Calcium in PDB 5v5x: Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure

The structure of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure, PDB code: 5v5x was solved by K.M.Goodman, S.Mannepalli, F.Bahna, B.Honig, L.Shapiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 3.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.242, 91.762, 452.991, 90.00, 90.00, 90.00
R / Rfree (%)	20.8 / 25.7

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Calcium atom in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure (pdb code 5v5x). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 36 binding sites of Calcium where determined in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure, PDB code: 5v5x:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca701 b:44.6 occ:1.00 OD2 A:ASP310 2.2 59.0 1.0 OD1 A:ASP276 2.5 71.6 1.0 OE1 A:GLU278 2.6 49.4 1.0 OE1 A:GLU223 2.7 90.7 1.0 CG A:ASP310 3.2 77.6 1.0 CD A:GLU223 3.2 90.5 1.0 OE2 A:GLU223 3.3 97.4 1.0 OD1 A:ASP310 3.5 70.6 1.0 CG A:ASP276 3.6 83.8 1.0 CD A:GLU278 3.8 70.8 1.0 CA A:CA702 4.0 39.6 1.0 N A:PHE277 4.2 73.6 1.0 CA A:ASP276 4.3 88.3 1.0 CB A:ASP276 4.3 88.8 1.0 OD2 A:ASP276 4.4 78.6 1.0 OE2 A:GLU278 4.4 50.3 1.0 CG A:GLU223 4.4 81.0 1.0 ND2 A:ASN311 4.5 88.2 1.0 CB A:ASP310 4.6 84.6 1.0 N A:GLU278 4.6 67.3 1.0 C A:ASP276 4.7 78.4 1.0 CG A:GLU278 4.7 79.7 1.0 OD1 A:ASN311 4.8 0.0 1.0 CB A:GLU278 4.9 77.7 1.0 CG A:ASN311 5.0 90.7 1.0

Calcium binding site 2 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca702 b:39.6 occ:1.00 OE2 A:GLU223 2.4 97.4 1.0 O A:GLU308 2.4 52.4 1.0 OE2 A:GLU278 2.5 50.3 1.0 OD1 A:ASP307 2.5 0.5 1.0 OD1 A:ASP310 2.5 70.6 1.0 OD1 A:ASP343 2.5 0.2 1.0 OE1 A:GLU278 3.2 49.4 1.0 CD A:GLU278 3.2 70.8 1.0 CD A:GLU223 3.4 90.5 1.0 CG A:ASP310 3.5 77.6 1.0 CG A:ASP343 3.5 88.2 1.0 C A:GLU308 3.5 65.5 1.0 N A:GLU308 3.6 75.2 1.0 CG A:ASP307 3.6 0.9 1.0 OE1 A:GLU223 3.7 90.7 1.0 OD2 A:ASP310 3.9 59.0 1.0 CA A:CA701 4.0 44.6 1.0 CA A:GLU308 4.1 68.4 1.0 CB A:ASP343 4.2 59.7 1.0 OD2 A:ASP307 4.3 0.3 1.0 N A:ASP310 4.3 54.9 1.0 OD2 A:ASP343 4.4 94.5 1.0 CA A:ASP343 4.4 60.7 1.0 C A:ASP307 4.5 86.4 1.0 CB A:PHE277 4.5 69.8 1.0 CA A:ASP307 4.6 82.9 1.0 CB A:ASP307 4.6 81.1 1.0 CG A:GLU278 4.6 79.7 1.0 N A:ASN309 4.7 77.3 1.0 CG A:GLU223 4.7 81.0 1.0 CB A:ASP310 4.7 84.6 1.0 CB A:GLU308 4.7 76.7 1.0 ND2 A:ASN311 4.9 88.2 1.0 CD2 A:PHE277 5.0 62.9 1.0

Calcium binding site 3 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca703 b:53.4 occ:1.00 OD2 A:ASP394 2.3 75.7 1.0 O A:ASN311 2.5 77.8 1.0 OD1 A:ASN309 2.5 76.5 1.0 O A:ASN347 2.5 47.4 1.0 OD2 A:ASP343 2.5 94.5 1.0 OD2 A:ASP341 2.7 46.0 1.0 OD1 A:ASP341 3.0 45.9 1.0 CG A:ASP341 3.2 43.5 1.0 CG A:ASP394 3.4 76.1 1.0 CG A:ASP343 3.6 88.2 1.0 C A:ASN347 3.6 63.2 1.0 CG A:ASN309 3.7 67.9 1.0 C A:ASN311 3.7 81.7 1.0 CB A:ASN347 3.8 73.7 1.0 CB A:ASP394 3.9 79.2 1.0 CB A:ASP343 3.9 59.7 1.0 CA A:ASN347 4.1 64.7 1.0 ND2 A:ASN309 4.4 98.5 1.0 OD1 A:ASP394 4.4 68.4 1.0 CA A:ARG312 4.5 70.3 1.0 N A:ARG312 4.5 77.5 1.0 CB A:ASP341 4.6 47.0 1.0 N A:ASN311 4.7 55.4 1.0 OD1 A:ASP343 4.7 0.2 1.0 CA A:ASN311 4.7 69.8 1.0 N A:ALA348 4.7 84.1 1.0 CA A:ASN309 4.8 64.2 1.0 CB A:ASN309 4.8 59.6 1.0 C A:ARG312 4.9 66.8 1.0 CD A:PRO313 5.0 46.9 1.0 N A:PRO313 5.0 70.2 1.0 CG A:ASN347 5.0 87.4 1.0

Calcium binding site 4 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca704 b:63.9 occ:1.00 OD2 A:ASP415 2.1 99.4 1.0 OD1 A:ASP379 2.5 80.9 1.0 OE1 A:GLU381 2.7 69.7 1.0 OE1 A:GLU326 2.8 95.2 1.0 CG A:ASP415 3.0 0.8 1.0 CD A:GLU326 3.2 91.4 1.0 OD1 A:ASP415 3.3 96.3 1.0 OE2 A:GLU326 3.4 98.5 1.0 CG A:ASP379 3.5 87.1 1.0 CD A:GLU381 3.8 70.3 1.0 OD1 A:ASN416 4.0 95.5 1.0 CA A:CA705 4.1 62.3 1.0 CA A:ASP379 4.2 97.0 1.0 CB A:ASP415 4.2 0.5 1.0 OD2 A:ASP379 4.3 91.1 1.0 CB A:ASP379 4.3 98.6 1.0 CG A:GLU326 4.4 84.8 1.0 OE2 A:GLU381 4.4 69.7 1.0 N A:ARG380 4.5 68.1 1.0 C A:ASP379 4.7 80.4 1.0 O A:LEU378 4.8 0.3 1.0 CG A:GLU381 4.9 80.1 1.0 N A:GLU381 5.0 68.5 1.0 CB A:GLU326 5.0 64.0 1.0

Calcium binding site 5 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca705 b:62.3 occ:1.00 OE2 A:GLU381 2.1 69.7 1.0 OE2 A:GLU326 2.2 98.5 1.0 OD1 A:ASP412 2.4 76.2 1.0 O A:VAL413 2.5 81.8 1.0 OD1 A:ASP415 2.6 96.3 1.0 OD1 A:ASP448 2.8 0.3 1.0 CD A:GLU381 3.0 70.3 1.0 OE1 A:GLU381 3.2 69.7 1.0 CD A:GLU326 3.3 91.4 1.0 CG A:ASP415 3.4 0.8 1.0 CG A:ASP412 3.6 81.1 1.0 C A:VAL413 3.6 77.9 1.0 N A:VAL413 3.6 88.9 1.0 OD2 A:ASP415 3.7 99.4 1.0 OE1 A:GLU326 3.7 95.2 1.0 CG A:ASP448 3.7 0.2 1.0 CA A:CA704 4.1 63.9 1.0 OD1 A:ASN416 4.1 95.5 1.0 N A:ASP415 4.2 94.4 1.0 CA A:VAL413 4.3 86.0 1.0 OD2 A:ASP412 4.3 90.6 1.0 CG A:GLU381 4.4 80.1 1.0 CB A:ASP448 4.4 0.5 1.0 CA A:ASP412 4.5 72.3 1.0 CG A:GLU326 4.5 84.8 1.0 CA A:ASP448 4.5 76.3 1.0 NE A:ARG380 4.5 62.4 1.0 C A:ASP412 4.6 80.4 1.0 OD2 A:ASP448 4.6 0.2 1.0 CB A:ASP412 4.6 69.2 1.0 CB A:ASP415 4.7 0.5 1.0 N A:ASN414 4.7 73.4 1.0 CA A:ASN414 5.0 83.4 1.0 CB A:VAL413 5.0 82.3 1.0 CA A:ASP415 5.0 0.7 1.0 N A:ASN416 5.0 72.1 1.0 NH1 A:ARG380 5.0 91.8 1.0

Calcium binding site 6 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca706 b:49.6 occ:1.00 OD2 A:ASP504 2.3 0.9 1.0 OD2 A:ASP448 2.3 0.2 1.0 OD2 A:ASP446 2.3 69.1 1.0 O A:ASN416 2.4 72.2 1.0 O A:ASN452 2.4 59.5 1.0 OD1 A:ASN414 2.6 83.3 1.0 OD1 A:ASP446 2.8 74.3 1.0 CG A:ASP446 2.9 67.4 1.0 CG A:ASP448 3.3 0.2 1.0 CG A:ASP504 3.3 0.4 1.0 C A:ASN416 3.6 82.9 1.0 C A:ASN452 3.6 81.4 1.0 CB A:ASP448 3.6 0.5 1.0 CG A:ASN414 3.7 89.3 1.0 CB A:ASP504 3.8 0.6 1.0 OD1 A:ASP504 4.4 0.4 1.0 ND2 A:ASN414 4.4 0.4 1.0 CB A:ASP446 4.4 76.7 1.0 OD1 A:ASP448 4.4 0.3 1.0 CA A:ASN452 4.4 82.1 1.0 CB A:ASN452 4.5 88.0 1.0 CD A:PRO418 4.5 79.5 1.0 CA A:ASN416 4.5 79.8 1.0 N A:ALA417 4.5 88.0 1.0 CA A:ALA417 4.5 78.5 1.0 N A:ASN416 4.6 72.1 1.0 N A:GLY453 4.6 74.8 1.0 CB A:ASN416 4.6 78.0 1.0 CA A:GLY453 4.7 72.5 1.0 N A:PRO418 4.8 79.1 1.0 C A:ALA417 4.8 74.5 1.0 CB A:ASN414 4.9 86.8 1.0 CA A:ASP448 4.9 76.3 1.0 N A:ASP448 4.9 68.1 1.0 CA A:ASN414 4.9 83.4 1.0

Calcium binding site 7 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca707 b:98.8 occ:1.00 OD2 A:ASP525 2.1 0.3 1.0 OD1 A:ASP489 2.4 0.9 1.0 OE1 A:GLU491 2.7 98.0 1.0 OE2 A:GLU431 2.7 0.1 1.0 CG A:ASP525 3.1 0.6 1.0 OD1 A:ASP525 3.4 98.5 1.0 CG A:ASP489 3.5 0.1 1.0 CD A:GLU491 3.6 99.1 1.0 OD1 A:ASN432 3.8 0.8 1.0 CD A:GLU431 3.8 0.2 1.0 OD2 A:ASP489 4.1 0.2 1.0 OE2 A:GLU491 4.1 98.8 1.0 CA A:CA708 4.1 80.7 1.0 ND2 A:ASN526 4.2 0.2 1.0 CB A:ASP525 4.3 0.3 1.0 OE1 A:GLU431 4.5 0.1 1.0 OD1 A:ASN526 4.5 0.7 1.0 CB A:ASP489 4.6 0.6 1.0 CG A:ASN526 4.6 0.9 1.0 N A:HIS490 4.7 93.5 1.0 CG A:ASN432 4.7 0.2 1.0 CG A:GLU491 4.7 0.4 1.0 CA A:ASP489 4.7 0.7 1.0 ND2 A:ASN432 4.8 0.0 1.0 CG A:GLU431 4.8 0.8 1.0 N A:GLU491 4.8 0.8 1.0 CB A:GLU491 4.8 0.9 1.0

Calcium binding site 8 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca708 b:80.7 occ:1.00 OE2 A:GLU491 2.1 98.8 1.0 OD1 A:ASP525 2.3 98.5 1.0 OD1 A:ASP522 2.4 95.6 1.0 O A:ARG523 2.5 0.2 1.0 OE1 A:GLU431 2.6 0.1 1.0 OD1 A:ASP565 2.9 0.3 1.0 CD A:GLU491 3.1 99.1 1.0 CG A:ASP525 3.2 0.6 1.0 CD A:GLU431 3.3 0.2 1.0 OE1 A:GLU491 3.3 98.0 1.0 OE2 A:GLU431 3.4 0.1 1.0 OD2 A:ASP525 3.5 0.3 1.0 CG A:ASP522 3.6 96.2 1.0 C A:ARG523 3.7 0.9 1.0 CG A:ASP565 3.7 0.3 1.0 N A:ARG523 3.8 92.9 1.0 CA A:CA707 4.1 98.8 1.0 N A:ASP525 4.1 0.9 1.0 OD2 A:ASP522 4.2 97.5 1.0 CA A:ARG523 4.4 94.9 1.0 CB A:ASP565 4.4 0.4 1.0 OD2 A:ASP565 4.4 0.2 1.0 CB A:ASP525 4.4 0.3 1.0 CG A:GLU491 4.4 0.4 1.0 CB A:HIS490 4.6 92.9 1.0 CA A:ASP522 4.6 0.7 1.0 CG A:GLU431 4.6 0.8 1.0 C A:ASP522 4.6 1.0 1.0 CB A:ASP522 4.7 0.7 1.0 N A:ASN524 4.7 0.3 1.0 CA A:ASP565 4.7 0.6 1.0 CD2 A:HIS490 4.8 0.5 1.0 ND2 A:ASN526 4.8 0.2 1.0 CA A:ASP525 4.8 0.4 1.0 N A:ASN526 4.8 0.4 1.0 CA A:ASN524 5.0 0.8 1.0

Calcium binding site 9 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:98.6 occ:1.00 OD2 A:ASP565 2.4 0.2 1.0 OD2 A:ASP616 2.5 0.9 1.0 O A:ASN526 2.5 0.1 1.0 O A:ASN569 2.5 1.0 1.0 OD1 A:ASN524 2.5 1.0 1.0 OD2 A:ASP563 2.6 0.0 1.0 OD1 A:ASP563 2.7 0.0 1.0 CG A:ASP563 2.9 0.7 1.0 CG A:ASP565 3.5 0.3 1.0 C A:ASN569 3.6 0.7 1.0 CG A:ASP616 3.6 98.9 1.0 CG A:ASN524 3.7 0.7 1.0 C A:ASN526 3.7 0.6 1.0 CB A:ASP565 4.0 0.4 1.0 CB A:ASN569 4.1 0.7 1.0 CA A:ASN569 4.2 0.4 1.0 CB A:ASP616 4.2 96.9 1.0 CB A:ASP563 4.3 99.1 1.0 ND2 A:ASN524 4.4 0.5 1.0 CD1 A:LEU622 4.5 0.6 1.0 OD1 A:ASP565 4.6 0.3 1.0 CA A:ALA527 4.6 0.6 1.0 N A:ALA527 4.6 0.9 1.0 N A:ALA570 4.6 0.2 1.0 OD1 A:ASP616 4.6 0.4 1.0 N A:ASN526 4.7 0.4 1.0 CA A:ASN526 4.7 0.6 1.0 CD A:PRO528 4.7 97.8 1.0 C A:ALA527 4.8 98.6 1.0 CB A:ASN524 4.8 0.6 1.0 CA A:ASN524 4.8 0.8 1.0 N A:PRO528 4.8 95.6 1.0 CA A:ALA570 4.9 0.6 1.0 CB A:LEU622 4.9 98.4 1.0

Calcium binding site 10 out of 36 in the Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Protocadherin GAMMAB7 EC3-6 Cis-Dimer Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca701 b:58.6 occ:1.00 OD2 B:ASP310 2.3 64.6 1.0 OD1 B:ASP276 2.5 89.2 1.0 OE1 B:GLU223 2.6 88.0 1.0 OE1 B:GLU278 2.6 48.1 1.0 CD B:GLU223 3.2 88.0 1.0 CG B:ASP310 3.3 84.7 1.0 OE2 B:GLU223 3.4 91.0 1.0 CG B:ASP276 3.5 83.8 1.0 OD1 B:ASP310 3.6 86.5 1.0 CD B:GLU278 3.8 64.7 1.0 CA B:CA702 4.1 44.7 1.0 CA B:ASP276 4.2 74.2 1.0 OD2 B:ASP276 4.3 93.2 1.0 CB B:ASP276 4.3 80.3 1.0 OE2 B:GLU278 4.3 51.3 1.0 N B:PHE277 4.3 75.3 1.0 CG B:GLU223 4.5 85.0 1.0 OD1 B:ASN311 4.5 83.8 1.0 CB B:ASP310 4.6 73.3 1.0 C B:ASP276 4.7 75.7 1.0 N B:GLU278 4.8 71.0 1.0 O B:LEU275 4.9 75.2 1.0 CG B:GLU278 4.9 88.9 1.0

K.M.Goodman, R.Rubinstein, H.Dan, F.Bahna, S.Mannepalli, G.Ahlsen, C.Aye Thu, R.V.Sampogna, T.Maniatis, B.Honig, L.Shapiro. Protocadherin Cis-Dimer Architecture and Recognition Unit Diversity. Proc. Natl. Acad. Sci. V. 114 E9829 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29087338
DOI: 10.1073/PNAS.1713449114