA A:CA1002 4.5 95.5 1.0 OD1 A:ASN692 4.5 0.2 1.0 N A:GLU658 4.5 0.3 1.0 CB A:GLU658 4.6 0.2 1.0 C A:ASP656 4.6 0.4 1.0 CG A:GLU606 4.6 0.9 1.0 OE2 A:GLU658 4.7 0.2 1.0 CB A:GLU606 5.0 0.6 1.0

Calcium binding site 4 out of 6 in the Crystal Structure of Mouse Protocadherin-15 EC4-7


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 Mouse Protocadherin-15 EC4-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1004 b:0.6 occ:1.00 OE1 A:GLU623 2.2 0.3 1.0 OD1 A:ASP621 2.3 0.1 1.0 OE1 A:GLN590 2.4 0.1 1.0 O A:SER591 2.5 0.5 1.0 OD2 A:ASP625 2.6 0.5 1.0 OD2 A:ASP621 2.8 0.7 1.0 CG A:ASP621 2.9 0.0 1.0 OD1 A:ASP671 3.0 0.1 1.0 CD A:GLN590 3.4 0.9 1.0 CD A:GLU623 3.4 0.9 1.0 CG A:ASP671 3.5 0.3 1.0 C A:SER591 3.5 0.8 1.0 OD2 A:ASP671 3.6 0.3 1.0 CG A:ASP625 3.7 0.1 1.0 N A:SER591 3.8 0.7 1.0 CB A:GLU623 4.0 0.4 1.0 NE2 A:GLN590 4.0 0.4 1.0 OG A:SER591 4.0 0.5 1.0 CG A:GLU623 4.1 0.1 1.0 O A:PRO592 4.1 0.2 1.0 C A:PRO592 4.2 0.8 1.0 CA A:SER591 4.3 0.8 1.0 CB A:ASP625 4.3 1.0 1.0 N A:GLU623 4.3 0.3 1.0 CB A:ASP621 4.3 0.7 1.0 OE2 A:GLU623 4.4 0.7 1.0 CG A:GLN590 4.4 0.3 1.0 CA A:PRO592 4.4 0.2 1.0 N A:PRO592 4.4 0.8 1.0 OD1 A:ASP625 4.6 0.6 1.0 N A:ARG622 4.6 0.5 1.0 N A:PRO593 4.6 0.1 1.0 CB A:ASP671 4.7 0.7 1.0 CA A:GLU623 4.7 0.6 1.0 CB A:SER591 4.8 0.1 1.0 CA A:ASP621 4.8 0.4 1.0 C A:ASP621 4.9 0.3 1.0 C A:GLN590 4.9 0.2 1.0

Calcium binding site 5 out of 6 in the Crystal Structure of Mouse Protocadherin-15 EC4-7


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 Mouse Protocadherin-15 EC4-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1005 b:87.3 occ:1.00 O A:ASN520 2.1 94.0 1.0 OD1 A:ASP514 2.2 98.5 1.0 O A:ASN484 2.4 0.9 1.0 OD1 A:ASN482 2.4 97.5 1.0 OD2 A:ASP514 2.6 98.7 1.0 OD2 A:ASP566 2.7 97.9 1.0 CG A:ASP514 2.7 99.0 1.0 OD2 A:ASP516 3.2 0.7 1.0 C A:ASN520 3.3 91.8 1.0 CB A:ASP516 3.4 0.1 1.0 C A:ASN484 3.4 0.2 1.0 CG A:ASN482 3.5 0.8 1.0 CG A:ASP566 3.7 0.6 1.0 CG A:ASP516 3.7 0.9 1.0 ND2 A:ASN482 3.8 97.3 1.0 CB A:ASN484 3.9 0.7 1.0 N A:ASN484 3.9 0.9 1.0 CA A:ASN484 4.0 0.6 1.0 CB A:ASP566 4.0 0.4 1.0 CB A:ASN520 4.1 95.2 1.0 N A:GLY521 4.2 89.7 1.0 CA A:ASN520 4.2 95.1 1.0 CB A:ASP514 4.2 0.1 1.0 CA A:GLY521 4.2 90.8 1.0 N A:THR485 4.6 0.0 1.0 CA A:ASP516 4.6 0.8 1.0 N A:ASP516 4.6 0.4 1.0 OD1 A:ASP566 4.7 0.1 1.0 CB A:ASN482 4.8 0.1 1.0 CD A:ARG574 4.9 0.3 1.0 OD1 A:ASP516 4.9 0.2 1.0 N A:ASP483 4.9 0.8 1.0

Calcium binding site 6 out of 6 in the Crystal Structure of Mouse Protocadherin-15 EC4-7


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 Mouse Protocadherin-15 EC4-7 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1007 b:0.1 occ:1.00 OE2 A:GLU385 2.2 0.8 1.0 OD1 A:ASP480 2.7 0.0 1.0 CG A:ASP480 3.1 0.6 1.0 OD2 A:ASP480 3.2 0.8 1.0 CD A:GLU385 3.3 0.8 1.0 N A:ALA481 3.8 0.4 1.0 OE1 A:GLU385 3.9 0.6 1.0 OD2 A:ASP483 3.9 1.0 1.0 O A:ALA481 4.2 0.4 1.0 CB A:ALA481 4.4 0.3 1.0 CB A:ASP480 4.4 0.4 1.0 OD1 A:ASP483 4.4 0.8 1.0 CG A:GLU385 4.5 0.1 1.0 CG A:ASP483 4.5 0.5 1.0 CA A:ALA481 4.5 0.0 1.0 CA A:ASP480 4.6 0.4 1.0 C A:ASP480 4.6 0.4 1.0 C A:ALA481 4.8 0.9 1.0 K A:K1006 5.0 0.5 1.0

C.Klanseck, B.L.Neel, M.Sotomayor. Crystal Structure of Mouse Protocadherin-15 EC4-7 To Be Published.